static RANDOM_FOREST *
train_rforest(MRI *mri_inputs[MAX_SUBJECTS][MAX_TIMEPOINTS], MRI *mri_segs[MAX_SUBJECTS][MAX_TIMEPOINTS], TRANSFORM *transforms[MAX_SUBJECTS][MAX_TIMEPOINTS],
int nsubjects, GCA *gca, RFA_PARMS *parms, float wm_thresh,
int wmsa_whalf, int ntp)
{
RANDOM_FOREST *rf ;
int nfeatures, x, y, z, ntraining, n, tvoxel_size, width, height, depth, xt, yt, zt ;
double xatlas, yatlas, zatlas ;
MRI *mri_in, *mri_seg, *mri_training_voxels, *mri_wmsa_possible ;
TRANSFORM *transform ;
double **training_data ;
int *training_classes, i, label, tlabel, nwmsa, nfuture, nnot, correct, label_time1, label_time2;
nwmsa = nnot = nfuture = 0 ;
/*
features are:
t1 intensity (3 vols)
3 priors
# of unknown voxels in the nbhd
# of neighboring wmsa voxels at t1
*/
nfeatures = parms->wsize*parms->wsize*parms->wsize*parms->nvols + 5 ;
rf = RFalloc(parms->ntrees, nfeatures, NCLASSES, parms->max_depth, single_classifier_names, max_steps) ;
if (rf == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not allocate random forest", Progname) ;
rf->min_step_size = 1 ;
tvoxel_size=1 ;
width = (int)ceil((float)mri_segs[0][0]->width/tvoxel_size) ;
height = (int)ceil((float)mri_segs[0][0]->height/tvoxel_size) ;
depth = (int)ceil((float)mri_segs[0][0]->depth/tvoxel_size) ;
mri_wmsa_possible = MRIalloc(width, height, depth, MRI_UCHAR) ;
GCAcopyDCToMRI(gca, mri_wmsa_possible) ;
mri_in = mri_inputs[0][0] ;
mri_training_voxels = MRIallocSequence(mri_in->width,mri_in->height, mri_in->depth,MRI_UCHAR,nsubjects) ;
#if 1
// update time 1 segmentation based on labels at time1 and time2
for (n = 0 ; n < nsubjects ; n++)
{
mri_seg = mri_segs[n][0] ;
for (x = 0 ; x < mri_in->width ; x++)
for (y = 0 ; y < mri_in->height ; y++)
for (z = 0 ; z < mri_in->depth ; z++)
{
label_time1 = MRIgetVoxVal(mri_segs[n][0], x, y, z, 0) ;
label_time2 = MRIgetVoxVal(mri_segs[n][1], x, y, z, 0) ;
if (IS_WMSA(label_time1))
MRIsetVoxVal(mri_segs[n][0], x, y, z, 0, label_time1) ;
else if (IS_WMSA(label_time2))
MRIsetVoxVal(mri_segs[n][0], x, y, z, 0, future_WMSA) ;
}
}
#endif
// build map of spatial locations that WMSAs can possibly occur in
for (n = 0 ; n < nsubjects ; n++)
{
mri_in = mri_inputs[n][1] ; transform = transforms[n][1] ;
for (x = 0 ; x < mri_in->width ; x++)
for (y = 0 ; y < mri_in->height ; y++)
for (z = 0 ; z < mri_in->depth ; z++)
if (is_possible_wmsa(gca, mri_in, transform, x, y, z, 0))
{
TransformSourceVoxelToAtlas(transform, mri_in, x, y, z, &xatlas, &yatlas, &zatlas) ;
xt = nint(xatlas/tvoxel_size) ;
yt = nint(yatlas/tvoxel_size) ;
zt = nint(zatlas/tvoxel_size) ;
if (xt == Gx && yt == Gy && zt == Gz)
DiagBreak() ;
MRIsetVoxVal(mri_wmsa_possible, xt, yt, zt, 0, 1) ;
}
}
for ( ; wmsa_whalf > 0 ; wmsa_whalf--)
MRIdilate(mri_wmsa_possible, mri_wmsa_possible) ;
// now build map of all voxels in training set
for (nnot = nwmsa = nfuture = ntraining = n = 0 ; n < nsubjects ; n++)
{
mri_in = mri_inputs[n][0] ; mri_seg = mri_segs[n][0] ; transform = transforms[n][0] ;
for (x = 0 ; x < mri_in->width ; x++)
for (y = 0 ; y < mri_in->height; y++)
for (z = 0 ; z < mri_in->depth; z++)
{
label = MRIgetVoxVal(mri_seg, x, y, z, 0) ;
TransformSourceVoxelToAtlas(transform, mri_in, x, y, z, &xatlas, &yatlas, &zatlas) ;
xt = nint(xatlas/tvoxel_size) ;
yt = nint(yatlas/tvoxel_size) ;
zt = nint(zatlas/tvoxel_size) ;
if (xt == Gx && yt == Gy && zt == Gz)
DiagBreak() ;
if ((IS_WMSA(label) == 0) &&
MRIgetVoxVal(mri_wmsa_possible,xt,yt, zt,0) == 0)
continue ;
if (NOT_TRAINING_LABEL(label))
continue ;
ntraining++ ;
if (IS_FUTURE_WMSA(label))
{
label = FUTURE_WMSA;
nfuture++ ;
}
else if (IS_WMSA(label))
{
label = WMSA ;
nwmsa++ ;
}
else
{
label = NOT_WMSA ;
nnot++ ;
}
// set label to one more than it will be for training so that 0 means this is not a training voxel
MRIsetVoxVal(mri_training_voxels, x, y, z, n, label+1) ;
}
}
correct = MRIcountNonzero(mri_training_voxels) ;
if (correct != ntraining)
DiagBreak() ;
printf("total training set size = %2.1fM\n", (float)ntraining/(1024.0f*1024.0f)) ;
printf("initial training set found with %dK FUTURE WMSA labels, %dK WMSA labels, and %dK non (ratio=%2.1f:%2.1f)\n",
nfuture/1000, nwmsa/1000, nnot/1000, (float)nnot/(float)nfuture, (float)nnot/(float)nwmsa) ;
MRIfree(&mri_wmsa_possible) ;
if (max_wm_wmsa_ratio*(nfuture+nwmsa) < nnot) // too many wm labels w.r.t. # of wmsas - remove some wm
{
int removed, total_to_remove = nnot - (max_wm_wmsa_ratio*(nfuture+nwmsa)) ;
double premove ;
premove = (double)total_to_remove / (double)nnot ;
printf("removing %dK WM indices to reduce training set imbalance (p < %f)\n", total_to_remove/1000, premove) ;
for (removed = n = 0 ; n < nsubjects ; n++)
for (x = 0 ; x < mri_in->width ; x++)
for (y = 0 ; y < mri_in->height; y++)
for (z = 0 ; z < mri_in->depth; z++)
{
label = MRIgetVoxVal(mri_training_voxels, x, y, z, n) ;
if (label == 1) // a WM voxel
{
if (randomNumber(0,1) < premove)
{
removed++ ;
MRIsetVoxVal(mri_training_voxels, x, y, z, n, 0) ; // remove it from training set
}
}
}
ntraining -= removed ;
printf("%d WM voxels removed, new training set size = %dM (ratio = %2.1f)\n",
removed, ntraining/(1024*1024), (double)(nnot-removed)/(double)(nwmsa+nfuture)) ;
}
correct = MRIcountNonzero(mri_training_voxels) ;
if (correct != ntraining)
DiagBreak() ;
// if (Gx >= 0)
{
int whalf = (parms->wsize-1)/2 ;
char buf[STRLEN] ;
rf->feature_names = (char **)calloc(rf->nfeatures, sizeof(char *)) ;
for (i = 0, x = -whalf ; x <= whalf ; x++)
for (y = -whalf ; y <= whalf ; y++)
for (z = -whalf ; z <= whalf ; z++)
for (n = 0 ; n < mri_in->nframes ; n++, i++)
{
switch (n)
{
default:
case 0: sprintf(buf, "T1(%d, %d, %d)", x, y, z) ; break ;
case 1: sprintf(buf, "T2(%d, %d, %d)", x, y, z) ;
break ;
case 2: sprintf(buf, "FLAIR(%d, %d, %d)", x, y, z) ;
if (x == 0 && y == 0 && z == 0)
Gdiag_no = i ;
break ;
}
rf->feature_names[i] = (char *)calloc(strlen(buf)+1, sizeof(char)) ;
strcpy(rf->feature_names[i], buf) ;
}
printf("FLAIR(0,0,0) = %dth feature\n", Gdiag_no) ;
sprintf(buf, "CSF voxels in nbhd") ;
rf->feature_names[i] = (char *)calloc(strlen(buf)+1, sizeof(char)) ;
strcpy(rf->feature_names[i], buf) ;
i++ ; sprintf(buf, "gm prior") ;
rf->feature_names[i] = (char *)calloc(strlen(buf)+1, sizeof(char)) ;
strcpy(rf->feature_names[i], buf) ;
i++ ; sprintf(buf, "wm prior") ;
rf->feature_names[i] = (char *)calloc(strlen(buf)+1, sizeof(char)) ;
strcpy(rf->feature_names[i], buf) ;
i++ ; sprintf(buf, "csf prior") ;
rf->feature_names[i] = (char *)calloc(strlen(buf)+1, sizeof(char)) ;
strcpy(rf->feature_names[i], buf) ;
i++ ; sprintf(buf, "WMSA in nbhd") ;
rf->feature_names[i] = (char *)calloc(strlen(buf)+1, sizeof(char)) ;
strcpy(rf->feature_names[i], buf) ;
if (Gdiag & DIAG_WRITE)
{
printf("writing training voxels to tv.mgz\n") ;
MRIwrite(mri_training_voxels, "tv.mgz") ;
}
}
// now build training features and classes
training_classes = (int *)calloc(ntraining, sizeof(training_classes[0])) ;
if (training_classes == NULL)
ErrorExit(ERROR_NOFILE, "train_rforest: could not allocate %d-length training buffers",ntraining);
training_data = (double **)calloc(ntraining, sizeof(training_data[0])) ;
if (training_classes == NULL)
ErrorExit(ERROR_NOFILE, "train_rforest: could not allocate %d-length training buffers",ntraining);
for (i = n = 0 ; n < nsubjects ; n++)
{
mri_in = mri_inputs[n][0] ; mri_seg = mri_segs[n][0] ; transform = transforms[n][0] ;
for (x = 0 ; x < mri_in->width ; x++)
for (y = 0 ; y < mri_in->height; y++)
for (z = 0 ; z < mri_in->depth; z++)
{
if ((int)MRIgetVoxVal(mri_training_voxels, x, y, z, n) == 0)
continue ;
label = MRIgetVoxVal(mri_seg, x, y, z, 0) ;
TransformSourceVoxelToAtlas(transform, mri_in, x, y, z, &xatlas, &yatlas, &zatlas) ;
xt = nint(xatlas/tvoxel_size) ; yt = nint(yatlas/tvoxel_size) ; zt = nint(zatlas/tvoxel_size) ;
if (IS_FUTURE_WMSA(label))
tlabel = FUTURE_WMSA ;
else if (IS_WMSA(label))
tlabel = WMSA ;
else
tlabel= NOT_WMSA ;
training_classes[i] = tlabel ;
training_data[i] = (double *)calloc(nfeatures, sizeof(double)) ;
if (training_data[i] == NULL)
ErrorExit(ERROR_NOMEMORY, "train_rforest: could not allocate %d-len feature vector #%d",
nfeatures, i) ;
training_classes[i] = training_classes[i] ;
// extract_feature(mri_in, parms->wsize, x, y, z, training_data[i], xatlas, yatlas, zatlas) ;
extract_long_features(mri_in, mri_seg, transform, gca, parms->wsize, x, y, z, training_data[i]) ;
if (training_data[i][Gdiag_no] < 80 && training_classes[i] == 1)
DiagBreak() ;
i++ ;
}
MRIfree(&mri_in) ; MRIfree(&mri_seg) ; TransformFree(&transform) ;
}
if (i < ntraining)
{
printf("warning!!!! i (%d) < ntraining (%d)! Setting ntraining=i\n", i, ntraining) ;
ntraining = i ;
}
printf("training random forest with %dK FUTURE WMSA labels, %dK WMSA labels, and %dK non (ratio=%2.1f:%2.1f)\n",
nfuture/1000, nwmsa/1000, nnot/1000, (float)nnot/(float)nfuture, (float)nnot/(float)nwmsa) ;
RFtrain(rf, parms->feature_fraction, parms->training_fraction, training_classes, training_data, ntraining);
correct = RFcomputeOutOfBagCorrect(rf, training_classes, training_data,ntraining);
printf("out of bag accuracy: %d of %d = %2.2f%%\n", correct, ntraining,
100.0*correct/ntraining) ;
if (log_file_name)
{
struct flock fl;
int fd;
char line[MAX_LINE_LEN] ;
printf("writing results to train.log file %s\n", log_file_name) ;
fd = open(log_file_name, O_WRONLY|O_APPEND|O_CREAT, S_IRWXU|S_IRWXG);
if (fd < 0)
ErrorExit(ERROR_NOFILE, "%s: could not open test log file %s",
Progname, log_file_name);
fcntl(fd, F_SETLKW, &fl); /* F_GETLK, F_SETLK, F_SETLKW */
sprintf(line, "%f %d %d %f\n",
rf->training_fraction,
rf->max_depth,
rf->ntrees,
100.0*correct/ntraining) ;
write(fd, line, (strlen(line))*sizeof(char)) ;
fl.l_type = F_UNLCK; /* tell it to unlock the region */
fcntl(fd, F_SETLK, &fl); /* set the region to unlocked */
close(fd) ;
}
for (i = 0 ; i < ntraining ; i++) // allow for augmenting with other wmsa examples
free(training_data[i]) ;
free(training_data) ;
free(training_classes) ;
MRIfree(&mri_training_voxels) ;
return(rf) ;
}
int main ( int argc, char** argv ) {
MRI* mri = NULL;
int zX = 256;
int zY = 256;
int zZ = 256;
int err = NO_ERROR;
int nX = 0;
int nY = 0;
int nZ = 0;
float sizeX = 1.0;
float sizeY = 1.0;
float sizeZ = 1.0;
int setMethod = SET_METHOD_XYZ;
int setValue = 0;
char fnVol[256] = "new_volume.mgz";
int i;
char* arg = NULL;
for ( i = 1; i < argc; i++ ) {
arg = argv[i];
if ( argv[i] && *argv[i] != '-' ) {
printf( "ERROR: Unrecognized argument %s\n", argv[i] );
PrintUsage( NULL );
exit( 1 );
}
while ( arg[0] == '-' )
arg = arg+1;
if ( strlen(arg) <= 0 )
continue;
if ( strcmp(arg,"h") == 0 ||
strcmp(arg,"help") == 0 ) {
PrintUsage( NULL );
exit( 0 );
}
if ( strcmp(arg,"f") == 0 ||
strcmp(arg,"filename") == 0 ) {
if ( i+1 >= argc ) {
PrintUsage( "No argument to filename option." );
exit( 1 );
}
strcpy( fnVol, argv[i+1] );
i++;
}
if ( strcmp(arg,"x") == 0 ||
strcmp(arg,"width") == 0 ) {
if ( i+1 >= argc ) {
PrintUsage( "No argument to width option." );
exit( 1 );
}
zX = atoi(argv[i+1]);
i++;
}
if ( strcmp(arg,"y") == 0 ||
strcmp(arg,"height") == 0 ) {
if ( i+1 >= argc ) {
PrintUsage( "No argument to height option." );
exit( 1 );
}
zY = atoi(argv[i+1]);
i++;
}
if ( strcmp(arg,"z") == 0 ||
strcmp(arg,"depth") == 0 ) {
if ( i+1 >= argc ) {
PrintUsage( "No argument to depth option." );
exit( 1 );
}
zZ = atoi(argv[i+1]);
i ++;
}
if ( strcmp(arg,"sizex") == 0 ) {
if ( i+1 >= argc ) {
PrintUsage( "No argument to sizex option." );
exit( 1 );
}
sizeX = atof(argv[i+1]);
i++;
}
if ( strcmp(arg,"sizey") == 0 ) {
if ( i+1 >= argc ) {
PrintUsage( "No argument to sizey option." );
exit( 1 );
}
sizeY = atof(argv[i+1]);
i++;
}
if ( strcmp(arg,"sizez") == 0 ) {
if ( i+1 >= argc ) {
PrintUsage( "No argument to sizez optoin." );
exit( 1 );
}
sizeZ = atof(argv[i+1]);
i++;
}
if ( strcmp(arg,"set-method") == 0 ) {
if ( i+1 >= argc ) {
PrintUsage( "No argument to set-method option." );
exit( 1 );
}
if ( strcmp( argv[i+1], "xyz" ) == 0 ) {
setMethod = SET_METHOD_XYZ;
i++;
printf( "set_method is xyz\n" );
} else if ( strcmp( argv[i+1], "random" ) == 0 ) {
setMethod = SET_METHOD_RANDOM;
i++;
printf( "set_method is random\n" );
} else if ( strncmp( argv[i+1], "constant", 9 ) == 0 ) {
if ( i+2 >= argc ) {
PrintUsage( "No value argument to constant method option." );
exit( 1 );
}
setMethod = SET_METHOD_CONSTANT;
setValue = atoi( argv[i+2] );
i+=2;
printf( "set_method is constant, %d\n", setValue );
} else {
PrintUsage( "Unrecognized argument to set-method option" );
exit( 1 );
}
}
}
printf( "Creating volume %s\n"
" width = %d height = %d depth = %d\n"
" xsize = %f ysize = %f zsize = %f\n"
" set method = %s, constant = %d\n",
fnVol, zX, zY, zZ,
sizeX, sizeY, sizeZ,
sSetMethods[setMethod], setValue );
mri = MRIalloc( zX, zY, zZ, MRI_UCHAR );
if ( NULL == mri ) {
fprintf( stderr, "Couldn't create volume.\n" );
return 1;
}
MRIsetResolution( mri, sizeX, sizeY, sizeZ );
switch ( setMethod ) {
case SET_METHOD_CONSTANT:
MRIvalueFill( mri, 0 );
break;
case SET_METHOD_RANDOM:
for ( nZ = 0; nZ < zZ; nZ++ ) {
for ( nY = 0; nY < zY; nY++ ) {
for ( nX = 0; nX < zX; nX++ ) {
MRIvox( mri, nX, nY, nZ ) = (int)((random()/(float)RAND_MAX)*255.0);
}
}
}
break;
case SET_METHOD_XYZ:
for ( nZ = 0; nZ < zZ; nZ++ ) {
for ( nY = 0; nY < zY; nY++ ) {
for ( nX = 0; nX < zX; nX++ ) {
MRIvox( mri, nX, nY, nZ ) =
(((float)nZ/(float)zZ)*255.0/3.0) +
(((float)nY/(float)zY)*255.0/3.0) +
(((float)nX/(float)zX)*255.0/3.0) ;
}
}
}
break;
default:
for ( nZ = (zZ/2) - (zZ/4); nZ < (zZ/2) + (zZ/4); nZ++ ) {
for ( nY = (zY/2) - (zY/4); nY < (zY/2) + (zY/4); nY++ ) {
for ( nX = (zX/2) - (zX/4); nX < (zX/2) + (zX/4); nX++ ) {
MRIvox( mri, nX, nY, nZ ) = 255;
}
}
}
}
err = MRIwrite( mri, fnVol );
if ( NO_ERROR != err ) {
fprintf( stderr, "Couldn't write volume.\n" );
return 1;
}
MRIfree( &mri );
return 0;
}
int
main(int argc, char *argv[]) {
char **av ;
int ac, nargs ;
MRI *mri_orig, *mri_norm, *mri_bias ;
int msec, minutes, seconds ;
struct timeb start ;
/* rkt: check for and handle version tag */
nargs = handle_version_option
(argc, argv,
"$Id: mri_apply_bias.c,v 1.5 2011/03/02 00:04:13 nicks Exp $",
"$Name: stable5 $");
if (nargs && argc - nargs == 1)
exit (0);
argc -= nargs;
Progname = argv[0] ;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
TimerStart(&start) ;
ac = argc ;
av = argv ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
if (argc < 4)
usage_exit(1) ;
mri_orig = MRIread(argv[1]) ;
if (mri_orig == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read %s",Progname, argv[1]) ;
mri_bias = MRIread(argv[2]) ;
if (mri_bias == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read %s",Progname, argv[2]) ;
if (xform_fname)
{
TRANSFORM *transform ;
MRI *mri ;
transform = TransformRead(xform_fname) ;
if (transform == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not load transform %s", Progname, xform_fname) ;
mri = MRIcloneDifferentType(mri_orig, MRI_FLOAT) ;
TransformApplyInverse(transform, mri_bias, mri) ;
MRIfree(&mri_bias) ; mri_bias = mri ;
}
mri_norm = apply_bias(mri_orig, NULL, mri_bias);
fprintf(stderr, "writing to %s...\n", argv[3]) ;
MRIwrite(mri_norm, argv[3]) ;
MRIfree(&mri_norm) ;
msec = TimerStop(&start) ;
seconds = nint((float)msec/1000.0f) ;
minutes = seconds / 60 ;
seconds = seconds % 60 ;
fprintf(stderr, "bias correction took %d minutes and %d seconds.\n",
minutes, seconds) ;
exit(0) ;
return(0) ;
}
/*---------------------------------------------------------------*/
int main(int argc, char *argv[]) {
int nargs, nthvtx, nnbrs1, nnbrs2, nthnbr, nbrvtxno1, nbrvtxno2;
int nthface, annot1, annot2;
VERTEX *vtx1, *vtx2;
FACE *face1, *face2;
float diff, maxdiff;
nargs = handle_version_option (argc, argv, vcid, "$Name: stable5 $");
if (nargs && argc - nargs == 1) exit (0);
argc -= nargs;
cmdline = argv2cmdline(argc,argv);
uname(&uts);
getcwd(cwd,2000);
Progname = argv[0] ;
argc --;
argv++;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
if (argc == 0) usage_exit();
parse_commandline(argc, argv);
check_options();
if (checkoptsonly) return(0);
SUBJECTS_DIR = getenv("SUBJECTS_DIR");
if (SUBJECTS_DIR == NULL) {
printf("INFO: SUBJECTS_DIR not defined in environment\n");
//exit(1);
}
if (SUBJECTS_DIR1 == NULL) SUBJECTS_DIR1 = SUBJECTS_DIR;
if (SUBJECTS_DIR2 == NULL) SUBJECTS_DIR2 = SUBJECTS_DIR;
if (surf1path == NULL && surfname == NULL) surfname = "orig";
if (surf1path == NULL) {
sprintf(tmpstr,"%s/%s/surf/%s.%s",SUBJECTS_DIR1,subject1,hemi,surfname);
surf1path = strcpyalloc(tmpstr);
}
if (surf2path == NULL) {
sprintf(tmpstr,"%s/%s/surf/%s.%s",SUBJECTS_DIR2,subject2,hemi,surfname);
surf2path = strcpyalloc(tmpstr);
}
dump_options(stdout);
//read-in each surface. notice that the random number generator is
//seeded with the same value prior to each read. this is because in
//the routine MRIScomputeNormals, if it finds a zero-length vertex
//normal, is adds a random value to the x,y,z and recomputes the normal.
//so if comparing identical surfaces, the seed must be the same so that
//any zero-length vertex normals appear the same.
setRandomSeed(seed) ;
surf1 = MRISread(surf1path);
if (surf1 == NULL) {
printf("ERROR: could not read %s\n",surf1path);
exit(1);
}
setRandomSeed(seed) ;
surf2 = MRISread(surf2path);
if (surf2 == NULL) {
printf("ERROR: could not read %s\n",surf2path);
exit(1);
}
printf("Number of vertices %d %d\n",surf1->nvertices,surf2->nvertices);
printf("Number of faces %d %d\n",surf1->nfaces,surf2->nfaces);
//Number of Vertices ----------------------------------------
if (surf1->nvertices != surf2->nvertices) {
printf("Surfaces differ in number of vertices %d %d\n",
surf1->nvertices,surf2->nvertices);
exit(101);
}
//Number of Faces ------------------------------------------
if (surf1->nfaces != surf2->nfaces) {
printf("Surfaces differ in number of faces %d %d\n",
surf1->nfaces,surf2->nfaces);
exit(101);
}
//surf1->faces[10000].area = 100;
//surf1->vertices[10000].x = 100;
if (ComputeNormalDist) {
double dist, dx, dy, dz, dot ;
MRI *mri_dist ;
mri_dist = MRIalloc(surf1->nvertices,1,1,MRI_FLOAT) ;
MRIScomputeMetricProperties(surf1) ;
MRIScomputeMetricProperties(surf2) ;
for (nthvtx=0; nthvtx < surf1->nvertices; nthvtx++) {
vtx1 = &(surf1->vertices[nthvtx]);
vtx2 = &(surf2->vertices[nthvtx]);
dx = vtx2->x-vtx1->x ;
dy = vtx2->y-vtx1->y ;
dz = vtx2->z-vtx1->z ;
dist = sqrt(dx*dx + dy*dy + dz*dz) ;
dot = dx*vtx1->nx + dy*vtx1->ny + dz*vtx1->nz ;
dist = dist * dot / fabs(dot) ;
MRIsetVoxVal(mri_dist, nthvtx, 0, 0, 0, dist) ;
}
MRIwrite(mri_dist, out_fname) ;
MRIfree(&mri_dist) ;
exit(0);
}
maxdiff=0;
//------------------------------------------------------------
if (CheckSurf) {
printf("Comparing surfaces\n");
// Loop over vertices ---------------------------------------
error_count=0;
for (nthvtx=0; nthvtx < surf1->nvertices; nthvtx++) {
vtx1 = &(surf1->vertices[nthvtx]);
vtx2 = &(surf2->vertices[nthvtx]);
if (vtx1->ripflag != vtx2->ripflag) {
printf("Vertex %d differs in ripflag %c %c\n",
nthvtx,vtx1->ripflag,vtx2->ripflag);
if (++error_count>=MAX_NUM_ERRORS) break;
}
if (CheckXYZ) {
diff=fabs(vtx1->x - vtx2->x);
if (diff>maxdiff) maxdiff=diff;
if (diff>thresh) {
printf("Vertex %d differs in x %g %g\t(%g)\n",
nthvtx,vtx1->x,vtx2->x,diff);
if (++error_count>=MAX_NUM_ERRORS) break;
}
diff=fabs(vtx1->y - vtx2->y);
if (diff>maxdiff) maxdiff=diff;
if (diff>thresh) {
printf("Vertex %d differs in y %g %g\t(%g)\n",
nthvtx,vtx1->y,vtx2->y,diff);
if (++error_count>=MAX_NUM_ERRORS) break;
}
diff=fabs(vtx1->z - vtx2->z);
if (diff>maxdiff) maxdiff=diff;
if (diff>thresh) {
printf("Vertex %d differs in z %g %g\t(%g)\n",
nthvtx,vtx1->z,vtx2->z,diff);
if (++error_count>=MAX_NUM_ERRORS) break;
}
}
if (CheckNXYZ) {
diff=fabs(vtx1->nx - vtx2->nx);
if (diff>maxdiff) maxdiff=diff;
if (diff>thresh) {
printf("Vertex %d differs in nx %g %g\t(%g)\n",
nthvtx,vtx1->nx,vtx2->nx,diff);
if (++error_count>=MAX_NUM_ERRORS) break;
}
diff=fabs(vtx1->ny - vtx2->ny);
if (diff>maxdiff) maxdiff=diff;
if (diff>thresh) {
printf("Vertex %d differs in ny %g %g\t(%g)\n",
nthvtx,vtx1->ny,vtx2->ny,diff);
if (++error_count>=MAX_NUM_ERRORS) break;
}
diff=fabs(vtx1->nz - vtx2->nz);
if (diff>maxdiff) maxdiff=diff;
if (diff>thresh) {
printf("Vertex %d differs in nz %g %g\t(%g)\n",
nthvtx,vtx1->nz,vtx2->nz,diff);
if (++error_count>=MAX_NUM_ERRORS) break;
}
}
nnbrs1 = surf1->vertices[nthvtx].vnum;
nnbrs2 = surf2->vertices[nthvtx].vnum;
if (nnbrs1 != nnbrs2) {
printf("Vertex %d has a different number of neighbors %d %d\n",
nthvtx,nnbrs1,nnbrs2);
if (++error_count>=MAX_NUM_ERRORS) break;
}
for (nthnbr=0; nthnbr < nnbrs1; nthnbr++) {
nbrvtxno1 = surf1->vertices[nthvtx].v[nthnbr];
nbrvtxno2 = surf2->vertices[nthvtx].v[nthnbr];
if (nbrvtxno1 != nbrvtxno2) {
printf("Vertex %d differs in the identity of the "
"%dth neighbor %d %d\n",nthvtx,nthnbr,nbrvtxno1,nbrvtxno2);
if (++error_count>=MAX_NUM_ERRORS) break;
}
}
if (error_count>=MAX_NUM_ERRORS) break;
}// loop over vertices
if (maxdiff>0) printf("maxdiff=%g\n",maxdiff);
if (error_count > 0) {
printf("Exiting after finding %d errors\n",error_count);
if (error_count>=MAX_NUM_ERRORS) {
printf("Exceeded MAX_NUM_ERRORS loop guard\n");
}
exit(103);
}
// Loop over faces ----------------------------------------
error_count=0;
for (nthface=0; nthface < surf1->nfaces; nthface++) {
face1 = &(surf1->faces[nthface]);
face2 = &(surf2->faces[nthface]);
if (CheckNXYZ) {
diff=fabs(face1->nx - face2->nx);
if (diff>maxdiff) maxdiff=diff;
if (diff>thresh) {
printf("Face %d differs in nx %g %g\t(%g)\n",
nthface,face1->nx,face2->nx,diff);
if (++error_count>=MAX_NUM_ERRORS) break;
}
diff=fabs(face1->ny - face2->ny);
if (diff>maxdiff) maxdiff=diff;
if (diff>thresh) {
printf("Face %d differs in ny %g %g\t(%g)\n",
nthface,face1->ny,face2->ny,diff);
if (++error_count>=MAX_NUM_ERRORS) break;
}
diff=fabs(face1->nz - face2->nz);
if (diff>maxdiff) maxdiff=diff;
if (diff>thresh) {
printf("Face %d differs in nz %g %g\t(%g)\n",
nthface,face1->nz,face2->nz,diff);
if (++error_count>=MAX_NUM_ERRORS) break;
}
}
diff=fabs(face1->area - face2->area);
if (diff>maxdiff) maxdiff=diff;
if (diff>thresh) {
printf("Face %d differs in area %g %g\t(%g)\n",
nthface,face1->area,face2->area,diff);
if (++error_count>=MAX_NUM_ERRORS) break;
}
if (face1->ripflag != face2->ripflag) {
printf("Face %d differs in ripflag %c %c\n",
nthface,face1->ripflag,face2->ripflag);
if (++error_count>=MAX_NUM_ERRORS) break;
}
for (nthvtx = 0; nthvtx < 3; nthvtx++) {
if (face1->v[nthvtx] != face2->v[nthvtx]) {
printf("Face %d differs in identity of %dth vertex %d %d\n",
nthface,nthvtx,face1->ripflag,face2->ripflag);
if (++error_count>=MAX_NUM_ERRORS) break;
}
} // end loop over nthface vertex
if (error_count>=MAX_NUM_ERRORS) break;
} // end loop over faces
if (maxdiff>0) printf("maxdiff=%g\n",maxdiff);
if (error_count > 0) {
printf("Exiting after finding %d errors\n",error_count);
if (error_count>=MAX_NUM_ERRORS) {
printf("Exceeded MAX_NUM_ERRORS loop guard\n");
}
exit(103);
}
printf("Surfaces are the same\n");
exit(0);
} // end check surf
// -----------------------------------------------------------------
if (CheckCurv) {
printf("Checking curv file %s\n",curvname);
sprintf(tmpstr,"%s/%s/surf/%s.%s",SUBJECTS_DIR1,subject1,hemi,curvname);
printf("Loading curv file %s\n",tmpstr);
if (MRISreadCurvatureFile(surf1, tmpstr) != 0) {
printf("ERROR: reading curvature file %s\n",tmpstr);
exit(1);
}
sprintf(tmpstr,"%s/%s/surf/%s.%s",SUBJECTS_DIR2,subject2,hemi,curvname);
printf("Loading curv file %s\n",tmpstr);
if (MRISreadCurvatureFile(surf2, tmpstr) != 0) {
printf("ERROR: reading curvature file %s\n",tmpstr);
exit(1);
}
error_count=0;
for (nthvtx=0; nthvtx < surf1->nvertices; nthvtx++) {
vtx1 = &(surf1->vertices[nthvtx]);
vtx2 = &(surf2->vertices[nthvtx]);
diff=fabs(vtx1->curv - vtx2->curv);
if (diff>maxdiff) maxdiff=diff;
if (diff > thresh) {
printf("curv files differ at vertex %d %g %g\t(%g)\n",
nthvtx,vtx1->curv,vtx2->curv,diff);
if (++error_count>=MAX_NUM_ERRORS) break;
}
} // end loop over vertices
if (maxdiff>0) printf("maxdiff=%g\n",maxdiff);
if (error_count > 0) {
printf("Exiting after finding %d errors\n",error_count);
if (error_count>=MAX_NUM_ERRORS) {
printf("Exceeded MAX_NUM_ERRORS loop guard\n");
}
exit(103);
}
printf("Curv files are the same\n");
exit(0);
} // end check curv
// ---------------------------------------------------------
if (CheckAParc) {
printf("Checking AParc %s\n",aparcname);
sprintf(tmpstr,"%s/%s/label/%s.%s.annot",
SUBJECTS_DIR1,subject1,hemi,aparcname);
printf("Loading aparc file %s\n",tmpstr);
fflush(stdout);
if (MRISreadAnnotation(surf1, tmpstr)) {
printf("ERROR: MRISreadAnnotation() failed %s\n",tmpstr);
exit(1);
}
if (aparc2name) aparcname = aparc2name;
sprintf(tmpstr,"%s/%s/label/%s.%s.annot",
SUBJECTS_DIR2,subject2,hemi,aparcname);
printf("Loading aparc file %s\n",tmpstr);
fflush(stdout);
if (MRISreadAnnotation(surf2, tmpstr)) {
printf("ERROR: MRISreadAnnotation() failed %s\n",tmpstr);
exit(1);
}
error_count=0;
for (nthvtx=0; nthvtx < surf1->nvertices; nthvtx++) {
annot1 = surf1->vertices[nthvtx].annotation;
annot2 = surf2->vertices[nthvtx].annotation;
if (annot1 != annot2) {
printf("aparc files differ at vertex %d: 1:%s 2:%s\n",
nthvtx,
CTABgetAnnotationName(surf1->ct,annot1),
CTABgetAnnotationName(surf2->ct,annot2));
if (++error_count>=MAX_NUM_ERRORS) break;
}
} // end loop over vertices
if (error_count > 0) {
printf("Exiting after finding %d errors\n",error_count);
if (error_count>=MAX_NUM_ERRORS) {
printf("Exceeded MAX_NUM_ERRORS loop guard\n");
}
exit(103);
}
printf("\n"
"AParc files are the same\n"
"------------------------\n");
exit(0);
}
return 0;
}
/*---------------------------------------------------------*/
int main(int argc, char **argv) {
int n,err, f, nhits, r,c,s;
float ipr, bpr, intensity;
float *framepower=NULL, val;
LTA *lta;
int nargs;
//int endian,roitype;
/* rkt: check for and handle version tag */
nargs = handle_version_option (argc, argv, "$Id: mri_vol2roi.c,v 1.32 2011/03/02 00:04:25 nicks Exp $", "$Name: stable5 $");
if (nargs && argc - nargs == 1)
exit (0);
argc -= nargs;
Progname = argv[0] ;
argc --;
argv++;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
if (argc == 0) usage_exit();
parse_commandline(argc, argv);
check_options();
printf("--------------------------------------------------------\n");
getcwd(tmpstr,2000);
printf("%s\n",tmpstr);
printf("%s\n",Progname);
for (n=0;n<argc;n++) printf(" %s",argv[n]);
printf("\n");
printf("version %s\n",vcid);
printf("--------------------------------------------------------\n");
dump_options(stdout);
/* --------- load in the (possibly 4-D) source volume --------------*/
printf("Loading volume %s ...",srcvolid);
mSrcVol = MRIread(srcvolid);
if(mSrcVol == NULL) exit(1);
printf("done\n");
/* Dsrc: read the source registration file */
if (srcregfile != NULL) {
err = regio_read_register(srcregfile, &srcsubject, &ipr, &bpr,
&intensity, &Dsrc, &float2int_src);
if (err) exit(1);
printf("srcreg Dsrc -------------\n");
MatrixPrint(stdout,Dsrc);
printf("----------------------------------\n");
} else Dsrc = NULL;
/* Wsrc: Get the source warping Transform */
Wsrc = NULL;
/* Fsrc: Get the source FOV registration matrix */
Fsrc = NULL;
/* Qsrc: Compute the quantization matrix for src volume */
Qsrc = FOVQuantMatrix(mSrcVol->width, mSrcVol->height, mSrcVol->depth,
mSrcVol->xsize, mSrcVol->ysize, mSrcVol->zsize);
printf("ras2vox src (tkreg) Qsrc -------------\n");
MatrixPrint(stdout,Qsrc);
printf("----------------------------------\n");
/* ----------- load in the label ----------------- */
if (labelfile != NULL) {
Label = LabelReadFile(labelfile);
if (Label == NULL) exit(1);
/* load in the source-to-label registration */
if (src2lblregfile != NULL) {
//err = regio_read_xfm(src2lblregfile, &Msrc2lbl);
//if(err) exit(1);
lta = LTAread(src2lblregfile);
if (lta->type == LINEAR_VOX_TO_VOX) {
printf("INFO: converting LTA to RAS\n");
LTAvoxelTransformToCoronalRasTransform(lta);
}
Msrc2lbl = MatrixCopy(lta->xforms[0].m_L,NULL);
} else if (labeltal) {
/* Load the talairach.xfm and make it approp for reg.dat*/
Msrc2lbl = DevolveXFM(srcsubject,NULL,talxfm);
if (Msrc2lbl==NULL) exit(1);
} else Msrc2lbl = NULL;
if (Msrc2lbl != NULL) {
printf("-- Source2Label %s ---- \n",src2lblregfile);
MatrixPrint(stdout,Msrc2lbl);
printf("-------------------------------\n");
}
} else {
Label = NULL;
Msrc2lbl = NULL;
}
/* -------------- load mask volume stuff -----------------------------*/
if (mskvolid != NULL) {
/* load the mask volume (single frame) */
printf("Reading %s\n",mskvolid);
mMskVol = MRIread(mskvolid);
if(mMskVol == NULL) exit(1);
if(mskframe > 0){
mritmp = fMRIframe(mMskVol, mskframe, NULL);
if(mritmp == NULL) exit(1);
MRIfree(&mMskVol);
mMskVol = mritmp;
}
/* Qmsk: Compute the quantization matrix for msk volume */
/* crsFOV = Qmsk*xyzFOV */
Qmsk = FOVQuantMatrix(mMskVol->width, mMskVol->height, mMskVol->depth,
mMskVol->xsize, mMskVol->ysize, mMskVol->zsize);
/* get the mask2source registration information */
/* xyzSrc = Mmsk2src * xyzMsk */
if (msk2srcregfile != NULL) {
err = regio_read_mincxfm(msk2srcregfile, &Mmsk2src, NULL);
if (err) exit(1);
} else Mmsk2src = NULL;
/* convert from Mask Anatomical to Src FOV */
if (!msksamesrc) {
mSrcMskVol = vol2vol_linear(mMskVol, Qmsk, NULL, NULL, Dmsk,
Qsrc, Fsrc, Wsrc, Dsrc,
mSrcVol->height, mSrcVol->width, mSrcVol->depth,
Mmsk2src, INTERP_NEAREST, float2int_msk);
if (mSrcMskVol == NULL) exit(1);
} else mSrcMskVol = mMskVol;
/* binarize the mask volume */
mri_binarize(mSrcMskVol, mskthresh, msktail, mskinvert,
mSrcMskVol, &nmskhits);
} else {
mSrcMskVol = NULL;
nmskhits = 0;
}
/*-------------- Done loading mask stuff -------------------------*/
/* If this is a statistical volume, raise each frame to it's appropriate
power (eg, stddev needs to be squared)*/
if (is_sxa_volume(srcvolid)) {
printf("INFO: Source volume detected as selxavg format\n");
sxa = ld_sxadat_from_stem(srcvolid);
if (sxa == NULL) exit(1);
framepower = sxa_framepower(sxa,&f);
if (f != mSrcVol->nframes) {
fprintf(stderr," number of frames is incorrect (%d,%d)\n",
f,mSrcVol->nframes);
exit(1);
}
printf("INFO: Adjusting Frame Power\n");
fflush(stdout);
mri_framepower(mSrcVol,framepower);
}
/*--------- Prepare the final mask ------------------------*/
if (Label != NULL) {
mFinalMskVol = label2mask_linear(mSrcVol, Qsrc, Fsrc, Wsrc,
Dsrc, mSrcMskVol,
Msrc2lbl, Label, labelfillthresh, float2int_src,
&nlabelhits, &nfinalhits);
if (mFinalMskVol == NULL) exit(1);
} else {
mFinalMskVol = mSrcMskVol;
nfinalhits = nmskhits;
}
if (!oldtxtstyle) {
/* count the number of functional voxels = 1 in the mask */
nfinalhits = 0;
for (r=0;r<mFinalMskVol->height;r++) {
for (c=0;c<mFinalMskVol->width;c++) {
for (s=0;s<mFinalMskVol->depth;s++) {
val = MRIgetVoxVal(mFinalMskVol,c,r,s,0);
if (val > 0.5) nfinalhits ++;
}
}
}
if (Label != NULL)
nlabelhits = CountLabelHits(mSrcVol, Qsrc, Fsrc,
Wsrc, Dsrc, Msrc2lbl,
Label, labelfillthresh,float2int_src);
else nlabelhits = 0;
}
/*-------------------------------------------------------*/
/*--------- Map the volume into the ROI -----------------*/
printf("Averging over ROI\n");
fflush(stdout);
mROI = vol2maskavg(mSrcVol, mFinalMskVol,&nhits);
if (mROI == NULL) exit(1);
printf("Done averging over ROI (nhits = %d)\n",nhits);
/*-------------------------------------------------------*/
/* ------- Save the final mask ------------------ */
if (finalmskvolid != 0) {
//mri_save_as_bvolume(mFinalMskVol,finalmskvolid,endian,BF_FLOAT);
//MRIwriteAnyFormat(mFinalMskVol,finalmskvolid,"bfloat",-1,NULL);
sprintf(tmpstr,"%s.%s",finalmskvolid,outext);
MRIwrite(mFinalMskVol,tmpstr);
}
/* ------- Save CRS of the the final mask ------------------ */
if (finalmskcrs != NULL) {
fp = fopen(finalmskcrs,"w");
if (fp==NULL) {
fprintf(stderr,"ERROR: cannot open %s\n",finalmskcrs);
exit(1);
}
for (r=0;r<mFinalMskVol->height;r++) {
for (c=0;c<mFinalMskVol->width;c++) {
for (s=0;s<mFinalMskVol->depth;s++) {
val = MRIgetVoxVal(mFinalMskVol,c,r,s,0);
if (val > 0.5) {
fprintf(fp,"%d %d %d\n",c,r,s);
}
}
}
}
fclose(fp);
}
/* If this is a statistical volume, lower each frame to it's appropriate
power (eg, variance needs to be sqrt'ed) */
if (is_sxa_volume(srcvolid)) {
printf("INFO: Readjusting Frame Power\n");
fflush(stdout);
for (f=0; f < mROI->nframes; f++) framepower[f] = 1.0/framepower[f];
mri_framepower(mROI,framepower);
}
/* save the target volume in an appropriate format */
if(roifile != NULL){
sprintf(tmpstr,"%s.%s",roifile,outext);
MRIwrite(mROI,tmpstr);
/* for a stat volume, save the .dat file */
if (is_sxa_volume(srcvolid)) {
sxa->nrows = 1;
sxa->ncols = 1;
sv_sxadat_by_stem(sxa,roifile);
}
}
/* save as text */
if(roitxtfile != NULL) {
fp = fopen(roitxtfile,"w");
if (fp==NULL) {
fprintf(stderr,"ERROR: cannot open %s\n",roitxtfile);
exit(1);
}
if (oldtxtstyle) {
printf("INFO: saving as old style txt\n");
fprintf(fp,"%d \n",nmskhits);
}
if (! plaintxtstyle ) {
fprintf(fp,"%d \n",nlabelhits);
fprintf(fp,"%d \n",nfinalhits);
}
for (f=0; f < mROI->nframes; f++)
fprintf(fp,"%f\n",MRIgetVoxVal(mROI,0,0,0,f));
fclose(fp);
}
/* ------- Mask the source and save it ------------------ */
if (srcmskvolid != 0) {
for (r=0;r<mFinalMskVol->height;r++) {
for (c=0;c<mFinalMskVol->width;c++) {
for (s=0;s<mFinalMskVol->depth;s++) {
val = MRIgetVoxVal(mFinalMskVol,c,r,s,0);
if (val < 0.5) {
for (f=0; f < mROI->nframes; f++)
MRIFseq_vox(mSrcVol,c,r,s,f) = 0.0;
}
}
}
}
MRIwrite(mSrcVol,srcmskvolid);
}
/* ------- Save as a text list ------------------ */
if (ListFile != 0) {
fp = fopen(ListFile,"w");
for (c=0;c<mFinalMskVol->width;c++) {
for (r=0;r<mFinalMskVol->height;r++) {
for (s=0;s<mFinalMskVol->depth;s++) {
val = MRIFseq_vox(mFinalMskVol,c,r,s,0);
if(val < 0.5) continue;
fprintf(fp,"%3d %3d %3d ",c,r,s);
for (f=0; f < mROI->nframes; f++){
val = MRIgetVoxVal(mSrcVol,c,r,s,f);
fprintf(fp,"%f ",val);
}
fprintf(fp,"\n");
}
}
}
fclose(fp);
}
return(0);
}
int
main(int argc, char *argv[])
{
char **av, fname[STRLEN] ;
int ac, nargs, i ;
char *subject, *cp, mdir[STRLEN], *out_fname, *name ;
int r, g, b, nedits = 0 ;
MRI *mri=NULL, *mri_edits=NULL, *mri_aseg_auto=NULL;
// default output file name:
out_fname = strcpyalloc("edits.mgz");
/* rkt: check for and handle version tag */
nargs = handle_version_option
(argc, argv,
"$Id: mri_compile_edits.c,v 1.6 2011/03/02 00:04:14 nicks Exp $",
"$Name: stable5 $");
if (nargs && argc - nargs == 1)
exit (0);
argc -= nargs;
Progname = argv[0] ;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
ac = argc ;
av = argv ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++)
{
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
if (argc < 2)
usage_exit(1) ;
if (strlen(sdir) == 0)
{
cp = getenv("SUBJECTS_DIR") ;
if (cp == NULL)
ErrorExit
(ERROR_BADPARM,
"%s: SUBJECTS_DIR must be defined in the env or on cmdline "
"with -sdir", Progname) ;
strcpy(sdir, cp) ;
}
subject = argv[1] ;
if (argv[2]) out_fname = argv[2] ;
printf("Compiling volume edits for subject %s...\n", subject) ;
fflush(stdout);
sprintf(mdir, "%s/%s/mri", sdir, subject) ;
/*
* brain.mgz
*/
sprintf(fname, "%s/brain.mgz", mdir) ;
mri = MRIread(fname) ;
if (mri)
{
if(NULL == mri_edits) mri_edits = MRIclone(mri, NULL) ;
int edits = MRIsetVoxelsWithValue(mri,
mri_edits,
WM_EDITED_OFF_VAL,
EDIT_BRAIN_OFF) ;
edits += MRIsetVoxelsWithValue(mri,
mri_edits,
WM_EDITED_ON_VAL,
EDIT_BRAIN_ON) ;
nedits += edits;
MRIfree(&mri) ;
if (edits) printf("Found %d edits in brain.mgz\n",edits);
fflush(stdout);
}
/*
* wm.mgz
*/
sprintf(fname, "%s/wm.mgz", mdir) ;
mri = MRIread(fname) ;
if (mri)
{
if(NULL == mri_edits) mri_edits = MRIclone(mri, NULL) ;
int edits = MRIsetVoxelsWithValue(mri,
mri_edits,
WM_EDITED_OFF_VAL,
EDIT_WM_OFF) ;
edits += MRIsetVoxelsWithValue(mri, mri_edits,
WM_EDITED_ON_VAL,
EDIT_WM_ON) ;
nedits += edits;
MRIfree(&mri) ;
if (edits) printf("Found %d edits in wm.mgz\n",edits);
fflush(stdout);
}
/*
* brainmask.mgz
*/
sprintf(fname, "%s/brainmask.mgz", mdir) ;
mri = MRIread(fname) ;
if (mri)
{
if(NULL == mri_edits) mri_edits = MRIclone(mri, NULL) ;
int edits = MRIsetVoxelsWithValue(mri,
mri_edits,
WM_EDITED_OFF_VAL,
EDIT_BRAINMASK_OFF) ;
edits += MRIsetVoxelsWithValue(mri, mri_edits,
WM_EDITED_ON_VAL,
EDIT_BRAINMASK_ON) ;
nedits += edits;
MRIfree(&mri) ;
if (edits) printf("Found %d edits in brainmask.mgz\n",edits);
fflush(stdout);
}
/*
* brain.finalsurfs.mgz
*/
sprintf(fname, "%s/brain.finalsurfs.mgz", mdir) ;
mri = MRIread(fname) ;
if (mri)
{
if(NULL == mri_edits) mri_edits = MRIclone(mri, NULL) ;
int edits = MRIsetVoxelsWithValue(mri,
mri_edits,
WM_EDITED_OFF_VAL,
EDIT_FINALSURFS_OFF) ;
edits += MRIsetVoxelsWithValue(mri,
mri_edits,
WM_EDITED_ON_VAL,
EDIT_FINALSURFS_ON) ;
nedits += edits;
MRIfree(&mri) ;
if (edits) printf("Found %d edits in brain.finalsurfs.mgz\n",edits);
fflush(stdout);
}
/*
* aseg.mgz
*/
sprintf(fname, "%s/aseg.mgz", mdir) ;
mri = MRIread(fname) ;
if (mri)
{
if(NULL == mri_edits) mri_edits = MRIclone(mri, NULL) ;
sprintf(fname, "%s/aseg.auto.mgz", mdir) ;
mri_aseg_auto = MRIread(fname) ;
if (mri_aseg_auto)
{
int edits = MRIsetDifferentVoxelsWithValue(mri,
mri_aseg_auto,
mri_edits,
EDIT_ASEG_CHANGED);
nedits += edits;
MRIfree(&mri) ;
MRIfree(&mri_aseg_auto) ;
if (edits) printf("Found %d edits in aseg.mgz\n",edits);
fflush(stdout);
}
}
if (mri_edits)
{
mri_edits->ct = CTABalloc(CTAB_ENTRIES) ;
strcpy (mri_edits->fname, "mri_compile_edits");
for (i = 0 ; i < CTAB_ENTRIES ; i++)
{
switch (i)
{
case EDIT_WM_OFF:
name = "wm-OFF" ;
r = 0 ;
g = 0 ;
b = 255 ;
break ;
case EDIT_WM_ON:
name = "wm-ON" ;
r = 255 ;
g = 0 ;
b = 0 ;
break ;
case EDIT_BRAIN_OFF:
name = "brain-OFF" ;
r = 0 ;
g = 255 ;
b = 255 ;
break ;
case EDIT_BRAIN_ON:
name = "brain-ON" ;
r = 255 ;
g = 255 ;
b = 0 ;
break ;
case EDIT_BRAINMASK_OFF:
name = "brainmask-OFF" ;
r = 0 ;
g = 64 ;
b = 255 ;
break ;
case EDIT_BRAINMASK_ON:
name = "brainmask-ON" ;
r = 255 ;
g = 26 ;
b = 0 ;
break ;
case EDIT_FINALSURFS_OFF:
name = "brain.finalsurf-OFF" ;
r = 0 ;
g = 128 ;
b = 255 ;
break ;
case EDIT_FINALSURFS_ON:
name = "brain.finalsurfs-ON" ;
r = 255 ;
g = 128 ;
b = 0 ;
break ;
case EDIT_ASEG_CHANGED:
name = "aseg-CHANGED" ;
r = 255 ;
g = 255 ;
b = 128 ;
break ;
default:
continue ;
}
strcpy(mri_edits->ct->entries[i]->name, name) ;
mri_edits->ct->entries[i]->ri = r ;
mri_edits->ct->entries[i]->gi = g ;
mri_edits->ct->entries[i]->bi = b ;
mri_edits->ct->entries[i]->ai = 255;
/* Now calculate the float versions. */
mri_edits->ct->entries[i]->rf =
(float)mri_edits->ct->entries[i]->ri / 255.0;
mri_edits->ct->entries[i]->gf =
(float)mri_edits->ct->entries[i]->gi / 255.0;
mri_edits->ct->entries[i]->bf =
(float)mri_edits->ct->entries[i]->bi / 255.0;
mri_edits->ct->entries[i]->af =
(float)mri_edits->ct->entries[i]->ai / 255.0;
}
}
// recon-all -show-edits greps on this text, so dont change it
if (nedits && mri_edits)
{
printf("%d mri_compile_edits_found, saving results to %s\n",
nedits, out_fname) ;
MRIwrite(mri_edits, out_fname);
printf("Edits can be viewed with command:\n");
printf("tkmedit %s T1.mgz -segmentation %s\n",subject,out_fname);
}
else
{
printf("0 mri_compile_edits_found\n") ;
}
exit(0) ;
return(0) ;
}
static int
normalize_timepoints(MRI *mri, double thresh, int nsoap)
{
int frame, x, y, z, skip, nvox ;
double target, val ;
MRI *mri_ctrl, *mri_bias, *mri_target, *mri_frame, *mri_kernel ;
mri_ctrl = MRIcloneDifferentType(mri, MRI_UCHAR) ;
mri_bias = MRIcloneDifferentType(mri, MRI_FLOAT) ;
mri_target = MRIcloneDifferentType(mri, MRI_FLOAT) ;
mri_kernel = MRIgaussian1d(sqrt(2.0*nsoap/M_PI), -1) ;
for (nvox = x = 0 ; x < mri->width ; x++)
for (y = 0 ; y < mri->height ; y++)
for (z = 0 ; z < mri->depth ; z++)
{
if (x == Gx && y == Gy && z == Gz)
DiagBreak() ;
for (target = 0.0, frame = 0 ; frame < mri->nframes ; frame++)
target += MRIgetVoxVal(mri, x, y, z, frame) ;
target /= mri->nframes ;
if (FZERO(target))
continue ; // both vals 0
skip = 0 ;
for (frame = 0 ; frame < mri->nframes ; frame++)
{
val = MRIgetVoxVal(mri, x, y, z, frame) ;
if (fabs(val-target) > thresh)
{
skip = 1 ;
break ;
}
}
if (skip)
continue ;
nvox++ ;
MRIsetVoxVal(mri_ctrl, x, y, z, 0, CONTROL_MARKED) ;
MRIsetVoxVal(mri_target, x, y, z, 0, target) ;
}
printf("%d voxels found to base intensity correction on\n", nvox) ;
// build a bias correction for each time point (which each has its own frame)
for (frame = 0 ; frame < mri->nframes ; frame++)
{
MRIclear(mri_bias) ;
for (x = 0 ; x < mri->width ; x++)
for (y = 0 ; y < mri->height ; y++)
for (z = 0 ; z < mri->depth ; z++)
{
target = MRIgetVoxVal(mri_target, x, y, z, 0) ;
val = MRIgetVoxVal(mri, x, y, z, frame) ;
if (FZERO(val))
val = 1.0 ;
MRIsetVoxVal(mri_bias, x, y, z, 0, target/val) ;
}
MRIbuildVoronoiDiagram(mri_bias, mri_ctrl, mri_bias) ;
MRIconvolveGaussian(mri_bias, mri_bias, mri_kernel) ;
// MRIsoapBubble(mri_bias, mri_ctrl, mri_bias, nsoap) ;
mri_frame = MRIcopyFrame(mri, NULL, frame, 0) ;
MRImultiply(mri_frame, mri_bias, mri_frame) ;
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
char fname[STRLEN] ;
sprintf(fname, "frame%d.mgz", frame) ;
MRIwrite(mri_frame, fname) ;
sprintf(fname, "bias%d.mgz", frame) ;
MRIwrite(mri_bias, fname) ;
sprintf(fname, "target%d.mgz", frame) ;
MRIwrite(mri_target, fname) ;
}
MRIcopyFrame(mri_frame, mri, 0, frame) ;
}
MRIfree(&mri_bias) ; MRIfree(&mri_kernel) ; MRIfree(&mri_target) ; MRIfree(&mri_ctrl) ;
return(NO_ERROR) ;
}
static int
MRIcheckRemovals(MRI *mri_T1, MRI *mri_dst, MRI *mri_labels, int wsize)
{
int x, y, z, width, depth, height, whalf, ntested, nchanged, on, vertex;
MRI *mri_tmp, *mri_region, *mri_plane, *mri_binary_plane ;
float min_on ;
whalf = (wsize-1)/2 ;
mri_tmp = MRIcopy(mri_dst, NULL) ;
mri_region = MRIalloc(wsize, wsize, wsize, MRI_UCHAR) ;
min_on = .1*wsize*wsize ;
MRIcopyLabel(mri_labels, mri_tmp, 255) ;
MRIbinarize(mri_tmp, mri_tmp, WM_MIN_VAL, 0, 100) ;
width = mri_T1->width ;
height = mri_T1->height ;
depth = mri_T1->depth ;
ntested = nchanged = 0 ;
if (Gdiag == 99)
{
MRIwrite(mri_tmp, "tmp.mgh") ;
}
for (z = 0 ; z < depth ; z++)
{
for (y = 0 ; y < height ; y++)
{
for (x = 0 ; x < width ; x++)
{
if (z == 87 && y == 88 && x == 163) /* test1 cs filled */
{
DiagBreak() ;
}
if (z == 88 && y == 89 && x == 163) /* test1 cs filled */
{
DiagBreak() ;
}
if (z == 101 && y == 133 && x == 152)
{
DiagBreak() ;
}
if (x == 157 && y == 143 && z == 98)
{
DiagBreak() ;
}
if (x == 156 && y == 143 && z == 98)
{
DiagBreak() ;
}
if (x == 154 && y == 167 && z == 128)
{
DiagBreak() ;
}
if (x == 136 && y == 147 && z == 28)
{
DiagBreak() ;
}
if (x == 163 && y == 88 && z == 86)
{
DiagBreak() ;
}
if ((x == 140 && y == 141 && z == 54) ||
(x == 140 && y == 141 && z == 53) ||
(x == 140 && y == 142 && z == 53) ||
(x == 140 && y == 142 && z == 54) ||
(x == 140 && y == 140 && z == 53))
{
DiagBreak() ; /* test4 cerebellum */
}
if (x == 142 && y == 139 && z == 54) /* test4 */
{
DiagBreak() ;
}
if (!MRIgetVoxVal(mri_labels, x, y, z, 0))
{
continue ;
}
ntested++ ;
MRIextract(mri_tmp, mri_region, x-whalf,y-whalf,z-whalf,
wsize, wsize, wsize) ;
vertex =
MRIcountCpolvOnAtVoxel(mri_region, whalf, whalf, whalf, wsize, &on) ;
mri_plane = MRIextractVertexPlane(mri_tmp, NULL, vertex,x,y,z,wsize);
MRIthreshold(mri_plane, mri_plane, 50) ;
MRIremove1dStructures(mri_plane,mri_plane, 10000,2,NULL);
mri_binary_plane = MRIfillFG(mri_plane, NULL, whalf, whalf, 0,
50, 128, &on) ;
if (on > min_on)
{
int xk, yk, i, ntransitions, i_prev ;
/*
now look at the winding # (number of white-black transitions
in a circle around the central point
*/
ntransitions = 0 ;
for (i = 0 ; i < NPTS ; i++)
{
xk = xpts[i] ;
yk = ypts[i] ;
i_prev = i-1 ;
if (i_prev < 0)
{
i_prev = NPTS-1 ;
}
if (MRIgetVoxVal(mri_binary_plane, whalf+xpts[i], whalf+ypts[i], 0, 0) !=
MRIgetVoxVal(mri_binary_plane,whalf+xpts[i_prev],
whalf+ypts[i_prev],0, 0))
{
ntransitions++ ;
}
}
if (ntransitions > 2) /* not planar */
{
nchanged++ ;
MRIsetVoxVal(mri_dst, x, y, z, 0, MRIgetVoxVal(mri_T1, x, y, z, 0)) ;
}
}
if (Gdiag & DIAG_WRITE)
{
MRIwrite(mri_region, "region.mgh") ;
MRIwrite(mri_plane, "plane.mgh") ;
MRIwrite(mri_binary_plane, "binary_plane.mgh") ;
}
MRIfree(&mri_plane) ;
MRIfree(&mri_binary_plane) ;
}
}
}
MRIfree(&mri_tmp) ;
MRIfree(&mri_region) ;
if (Gdiag & DIAG_SHOW)
{
fprintf(stderr, " %8d voxels tested (%2.2f%%)\n",
ntested, 100.0f*(float)ntested/ (float)(width*height*depth));
fprintf(stderr, " %8d voxels restored (%2.2f%%)\n",
nchanged, 100.0f*(float)nchanged/ (float)(width*height*depth));
}
return(NO_ERROR) ;
}
MRI *
MRIfindBrightNonWM(MRI *mri_T1, MRI *mri_wm)
{
int width, height, depth, x, y, z, nlabeled, nwhite,
xk, yk, zk, xi, yi, zi;
BUFTYPE val, wm ;
MRI *mri_labeled, *mri_tmp ;
mri_labeled = MRIclone(mri_T1, NULL) ;
width = mri_T1->width ;
height = mri_T1->height ;
depth = mri_T1->depth ;
for (z = 0 ; z < depth ; z++)
{
for (y = 0 ; y < height ; y++)
{
for (x = 0 ; x < width ; x++)
{
val = MRIgetVoxVal(mri_T1, x, y, z, 0) ;
wm = MRIgetVoxVal(mri_wm, x, y, z, 0) ;
if (x == 110 && y == 125 && z == 172) /* T1=148 */
{
DiagBreak() ;
}
/* not white matter and bright (e.g. eye sockets) */
if ((wm < WM_MIN_VAL) && (val > 125))
{
nwhite = 0 ;
for (xk = -1 ; xk <= 1 ; xk++)
{
xi = mri_T1->xi[x+xk] ;
for (yk = -1 ; yk <= 1 ; yk++)
{
yi = mri_T1->yi[y+yk] ;
for (zk = -1 ; zk <= 1 ; zk++)
{
zi = mri_T1->zi[z+zk] ;
if (MRIgetVoxVal(mri_wm, xi, yi, zi, 0) >= WM_MIN_VAL)
{
nwhite++ ;
}
}
}
}
#define MIN_WHITE ((3*3*3-1)/2)
if (nwhite < MIN_WHITE)
{
MRIsetVoxVal(mri_labeled, x, y, z, 0, BRIGHT_LABEL) ;
}
}
}
}
}
/* find all connected voxels that are above 115 */
MRIdilateThreshLabel(mri_labeled, mri_T1, NULL, BRIGHT_LABEL, 10,115);
MRIclose(mri_labeled, mri_labeled) ;
/* expand once more to all neighboring voxels that are bright. At
worst we will erase one voxel of white matter.
*/
mri_tmp =
MRIdilateThreshLabel(mri_labeled, mri_T1, NULL, BRIGHT_LABEL,1,100);
MRIxor(mri_labeled, mri_tmp, mri_tmp, 1, 255) ;
MRIreplaceValues(mri_tmp, mri_tmp, 1, BRIGHT_BORDER_LABEL) ;
MRIunion(mri_tmp, mri_labeled, mri_labeled) ;
#if 0
fprintf(stderr, "selectively smoothing volume....\n") ;
MRIsoapBubbleLabel(mri_T1, mri_labeled, mri_T1, BRIGHT_LABEL, 200) ;
#endif
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
MRIwrite(mri_labeled, "label.mgh") ;
}
/* MRIwrite(mri_tmp, "tmp.mgh") ;*/
nlabeled = MRIvoxelsInLabel(mri_labeled, BRIGHT_LABEL) ;
fprintf(stderr, "%d bright non-wm voxels segmented.\n", nlabeled) ;
MRIfree(&mri_tmp) ;
return(mri_labeled) ;
}
MRI *
MRIfillVentricles(MRI *mri_src, MRI *mri_dst)
{
int width, height, depth, x, y, z, xk, yk, xi, yi, nfilled, total, s ;
MRI *mri_filled, *mri_ventricles = NULL ;
MRI_SEGMENTATION *mriseg ;
MRI_SEGMENT *mseg ;
Real xt, yt, zt ;
if (!mri_dst)
{
mri_dst = MRIclone(mri_src, NULL) ;
}
width = mri_src->width ;
height = mri_src->height ;
depth = mri_src->depth ;
MRIcopy(mri_src, mri_dst) ;
mri_filled = MRIcopy(mri_src, NULL) ;
MRIreplaceValues(mri_filled, mri_filled, VENTRICLE_FILL,
VENTRICLE_FILL-1) ;
/* first fill each coronal slice starting from a background seed */
for (z = 0 ; z < depth ; z++)
{
total = 0 ;
do
{
nfilled = 0 ;
MRIsetVoxVal(mri_filled, 0, 0, z, 0, VENTRICLE_FILL) ;
for (y = 0 ; y < height ; y++)
{
for (x = 0 ; x < width ; x++)
{
if (MRIgetVoxVal(mri_filled, x, y, z, 0) == VENTRICLE_FILL)
{
for (yk = -1 ; yk <= 1 ; yk++)
{
yi = mri_src->yi[y+yk] ;
for (xk = -1 ; xk <= 1 ; xk++)
{
xi = mri_src->xi[x+xk] ;
if (!MRIgetVoxVal(mri_filled, xi, yi, z, 0))
{
nfilled++ ;
MRIsetVoxVal(mri_filled, xi, yi, z, 0, VENTRICLE_FILL) ;
}
}
}
}
}
}
total += nfilled ;
}
while (nfilled > 0) ;
}
MRIcomplement(mri_filled, mri_filled) ;
MRIreplaceValues(mri_filled, mri_filled, 1, VENTRICLE_FILL) ;
mriseg = MRIsegment(mri_filled, 1, 255) ;
fprintf(stderr, "%d segments found...\n", mriseg->nsegments) ;
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
MRIwrite(mri_filled, "exterior_filled.mgh") ;
}
for (s = 0 ; s < mriseg->nsegments ; s++)
{
mseg = &mriseg->segments[s] ;
if (mseg->nvoxels < 100 ||
mseg->z1-mseg->z0 < 7)
{
continue ;
}
MRIvoxelToTalairach(mri_src, mseg->cx, mseg->cy, mseg->cz, &xt, &yt, &zt);
fprintf(stderr, "added segment %d, nvox=%d, bbox [%d:%d, %d:%d, %d:%d]\n"
"\tc = %2.1f, %2.1f, %2.1f (tal = %2.1f, %2.1f, %2.1f)\n",
s, mseg->nvoxels, mseg->x0, mseg->x1, mseg->y0,mseg->y1,mseg->z0,
mseg->z1, mseg->cx, mseg->cy, mseg->cz, xt, yt, zt) ;
mri_ventricles = MRIsegmentToImage(mri_filled, mri_ventricles, mriseg, s) ;
}
MRIfree(&mri_filled) ;
MRIsegmentFree(&mriseg) ;
/* remove voxels close to the midline so that the cc can still be found */
for (z = 0 ; z < depth ; z++)
{
for (y = 0 ; y < height ; y++)
{
for (x = 0 ; x < width ; x++)
{
MRIvoxelToTalairach(mri_src, x, y, z, &xt, &yt, &zt);
if (fabs(xt) < 5)
{
MRIsetVoxVal(mri_ventricles, x, y, z, 0, 0) ;
}
}
}
}
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
MRIwrite(mri_ventricles, "ventricles.mgh") ;
}
MRIunion(mri_ventricles, mri_dst, mri_dst) ;
MRIfree(&mri_ventricles) ;
return(mri_dst) ;
}
int
main(int argc, char *argv[])
{
MRI *mri_src, *mri_dst, *mri_tmp, *mri_labeled, *mri_labels;
char *input_file_name, *output_file_name ;
int nargs, i, msec ;
struct timeb then ;
float white_mean, white_sigma, gray_mean, gray_sigma ;
char cmdline[CMD_LINE_LEN] ;
TAGmakeCommandLineString(argc, argv, cmdline) ;
/* rkt: check for and handle version tag */
nargs = handle_version_option
(argc, argv,
"$Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $",
"$Name: stable5 $");
if (nargs && argc - nargs == 1)
{
exit (0);
}
argc -= nargs;
Progname = argv[0] ;
DiagInit(NULL, NULL, NULL) ;
ErrorInit(NULL, NULL, NULL) ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++)
{
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
if (argc < 3)
{
usage_exit(1);
}
TimerStart(&then) ;
input_file_name = argv[1] ;
output_file_name = argv[2] ;
mri_src = MRIread(input_file_name) ;
if (!mri_src)
ErrorExit(ERROR_NOFILE, "%s: could not read source volume from %s",
Progname, input_file_name) ;
MRIaddCommandLine(mri_src, cmdline) ;
if (mri_src->type != MRI_UCHAR)
{
MRI *mri_tmp ;
printf("changing input type from %d to UCHAR\n", mri_src->type) ;
mri_tmp = MRIchangeType(mri_src, MRI_UCHAR, 0, 1000, 1) ;
MRIfree(&mri_src) ;
mri_src = mri_tmp ;
}
if (thicken > 1)
{
mri_dst = MRIcopy(mri_src, NULL) ;
/* MRIfilterMorphology(mri_dst, mri_dst) ;*/
fprintf(stderr, "removing 1-dimensional structures...\n") ;
MRIremove1dStructures(mri_dst, mri_dst, 10000, 2, NULL) ;
#if 0
MRIcheckRemovals(mri_src, mri_dst, mri_labels, 5) ;
fprintf(stderr, "thickening thin strands....\n") ;
MRIthickenThinWMStrands(mri_src, mri_dst, mri_dst, thickness, nsegments,
wm_hi) ;
#endif
MRIwrite(mri_dst, output_file_name) ;
exit(0) ;
}
mri_labels = MRIclone(mri_src, NULL) ;
if (auto_detect_stats && !wm_low_set) /* widen range to allow
for more variability */
{
wm_low -= 10 ;
}
fprintf(stderr, "doing initial intensity segmentation...\n") ;
mri_tmp = MRIintensitySegmentation(mri_src, NULL, wm_low, wm_hi, gray_hi);
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
MRIwrite(mri_tmp, "tmp1.mgz") ;
}
fprintf(stderr, "using local statistics to label ambiguous voxels...\n") ;
MRIhistoSegment(mri_src, mri_tmp, wm_low, wm_hi, gray_hi, wsize, 3.0f) ;
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
MRIwrite(mri_tmp, "tmp2.mgz") ;
}
if (auto_detect_stats)
{
fprintf(stderr, "computing class statistics for intensity windows...\n") ;
MRIcomputeClassStatistics(mri_src, mri_tmp, gray_low, WHITE_MATTER_MEAN,
&white_mean, &white_sigma, &gray_mean,
&gray_sigma) ;
if (!finite(white_mean) || !finite(white_sigma) ||
!finite(gray_mean) || !finite(gray_sigma))
ErrorExit
(ERROR_BADPARM,
"%s: class statistics not finite - check input volume!",
Progname);
if (!wm_low_set)
{
if (FZERO(gray_sigma))
{
wm_low = (white_mean+gray_mean) / 2 ;
}
else
{
wm_low = gray_mean + gray_sigma ;
}
}
if (!gray_hi_set)
{
gray_hi = gray_mean + 2*gray_sigma ;
#if 1
if (gray_hi >= white_mean)
{
gray_hi = white_mean-1 ;
}
#endif
}
fprintf(stderr, "setting bottom of white matter range to %2.1f\n",wm_low);
fprintf(stderr, "setting top of gray matter range to %2.1f\n", gray_hi) ;
if (log_stats)
{
FILE *fp ;
fp = fopen("segment.dat", "w") ;
if (fp)
{
fprintf(fp, "WM: %2.1f +- %2.1f\n",white_mean, white_sigma) ;
fprintf(fp, "GM: %2.1f +- %2.1f\n",gray_mean, gray_sigma) ;
fprintf(fp, "setting bottom of white matter range to %2.1f\n",wm_low);
fprintf(fp, "setting top of gray matter range to %2.1f\n", gray_hi) ;
fclose(fp) ;
}
}
fprintf(stderr, "doing initial intensity segmentation...\n") ;
mri_tmp = MRIintensitySegmentation(mri_src, NULL, wm_low, wm_hi, gray_hi);
fprintf(stderr, "using local statistics to label ambiguous voxels...\n") ;
MRIhistoSegment(mri_src, mri_tmp, wm_low, wm_hi, gray_hi, wsize, 3.0f) ;
}
else
{
/* just some not-too-dopey defaults - won't really be used */
white_mean = 110 ;
white_sigma = 5.0 ;
gray_mean = 65 ;
gray_sigma = 12 ;
}
fprintf(stderr,
"using local geometry to label remaining ambiguous voxels...\n") ;
mri_labeled = MRIcpolvMedianCurveSegment(mri_src, mri_tmp, NULL, 5, 3,
gray_hi, wm_low);
fprintf(stderr,
"\nreclassifying voxels using Gaussian border classifier...\n") ;
/*
now use the gray and white matter border voxels to build a Gaussian
classifier at each point in space and reclassify all voxels in the
range [wm_low-5,gray_hi].
*/
for (i = 0 ; i < niter ; i++)
{
MRIreclassify(mri_src, mri_labeled, mri_labeled, wm_low-5,gray_hi,wsize);
}
MRIfree(&mri_tmp) ;
mri_dst = MRImaskLabels(mri_src, mri_labeled, NULL) ;
MRIfree(&mri_labeled) ;
MRIrecoverBrightWhite(mri_src, mri_dst,mri_dst,wm_low,wm_hi,white_sigma,.33);
fprintf(stderr,
"\nremoving voxels with positive offset direction...\n") ;
#if 0
MRIremoveWrongDirection(mri_dst, mri_dst, 3, wm_low-5, gray_hi, mri_labels) ;
#else
MRIremoveWrongDirection(mri_dst, mri_dst, 3, wm_low-5, gray_hi, NULL) ;
#endif
if (thicken)
{
/* MRIfilterMorphology(mri_dst, mri_dst) ;*/
fprintf(stderr, "removing 1-dimensional structures...\n") ;
MRIremove1dStructures(mri_dst, mri_dst, 10000, 2, mri_labels) ;
#if 0
MRIcheckRemovals(mri_src, mri_dst, mri_labels, 5) ;
#endif
fprintf(stderr, "thickening thin strands....\n") ;
MRIthickenThinWMStrands(mri_src, mri_dst, mri_dst, thickness, nsegments,
wm_hi) ;
}
mri_tmp = MRIfindBrightNonWM(mri_src, mri_dst) ;
MRIbinarize(mri_tmp, mri_tmp, WM_MIN_VAL, 255, 0) ;
MRImaskLabels(mri_dst, mri_tmp, mri_dst) ;
MRIfilterMorphology(mri_dst, mri_dst) ;
if (fill_bg)
{
fprintf(stderr, "filling basal ganglia....\n") ;
MRIfillBasalGanglia(mri_src, mri_dst) ;
}
if (fill_ventricles)
{
fprintf(stderr, "filling ventricles....\n") ;
MRIfillVentricles(mri_dst, mri_dst) ;
}
MRIfree(&mri_src) ;
msec = TimerStop(&then) ;
fprintf(stderr, "white matter segmentation took %2.1f minutes\n",
(float)msec/(1000.0f*60.0f));
fprintf(stderr, "writing output to %s...\n", output_file_name) ;
if (keep_edits)
{
MRI *mri_old ;
mri_old = MRIread(output_file_name) ;
if (!mri_old)
{
ErrorPrintf
(ERROR_NOFILE, "%s: could not read file %s to preserve edits",
Progname, output_file_name) ;
exit(1);
}
else
{
MRIcopyLabel(mri_old, mri_dst, WM_EDITED_ON_VAL) ;
MRIcopyLabel(mri_old, mri_dst, WM_EDITED_OFF_VAL) ;
MRIfree(&mri_old) ;
}
}
MRIwrite(mri_dst, output_file_name) ;
MRIfree(&mri_dst) ;
exit(0) ;
return(0) ;
}
static int
MRISrepositionToInnerSkull(MRI_SURFACE *mris, MRI *mri_smooth, INTEGRATION_PARMS *parms) {
MRI *mri_dist, *mri_bin, *mri_kernel, *mri_bin_smooth, *mri_dist_smooth ;
float l_spring, sigma ;
int i, ic_order, avgs ;
parms->niterations = 1000 ;
if (parms->momentum < 0.0)
parms->momentum = 0.0 /*0.75*/ ;
mri_bin = MRIbinarize(mri_smooth, NULL, 15, 0, TARGET_VAL) ;
mri_dist = MRIdistanceTransform(mri_bin, NULL, TARGET_VAL, 10*mri_bin->width, DTRANS_MODE_SIGNED, NULL) ;
MRIwrite(mri_bin, "bin.mgz") ;
MRIwrite(mri_dist, "dist.mgz") ;
MRISscaleBrain(mris, mris, 0.5) ; // start inside
mri_kernel = MRIgaussian1d(2, 0) ;
mri_bin_smooth = MRIconvolveGaussian(mri_bin, NULL, mri_kernel) ;
MRIwrite(mri_bin_smooth, "bin_smooth.mgz") ;
MRISfindOptimalRigidPosition(mris, mri_bin_smooth, parms) ;
MRIfree(&mri_kernel) ;
MRIfree(&mri_bin_smooth) ;
avgs = parms->n_averages = 32 ;
l_spring = parms->l_spring_norm ;
for (ic_order = 3 ; ic_order <= 3 ; ic_order++) {
if (ic_order != ic_init) {
MRI_SURFACE *mris_new ;
char fname[STRLEN], *mdir ;
mdir = getenv("FREESURFER_HOME") ;
if (!mdir)
ErrorExit(ERROR_BADPARM, "FREESURFER_HOME not defined in environment") ;
sprintf(fname, "%s/lib/bem/ic%d.tri", mdir, ic_order) ;
mris_new = MRISread(fname) ;
MRISupsampleIco(mris, mris_new) ;
MRISfree(&mris) ;
mris = mris_new ;
}
printf("********************** using ICO order %d *********************\n", ic_order) ;
parms->n_averages = avgs ;
parms->l_spring_norm = l_spring ;
for (sigma = 16.0, i = 0 ; i < 7 ; i++, sigma /= 2) {
printf("******************** pass %d, sigma = %2.2f, avgs = %d ******************\n",
i+1, sigma, parms->n_averages) ;
parms->sigma = sigma ;
MRISsetVals(mris,parms->sigma) ;
MRIScopyValToVal2(mris) ;
MRISsetVals(mris, 0) ; // 0 mm from fat
parms->mri_brain = mri_dist ;
mri_kernel = MRIgaussian1d(sigma, 0) ;
mri_dist_smooth = MRIconvolveGaussian(mri_dist, NULL, mri_kernel) ;
MRIfree(&mri_kernel) ;
if (i == 0) {
MRIwrite(mri_dist_smooth, "dist_smooth.mgz") ;
MRISwrite(mris, "lh.0000") ;
}
MRISsetVals(mris, 0) ;
MRISpositionSurface(mris, mri_dist, mri_dist_smooth, parms) ;
parms->l_spring_norm /= 2;
parms->n_averages /= 2 ;
}
}
MRIfree(&mri_bin) ;
MRIfree(&mri_dist) ;
return(NO_ERROR) ;
}
static int
initialize_surface_position(MRI_SURFACE *mris, MRI *mri_masked, int outside, INTEGRATION_PARMS *parms) {
MRI *mri_dilated ;
int x, y, z, vno ;
double x0, y0, z0, radius = 0, dist, num ;
Real xs, ys, zs ;
VERTEX *v ;
if (outside) {
mri_dilated = MRIdilate(mri_masked, NULL) ;
MRIsubtract(mri_dilated, mri_masked, mri_dilated) ;
MRIwrite(mri_dilated, "outside.mgz") ;
num = x0 = y0 = z0 = 0 ;
for (x = 0 ; x < mri_dilated->width ; x++) {
for (y = 0 ; y < mri_dilated->height ; y++) {
for (z = 0 ; z < mri_dilated->depth ; z++) {
if (MRIgetVoxVal(mri_dilated, x, y, z,0) > 0) {
MRIvoxelToSurfaceRAS(mri_dilated, x, y, z, &xs, &ys, &zs) ;
x0 += xs ;
y0 += ys ;
z0 += zs ;
num++ ;
}
}
}
}
x0 /= num ;
y0 /= num ;
z0 /= num ;
printf("centroid at (%2.1f, %2.1f, %2.1f)\n", x0, y0, z0) ;
num = radius = 0 ;
for (x = 0 ; x < mri_dilated->width ; x++) {
for (y = 0 ; y < mri_dilated->height ; y++) {
for (z = 0 ; z < mri_dilated->depth ; z++) {
if (MRIgetVoxVal(mri_dilated, x, y, z,0) > 0) {
MRIvoxelToSurfaceRAS(mri_dilated, x, y, z, &xs, &ys, &zs) ;
dist = sqrt(SQR(xs-x0)+SQR(ys-y0)+SQR(zs-z0)) ;
radius += dist ;
num++ ;
}
}
}
}
radius /= num ;
printf("average radius = %2.3f\n", radius) ;
MRIfree(&mri_dilated) ;
MRISprojectOntoSphere(mris, mris, radius*1.25) ;
for (vno = 0 ; vno < mris->nvertices ; vno++) {
v = &mris->vertices[vno] ;
v->x += x0 ;
v->y += y0 ;
v->z += z0 ;
}
MRIScomputeMetricProperties(mris) ;
}
parms->target_radius = radius ;
MRISsaveVertexPositions(mris, ORIGINAL_VERTICES) ;
return(NO_ERROR) ;
}
int
main(int argc, char *argv[]) {
char **av, fname[STRLEN], *T1_fname, *PD_fname, *output_dir, *mdir ;
int ac, nargs, msec, s ;
MRI_SURFACE *mris ;
MRI *mri_flash1, *mri_flash2, *mri_masked, *mri_masked_smooth, *mri_kernel,
*mri_mean, *mri_dif, *mri_binary, *mri_distance ;
MRI *mri_smooth, *mri_grad, *mri_inner ;
struct timeb then ;
double l_spring ;
MRI_SEGMENTATION *mriseg ;
/* rkt: check for and handle version tag */
nargs = handle_version_option (argc, argv, "$Id: mris_AA_shrinkwrap.c,v 1.5 2011/03/02 00:04:34 nicks Exp $", "$Name: stable5 $");
if (nargs && argc - nargs == 1)
exit (0);
argc -= nargs;
Gdiag |= DIAG_SHOW ;
Progname = argv[0] ;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
memset(&parms, 0, sizeof(parms)) ;
parms.projection = NO_PROJECTION ;
parms.tol = 0.05 ;
parms.check_tol = 1 ;
parms.ignore_energy = 1 ;
parms.dt = 0.5f ;
parms.base_dt = BASE_DT_SCALE*parms.dt ;
parms.l_spring_norm = 1 ;
parms.l_shrinkwrap = 0 ;
parms.l_intensity = 1 ;
parms.niterations = 0 ;
parms.write_iterations = 0 /*WRITE_ITERATIONS */;
parms.integration_type = INTEGRATE_MOMENTUM ;
parms.momentum = 0.0 /*0.8*/ ;
parms.l_intensity = 1 ;
parms.dt_increase = 1.0 /* DT_INCREASE */;
parms.dt_decrease = 0.50 /* DT_DECREASE*/ ;
parms.error_ratio = 50.0 /*ERROR_RATIO */;
/* parms.integration_type = INTEGRATE_LINE_MINIMIZE ;*/
parms.l_surf_repulse = 0.0 ;
parms.l_repulse = 0 /*1*/ ;
ac = argc ;
av = argv ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
mdir = getenv("FREESURFER_HOME") ;
if (!mdir)
ErrorExit(ERROR_BADPARM, "FREESURFER_HOME not defined in environment") ;
if (argc < 4)
usage_exit() ;
/* set default parameters for white and gray matter surfaces */
parms.niterations = 1000 ;
if (parms.momentum < 0.0)
parms.momentum = 0.0 /*0.75*/ ;
TimerStart(&then) ;
T1_fname = argv[1] ;
PD_fname = argv[2] ;
output_dir = argv[3] ;
fprintf(stderr, "reading volume %s...\n", T1_fname) ;
mri_flash1 = MRIread(T1_fname) ;
if (!mri_flash1)
ErrorExit(ERROR_NOFILE, "%s: could not read input volume %s", Progname, T1_fname) ;
mri_flash2 = MRIread(PD_fname) ;
if (!mri_flash2)
ErrorExit(ERROR_NOFILE, "%s: could not read input volume %s", Progname, T1_fname) ;
// setMRIforSurface(mri_flash1);
sprintf(fname, "%s/lib/bem/ic%d.tri", mdir, ic_init) ;
mris = MRISread(fname) ;
if (!mris)
ErrorExit(ERROR_NOFILE, "%s: could not read icosahedron %s", Progname, fname) ;
mri_mean = MRImean(mri_flash1, NULL, 5) ;
MRIwrite(mri_mean, "mean.mgz") ;
mri_dif = MRIabsdiff(mri_flash1, mri_flash2, NULL) ;
MRIwrite(mri_dif, "dif.mgz") ;
mriseg = MRIsegment(mri_mean, 30, 100000) ;
s = MRIsegmentMax(mriseg) ;
mri_masked = MRIsegmentToImage(mri_flash1, NULL, mriseg, s) ;
MRIwrite(mri_masked, "mask.mgz") ;
MRIsegmentFree(&mriseg) ;
// MRIthresholdMask(mri_dif, mri_masked, mri_dif, 1, 0) ;
// MRIwrite(mri_dif, "dif_masked.mgz") ;
mri_kernel = MRIgaussian1d(2, 0) ;
mri_smooth = MRIconvolveGaussian(mri_dif, NULL, mri_kernel) ;
MRIwrite(mri_smooth, "smooth.mgz") ;
MRIScopyVolGeomFromMRI(mris, mri_smooth) ;
mris->useRealRAS = 1 ;
initialize_surface_position(mris, mri_dif, 1, &parms) ;
MRISwrite(mris, "init") ;
MRISrepositionToInnerSkull(mris, mri_smooth, &parms) ;
exit(0) ;
mri_grad = MRIsobel(mri_smooth, NULL, NULL) ;
MRIwrite(mri_grad, "grad.mgz") ;
mri_inner = MRIfindInnerBoundary(mri_dif, mri_grad, NULL, 5.0) ;
MRIwrite(mri_inner, "inner.mgz") ;
MRIbinarize(mri_inner, mri_inner, 10, 0, 128) ;
MRISpositionOptimalSphere(mris, mri_inner, 6) ;
MRISwrite(mris, "optimal") ;
exit(0) ;
parms.sigma = 4 / mri_flash1->xsize ;
// mri_dist = create_distance_map(mri_masked, NULL, BORDER_VAL, OUTSIDE_BORDER_STEP) ;
MRISsetVals(mris,parms.sigma) ;
MRIScopyValToVal2(mris) ;
MRISsetVals(mris, 0) ;
sprintf(parms.base_name, "%s_inner_skull%s%s", "test", output_suffix, suffix) ;
parms.mri_brain = mri_masked ;
l_spring = parms.l_spring_norm ;
mri_kernel = MRIgaussian1d(parms.sigma, 0) ;
mri_binary = MRIbinarize(mri_dif, mri_binary, 40, 0, 128) ;
MRIwrite(mri_binary, "bin.mgz") ;
mri_distance = MRIdistanceTransform(mri_binary, NULL, 128, 100, DTRANS_MODE_SIGNED, NULL) ;
MRIwrite(mri_distance, "dist.mgz") ;
mri_masked_smooth = MRIconvolveGaussian(mri_distance, NULL, mri_kernel) ;
MRIfree(&mri_kernel) ;
MRIwrite(mri_masked_smooth, "dif_smooth.mgz") ;
MRISwrite(mris, "inner_skull.tri") ;
msec = TimerStop(&then) ;
fprintf(stderr,"positioning took %2.1f minutes\n", (float)msec/(60*1000.0f));
exit(0) ;
return(0) ; /* for ansi */
}
int
main(int argc, char *argv[]) {
char **av, fname[STRLEN] ;
int ac, nargs, i ;
MRI *mri_flash[MAX_IMAGES], *mri_T1, *mri_PD ;
char *in_fname, *out_PD_fname, *out_T1_fname ;
int msec, minutes, seconds, nvolumes ;
struct timeb start ;
/* rkt: check for and handle version tag */
nargs = handle_version_option (argc, argv, "$Id: mri_estimate_tissue_parms.c,v 1.9 2011/03/02 00:04:15 nicks Exp $", "$Name: $");
if (nargs && argc - nargs == 1)
exit (0);
argc -= nargs;
Progname = argv[0] ;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
TimerStart(&start) ;
parms.dt = 1e-6 ;
parms.tol = 1e-5 ;
parms.momentum = 0.0 ;
parms.niterations = 20 ;
ac = argc ;
av = argv ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
if (argc < 4)
usage_exit(1) ;
out_T1_fname = argv[argc-2] ;
out_PD_fname = argv[argc-1] ;
FileNameOnly(out_T1_fname, fname) ;
FileNameRemoveExtension(fname, fname) ;
strcpy(parms.base_name, fname) ;
nvolumes = 0 ;
for (i = 1 ; i < argc-2 ; i++) {
if (argv[i][0] == '-') {
if (!stricmp(argv[i]+1, "te"))
te = atof(argv[i+1]) ;
else if (!stricmp(argv[i]+1, "tr"))
tr = atof(argv[i+1]) ;
else if (!stricmp(argv[i]+1, "fa"))
fa = RADIANS(atof(argv[i+1])) ;
else
ErrorExit(ERROR_BADPARM, "%s: unsupported MR parameter %s",
Progname, argv[i]+1) ;
i++ ; /* skip parameter */
continue ;
}
in_fname = argv[i] ;
printf("reading %s...", in_fname) ;
mri_flash[nvolumes] = MRIread(in_fname) ;
if (!mri_flash[nvolumes])
ErrorExit(Gerror, "%s: MRIread(%s) failed", Progname, in_fname) ;
if (tr > 0) {
mri_flash[nvolumes]->tr = tr ;
tr = 0 ;
}
if (te > 0) {
mri_flash[nvolumes]->te = te ;
te = 0 ;
}
if (fa > 0) {
mri_flash[nvolumes]->flip_angle = fa ;
fa = 0 ;
}
printf("TE = %2.2f, TR = %2.2f, alpha = %2.2f\n", mri_flash[nvolumes]->te,
mri_flash[nvolumes]->tr, DEGREES(mri_flash[nvolumes]->flip_angle)) ;
mri_flash[nvolumes]->flip_angle = mri_flash[nvolumes]->flip_angle;
if (conform) {
MRI *mri_tmp ;
printf("embedding and interpolating volume\n") ;
mri_tmp = MRIconform(mri_flash[nvolumes]) ;
/* MRIfree(&mri_src) ;*/
mri_flash[nvolumes] = mri_tmp ;
}
if (FZERO(mri_flash[nvolumes]->tr) ||
FZERO(mri_flash[nvolumes]->flip_angle))
ErrorExit(ERROR_BADPARM, "%s: invalid TR or FA for image %d:%s",
Progname, nvolumes, in_fname) ;
nvolumes++ ;
}
printf("using %d FLASH volumes to estimate tissue parameters.\n", nvolumes) ;
mri_T1 = MRIclone(mri_flash[0], NULL) ;
mri_PD = MRIclone(mri_flash[0], NULL) ;
{
double sse, last_T1, last_PD, total_rms, avg_rms ;
int x, y, z, width, height, depth, total_vox, ignored, nvox ;
struct timeb first_slice ;
Progname = argv[0] ;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
TimerStart(&first_slice) ;
last_T1 = last_PD = 1000 ;
sse = 0.0 ;
width = mri_T1->width ;
height = mri_T1->height ;
depth = mri_T1->depth ;
total_vox = width*depth*height ;
#if 0
estimateVoxelParameters(mri_flash, nvolumes, width/2, height/2, depth/2,
mri_T1, mri_PD, last_T1, last_PD) ;
#endif
if (Gdiag_no == 999) {
x = 130 ;
y = 124 ;
z = 74 ; /* CSF */
computeErrorSurface("error_surf_csf.dat",mri_flash,nvolumes,x,y,z,500,3000,500,3000);
x = 161 ;
y = 157 ;
z = 63 ; /* wm */
computeErrorSurface("error_surf_wm.dat",mri_flash,nvolumes,x,y,z,250,3000,250,3000);
x = 166 ;
y = 153 ;
z = 63 ; /* gm */
computeErrorSurface("error_surf_gm.dat",mri_flash,nvolumes,x,y,z,250,3000,250,3000);
}
avg_rms = 0 ;
for (ignored = z = 0 ; z < depth ; z++) {
if (z > 0)
printf("z = %d, avg rms=%2.1f, T1=%2.0f, PD=%2.0f...\n",
z, avg_rms, last_T1, last_PD) ;
#if 0
if (z > 0 && z*width*height - ignored > 0) {
int processed = z*width*height - ignored, hours ;
msec = TimerStop(&first_slice) ;
seconds = nint((float)msec/1000.0f) ;
minutes = seconds / 60 ;
seconds = seconds % 60 ;
hours = minutes / 60 ;
minutes = minutes % 60 ;
printf("%02d:%02d:%02d total processing time ... ",
hours,minutes,seconds);
msec = (int)((float)(total_vox-ignored)*msec/(float)processed) ;
seconds = nint((float)msec/1000.0f) ;
minutes = seconds / 60 ;
seconds = seconds % 60 ;
hours = minutes / 60 ;
minutes = minutes % 60 ;
printf("estimate %02d:%02d:%02d remaining.\n", hours,minutes, seconds);
}
#endif
if (write_iterations > 0 && z > 0 && !(z%write_iterations)) {
printf("writing T1 esimates to %s...\n", out_T1_fname) ;
printf("writing PD estimates to %s...\n", out_PD_fname) ;
MRIwrite(mri_T1, out_T1_fname) ;
MRIwrite(mri_PD, out_PD_fname) ;
printf("writing residuals to %s...\n", residual_name) ;
if (residual_name) {
MRI *mri_res, *mri_res_total = NULL ;
for (i = 0 ; i < nvolumes ; i++) {
mri_res = compute_residuals(mri_flash[i], mri_T1, mri_PD) ;
sprintf(fname, "%s%d.mgh", residual_name, i) ;
#if 0
MRIwrite(mri_res, fname) ;
#endif
if (!mri_res_total) {
mri_res_total = MRIcopy(mri_res, NULL) ;
} else {
MRIsadd(mri_res, mri_res_total, mri_res_total) ;
}
MRIfree(&mri_res) ;
}
MRIsscalarMul(mri_res_total, mri_res_total, 1.0/(float)nvolumes) ;
MRIssqrt(mri_res_total, mri_res_total) ;
sprintf(fname, "%s.mgh", residual_name) ;
MRIwrite(mri_res_total, fname) ;
}
}
nvox = 0 ;
total_rms = 0 ;
for (y = 0 ; y < height ; y++) {
#if 0
if (y%32 == 0 && nvox > 0)
printf("z = %d, y = %d, avg rms=%2.1f, T1=%2.0f, PD=%2.0f...\n",
z, y, total_rms/(double)nvox, last_T1, last_PD) ;
#endif
for (x = 0 ; x < width ; x++) {
#if 0
for (i = 0 ; i < nvolumes ; i++)
if (MRISvox(mri_flash[i],x,y,z) > thresh)
break ;
if (i >= nvolumes)
#else
if (no_valid_data(mri_flash, nvolumes, x, y, z, thresh))
#endif
{
ignored++ ;
MRISvox(mri_T1, x, y, z) = MRISvox(mri_PD, x, y, z) = 0 ;
/* last_T1 = last_PD = 1000 ;*/
continue ;
}
#if 0
sse = findInitialParameters(mri_flash, nvolumes, x, y, z,
last_PD-1000, last_PD+1000,
last_T1-1000, last_T1+1000,
&last_PD, &last_T1, 10) ;
#endif
#if 0
sse = findInitialParameters(mri_flash, nvolumes, x, y, z,
last_PD-100, last_PD+100,
last_T1-100, last_T1+100,
&last_PD, &last_T1, 10) ;
if (last_T1 <= MIN_T1 || last_PD <= 0) {
ignored++ ;
MRISvox(mri_T1, x, y, z) = MRISvox(mri_PD, x, y, z) = 0 ;
/* last_T1 = last_PD = 1000 ;*/
continue ;
}
#endif
sse = estimateVoxelParameters(mri_flash, nvolumes, x, y, z,
mri_T1, mri_PD, nsteps) ;
nvox++ ;
last_T1 = MRISvox(mri_T1, x, y, z) ;
last_PD = MRISvox(mri_PD, x, y, z) ;
total_rms += sqrt(sse/nvolumes) ;
if (!finite(total_rms))
DiagBreak() ;
}
}
avg_rms = total_rms / nvox ;
if (!finite(avg_rms))
DiagBreak() ;
}
}
printf("writing T1 esimates to %s...\n", out_T1_fname) ;
printf("writing PD estimates to %s...\n", out_PD_fname) ;
MRIwrite(mri_T1, out_T1_fname) ;
MRIwrite(mri_PD, out_PD_fname) ;
if (residual_name) {
MRI *mri_res_total = NULL ;
for (i = 0 ; i < nvolumes ; i++) {
MRI *mri_res ;
mri_res = compute_residuals(mri_flash[i], mri_T1, mri_PD) ;
#if 0
sprintf(fname, "%s%d.mgh", residual_name, i) ;
MRIwrite(mri_res, fname) ;
#endif
if (!mri_res_total) {
mri_res_total = MRIcopy(mri_res, NULL) ;
} else {
MRIsadd(mri_res, mri_res_total, mri_res_total) ;
}
MRIfree(&mri_res) ;
}
MRIsscalarMul(mri_res_total, mri_res_total, 1.0/(float)nvolumes) ;
MRIssqrt(mri_res_total, mri_res_total) ;
sprintf(fname, "%s.mgh", residual_name) ;
MRIwrite(mri_res_total, fname) ;
}
MRIfree(&mri_T1) ;
MRIfree(&mri_PD) ;
msec = TimerStop(&start) ;
seconds = nint((float)msec/1000.0f) ;
minutes = seconds / 60 ;
seconds = seconds % 60 ;
printf("parameter estimation took %d minutes and %d seconds.\n",
minutes, seconds) ;
exit(0) ;
return(0) ;
}
int
main(int argc, char *argv[]) {
char **av, *out_fname, *T1_fname, *PD_fname ;
int ac, nargs ;
MRI *mri_T1, *mri_PD, *mri_out, *mri_T2star = NULL ;
float TR, TE, alpha ;
char cmdline[CMD_LINE_LEN] ;
make_cmd_version_string (argc, argv, "$Id: mri_synthesize.c,v 1.18 2011/03/02 00:04:25 nicks Exp $", "$Name: $", cmdline);
/* rkt: check for and handle version tag */
nargs = handle_version_option (argc, argv, "$Id: mri_synthesize.c,v 1.18 2011/03/02 00:04:25 nicks Exp $", "$Name: $");
if (nargs && argc - nargs == 1)
exit (0);
argc -= nargs;
Progname = argv[0] ;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
ac = argc ;
av = argv ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
if (argc < 7)
usage_exit() ;
TR = atof(argv[1]) ;
alpha = atof(argv[2]) ;
TE = atof(argv[3]) ;
T1_fname = argv[4] ;
PD_fname = argv[5] ;
out_fname = argv[6] ;
printf("reading T1 volume from %s...\n", T1_fname) ;
mri_T1 = MRIread(T1_fname) ;
if (!mri_T1)
ErrorExit(ERROR_NOFILE, "%s: could not read T1 volume %s", Progname,
T1_fname) ;
if (extract) {
MRI *mri_tmp ;
int dx, dy, dz ;
dx = mri_T1->width/2 ;
dy = mri_T1->height/2 ;
dz = mri_T1->depth/2 ;
printf("extracting interior %dx%dx%d\n", dx, dy, dz) ;
mri_tmp = MRIextract(mri_T1, NULL, dx/2, dy/2, dz/2, dx, dy, dz) ;
MRIfree(&mri_T1) ;
mri_T1 = mri_tmp ;
}
if (jpdf_name) {
transform_T1_values_using_joint_pdf(mri_T1, jpdf_name, invert) ;
}
printf("reading PD volume from %s...\n", PD_fname) ;
mri_PD = MRIread(PD_fname) ;
if (!mri_PD)
ErrorExit(ERROR_NOFILE, "%s: could not read PD volume %s", Progname,
PD_fname) ;
if (T2star_fname != NULL) {
printf("reading T2* volume from %s...\n", T2star_fname) ;
mri_T2star = MRIread(T2star_fname) ;
if (!mri_T2star)
ErrorExit(ERROR_NOFILE, "%s: could not read T2* volume %s", Progname,
T2star_fname) ;
}
if (PDsat > 0)
saturate_PD(mri_PD, PDsat) ;
if (extract) {
MRI *mri_tmp ;
int dx, dy, dz ;
dx = mri_PD->width/2 ;
dy = mri_PD->height/2 ;
dz = mri_PD->depth/2 ;
mri_tmp = MRIextract(mri_PD, NULL, dx/2, dy/2, dz/2, dx, dy, dz) ;
MRIfree(&mri_PD) ;
mri_PD = mri_tmp ;
}
if (use_weighting) {
mri_out = MRIsynthesizeWeightedVolume(mri_T1, mri_PD, w5, TR, w30, TR, 110,TE);
} else {
printf("synthesizing volume with TR=%2.1f msec, TE=%2.1f msec, and alpha=%2.2f degrees...\n",
TR, TE, alpha) ;
if (normalize)
normalize_PD(mri_PD, 1000) ;
if (discard)
discard_PD(mri_PD, 250, 1500) ;
if (nl_remap_T1)
remap_T1(mri_T1, nl_mean, nl_scale) ;
if (nfaf > 0)
mri_out = MRIsynthesizeWithFAF(mri_T1, mri_PD, NULL, TR, RADIANS(alpha), TE, nfaf, faf_coefs) ;
else
mri_out = MRIsynthesize(mri_T1, mri_PD, mri_T2star, NULL, TR, RADIANS(alpha), TE) ;
}
if (nbias > 0)
apply_bias_field(mri_out, nbias, bias_coefs) ;
printf("writing output to %s.\n", out_fname) ;
MRIaddCommandLine(mri_out, cmdline) ;
MRIwrite(mri_out, out_fname) ;
exit(0) ;
return(0) ; /* for ansi */
}
/*--------------------------------------------------*/
int main(int argc, char **argv)
{
int nargs, nthin, nframestot=0, nr=0,nc=0,ns=0, fout;
int r,c,s,f,outf,nframes,err,nthrep;
double v, v1, v2, vavg, vsum;
int inputDatatype=MRI_UCHAR;
MATRIX *Upca=NULL,*Spca=NULL;
MRI *Vpca=NULL;
char *stem;
/* rkt: check for and handle version tag */
nargs = handle_version_option (argc, argv, vcid, "$Name: stable5 $");
if (nargs && argc - nargs == 1)
{
exit (0);
}
argc -= nargs;
Progname = argv[0] ;
argc --;
argv++;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
if (argc == 0)
{
usage_exit();
}
parse_commandline(argc, argv);
check_options();
dump_options(stdout);
if(maskfile)
{
printf("Loading mask %s\n",maskfile);
mask = MRIread(maskfile);
if(mask == NULL)
{
exit(1);
}
}
printf("ninputs = %d\n",ninputs);
if(DoCheck)
{
printf("Checking inputs\n");
for(nthin = 0; nthin < ninputs; nthin++)
{
if(Gdiag_no > 0 || debug)
{
printf("Checking %2d %s\n",nthin,inlist[nthin]);
fflush(stdout);
}
mritmp = MRIreadHeader(inlist[nthin],MRI_VOLUME_TYPE_UNKNOWN);
if (mritmp == NULL)
{
printf("ERROR: reading %s\n",inlist[nthin]);
exit(1);
}
if (nthin == 0)
{
nc = mritmp->width;
nr = mritmp->height;
ns = mritmp->depth;
}
if (mritmp->width != nc ||
mritmp->height != nr ||
mritmp->depth != ns)
{
printf("ERROR: dimension mismatch between %s and %s\n",
inlist[0],inlist[nthin]);
exit(1);
}
nframestot += mritmp->nframes;
inputDatatype = mritmp->type; // used by DoKeepDatatype option
MRIfree(&mritmp);
}
}
else
{
printf("NOT Checking inputs, assuming nframestot = ninputs\n");
nframestot = ninputs;
mritmp = MRIreadHeader(inlist[0],MRI_VOLUME_TYPE_UNKNOWN);
if (mritmp == NULL)
{
printf("ERROR: reading %s\n",inlist[0]);
exit(1);
}
nc = mritmp->width;
nr = mritmp->height;
ns = mritmp->depth;
MRIfree(&mritmp);
}
printf("nframestot = %d\n",nframestot);
if (DoRMS)
{
if (ninputs != 1)
{
printf("ERROR: --rms supports only single input w/ multiple frames\n");
exit (1);
}
if (nframestot == 1)
{
printf("ERROR: --rms input must have multiple frames\n");
exit (1);
}
}
if(ngroups != 0)
{
printf("Creating grouped mean matrix ngroups=%d, nper=%d\n",
ngroups,nframestot/ngroups);
M = GroupedMeanMatrix(ngroups,nframestot);
if(M==NULL)
{
exit(1);
}
if(debug)
{
MatrixPrint(stdout,M);
}
}
if(M != NULL)
{
if(nframestot != M->cols)
{
printf("ERROR: dimension mismatch between inputs (%d) and matrix (%d)\n",
nframestot,M->rows);
exit(1);
}
}
if (DoPaired)
{
if (remainder(nframestot,2) != 0)
{
printf("ERROR: --paired-xxx specified but there are an "
"odd number of frames\n");
exit(1);
}
}
printf("Allocing output\n");
fflush(stdout);
int datatype=MRI_FLOAT;
if (DoKeepDatatype)
{
datatype = inputDatatype;
}
if (DoRMS)
{
// RMS always has single frame output
mriout = MRIallocSequence(nc,nr,ns,datatype,1);
}
else
{
mriout = MRIallocSequence(nc,nr,ns,datatype,nframestot);
}
if (mriout == NULL)
{
exit(1);
}
printf("Done allocing\n");
fout = 0;
for (nthin = 0; nthin < ninputs; nthin++)
{
if (DoRMS) break; // MRIrms reads the input frames
if(Gdiag_no > 0 || debug)
{
printf("Loading %dth input %s\n",
nthin+1,fio_basename(inlist[nthin],NULL));
fflush(stdout);
}
mritmp = MRIread(inlist[nthin]);
if(mritmp == NULL)
{
printf("ERROR: loading %s\n",inlist[nthin]);
exit(1);
}
if(nthin == 0)
{
MRIcopyHeader(mritmp, mriout);
//mriout->nframes = nframestot;
}
if(DoAbs)
{
if(Gdiag_no > 0 || debug)
{
printf("Removing sign from input\n");
}
MRIabs(mritmp,mritmp);
}
if(DoPos)
{
if(Gdiag_no > 0 || debug)
{
printf("Setting input negatives to 0.\n");
}
MRIpos(mritmp,mritmp);
}
if(DoNeg)
{
if(Gdiag_no > 0 || debug)
{
printf("Setting input positives to 0.\n");
}
MRIneg(mritmp,mritmp);
}
for(f=0; f < mritmp->nframes; f++)
{
for(c=0; c < nc; c++)
{
for(r=0; r < nr; r++)
{
for(s=0; s < ns; s++)
{
v = MRIgetVoxVal(mritmp,c,r,s,f);
MRIsetVoxVal(mriout,c,r,s,fout,v);
}
}
}
fout++;
}
MRIfree(&mritmp);
}
if(DoCombine)
{
// Average frames from non-zero voxels
int nhits;
mritmp = MRIallocSequence(nc,nr,ns,MRI_FLOAT,1);
MRIcopyHeader(mritmp,mriout);
for(c=0; c < nc; c++)
{
for(r=0; r < nr; r++)
{
for(s=0; s < ns; s++)
{
nhits = 0;
vsum = 0;
for(f=0; f < mriout->nframes; f++)
{
v = MRIgetVoxVal(mriout,c,r,s,f);
if (v > 0)
{
vsum += v;
nhits ++;
}
}
if(nhits > 0 )
{
MRIsetVoxVal(mritmp,c,r,s,0,vsum/nhits);
}
} // for s
}// for r
} // for c
MRIfree(&mriout);
mriout = mritmp;
} // do combine
if(DoPrune)
{
// This computes the prune mask, applied below
printf("Computing prune mask \n");
PruneMask = MRIframeBinarize(mriout,FLT_MIN,NULL);
printf("Found %d voxels in prune mask\n",MRInMask(PruneMask));
}
if(DoNormMean)
{
printf("Normalizing by mean across frames\n");
MRInormalizeFramesMean(mriout);
}
if(DoNorm1)
{
printf("Normalizing by first across frames\n");
MRInormalizeFramesFirst(mriout);
}
if(DoASL)
{
printf("Computing ASL matrix matrix\n");
M = ASLinterpMatrix(mriout->nframes);
}
if(M != NULL)
{
printf("Multiplying by matrix\n");
mritmp = fMRImatrixMultiply(mriout, M, NULL);
if(mritmp == NULL)
{
exit(1);
}
MRIfree(&mriout);
mriout = mritmp;
}
if(DoPaired)
{
printf("Combining pairs\n");
mritmp = MRIcloneBySpace(mriout,-1,mriout->nframes/2);
for (c=0; c < nc; c++)
{
for (r=0; r < nr; r++)
{
for (s=0; s < ns; s++)
{
fout = 0;
for (f=0; f < mriout->nframes; f+=2)
{
v1 = MRIgetVoxVal(mriout,c,r,s,f);
v2 = MRIgetVoxVal(mriout,c,r,s,f+1);
v = 0;
if(DoPairedAvg)
{
v = (v1+v2)/2.0;
}
if(DoPairedSum)
{
v = (v1+v2);
}
if(DoPairedDiff)
{
v = v1-v2; // difference
}
if(DoPairedDiffNorm)
{
v = v1-v2; // difference
vavg = (v1+v2)/2.0;
if (vavg != 0.0)
{
v = v/vavg;
}
}
if(DoPairedDiffNorm1)
{
v = v1-v2; // difference
if (v1 != 0.0)
{
v = v/v1;
}
else
{
v = 0;
}
}
if(DoPairedDiffNorm2)
{
v = v1-v2; // difference
if (v2 != 0.0)
{
v = v/v2;
}
else
{
v = 0;
}
}
MRIsetVoxVal(mritmp,c,r,s,fout,v);
fout++;
}
}
}
}
MRIfree(&mriout);
mriout = mritmp;
}
nframes = mriout->nframes;
printf("nframes = %d\n",nframes);
if(DoBonfCor)
{
DoAdd = 1;
AddVal = -log10(mriout->nframes);
}
if(DoMean)
{
printf("Computing mean across frames\n");
mritmp = MRIframeMean(mriout,NULL);
MRIfree(&mriout);
mriout = mritmp;
}
if(DoMedian)
{
printf("Computing median across frames\n");
mritmp = MRIframeMedian(mriout,NULL);
MRIfree(&mriout);
mriout = mritmp;
}
if(DoMeanDivN)
{
printf("Computing mean2 = sum/(nframes^2)\n");
mritmp = MRIframeSum(mriout,NULL);
MRIfree(&mriout);
mriout = mritmp;
MRImultiplyConst(mriout, 1.0/(nframes*nframes), mriout);
}
if(DoSum)
{
printf("Computing sum across frames\n");
mritmp = MRIframeSum(mriout,NULL);
MRIfree(&mriout);
mriout = mritmp;
}
if(DoTAR1)
{
printf("Computing temoral AR1 %d\n",mriout->nframes-TAR1DOFAdjust);
mritmp = fMRItemporalAR1(mriout,TAR1DOFAdjust,NULL,NULL);
MRIfree(&mriout);
mriout = mritmp;
}
if(DoStd || DoVar)
{
printf("Computing std/var across frames\n");
if(mriout->nframes < 2)
{
printf("ERROR: cannot compute std from one frame\n");
exit(1);
}
//mritmp = fMRIvariance(mriout, -1, 1, NULL);
mritmp = fMRIcovariance(mriout, 0, -1, NULL, NULL);
if(DoStd)
{
MRIsqrt(mritmp, mritmp);
}
MRIfree(&mriout);
mriout = mritmp;
}
if(DoMax)
{
printf("Computing max across all frames \n");
mritmp = MRIvolMax(mriout,NULL);
MRIfree(&mriout);
mriout = mritmp;
}
if(DoMaxIndex)
{
printf("Computing max index across all frames \n");
mritmp = MRIvolMaxIndex(mriout,1,NULL,NULL);
MRIfree(&mriout);
mriout = mritmp;
}
if(DoConjunction)
{
printf("Computing conjunction across all frames \n");
mritmp = MRIconjunct(mriout,NULL);
MRIfree(&mriout);
mriout = mritmp;
}
if(DoMin)
{
printf("Computing min across all frames \n");
mritmp = MRIvolMin(mriout,NULL);
MRIfree(&mriout);
mriout = mritmp;
}
if(DoSort)
{
printf("Sorting \n");
mritmp = MRIsort(mriout,mask,NULL);
MRIfree(&mriout);
mriout = mritmp;
}
if(DoVote)
{
printf("Voting \n");
mritmp = MRIvote(mriout,mask,NULL);
MRIfree(&mriout);
mriout = mritmp;
}
if(DoMultiply)
{
printf("Multiplying by %lf\n",MultiplyVal);
MRImultiplyConst(mriout, MultiplyVal, mriout);
}
if(DoAdd)
{
printf("Adding %lf\n",AddVal);
MRIaddConst(mriout, AddVal, mriout);
}
if(DoSCM)
{
printf("Computing spatial correlation matrix (%d)\n",mriout->nframes);
mritmp = fMRIspatialCorMatrix(mriout);
if(mritmp == NULL)
{
exit(1);
}
MRIfree(&mriout);
mriout = mritmp;
}
if(DoPCA)
{
// Saves only non-zero components
printf("Computing PCA\n");
if(PCAMaskFile)
{
printf(" PCA Mask %s\n",PCAMaskFile);
PCAMask = MRIread(PCAMaskFile);
if(PCAMask == NULL)
{
exit(1);
}
}
err=MRIpca(mriout, &Upca, &Spca, &Vpca, PCAMask);
if(err)
{
exit(1);
}
stem = IDstemFromName(out);
sprintf(tmpstr,"%s.u.mtx",stem);
MatrixWriteTxt(tmpstr, Upca);
sprintf(tmpstr,"%s.stats.dat",stem);
WritePCAStats(tmpstr,Spca);
MRIfree(&mriout);
mriout = Vpca;
}
if(NReplications > 0)
{
printf("NReplications %d\n",NReplications);
mritmp = MRIallocSequence(mriout->width,
mriout->height,
mriout->depth,
mriout->type,
mriout->nframes*NReplications);
if(mritmp == NULL)
{
exit(1);
}
printf("Done allocing\n");
MRIcopyHeader(mriout,mritmp);
for(c=0; c < mriout->width; c++)
{
for(r=0; r < mriout->height; r++)
{
for(s=0; s < mriout->depth; s++)
{
outf = 0;
for(nthrep = 0; nthrep < NReplications; nthrep++)
{
for(f=0; f < mriout->nframes; f++)
{
v = MRIgetVoxVal(mriout,c,r,s,f);
MRIsetVoxVal(mritmp,c,r,s,outf,v);
outf ++;
}
}
}
}
}
MRIfree(&mriout);
mriout = mritmp;
}
if(DoPrune)
{
// Apply prune mask that was computed above
printf("Applying prune mask \n");
MRImask(mriout, PruneMask, mriout, 0, 0);
}
if(DoRMS)
{
printf("Computing RMS across input frames\n");
mritmp = MRIread(inlist[0]);
MRIcopyHeader(mritmp, mriout);
MRIrms(mritmp,mriout);
}
printf("Writing to %s\n",out);
err = MRIwrite(mriout,out);
if(err)
{
exit(err);
}
return(0);
}
int
main(int argc, char *argv[]) {
char **av, fname[STRLEN] ;
int ac, nargs ;
char *reg_fname, *in_fname, *out_stem, *cp ;
int msec, minutes, seconds, nvox, float2int ;
struct timeb start ;
MRI_SURFACE *mris_lh_white, *mris_rh_white, *mris_lh_pial, *mris_rh_pial ;
MRI *mri_aseg, *mri_seg, *mri_pial, *mri_tmp, *mri_ribbon, *mri_in, *mri_cortex,
*mri_subcort_gm, *mri_wm, *mri_csf ;
MATRIX *m_regdat ;
float intensity, betplaneres, inplaneres ;
/* rkt: check for and handle version tag */
nargs = handle_version_option (argc, argv, "$Id: mri_compute_volume_fractions.c,v 1.9 2012/11/07 18:58:02 greve Exp $", "$Name: $");
if (nargs && argc - nargs == 1)
exit (0);
argc -= nargs;
Progname = argv[0] ;
ac = argc ;
av = argv ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
if (argc < 4)
usage_exit(1) ;
if (!strlen(sdir)) {
cp = getenv("SUBJECTS_DIR") ;
if (!cp)
ErrorExit(ERROR_BADPARM,
"%s: SUBJECTS_DIR not defined in environment.\n", Progname) ;
strcpy(sdir, cp) ;
}
reg_fname = argv[1] ; in_fname = argv[2] ;
out_stem = argv[3] ; Progname = argv[0] ;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
TimerStart(&start) ;
if (stricmp(reg_fname, "identity.nofile") == 0)
{
printf("using identity transform\n") ;
m_regdat = NULL ;
inplaneres = betplaneres = intensity = 1 ;
float2int = 0 ;
if (subject == NULL)
subject = "unknown" ;
}
else
{
char *saved_subject = subject ;
printf("reading registration file %s\n", reg_fname) ;
regio_read_register(reg_fname, &subject, &inplaneres,
&betplaneres, &intensity, &m_regdat,
&float2int);
if (saved_subject) // specified on cmdline
subject = saved_subject ;
m_regdat = regio_read_registermat(reg_fname) ;
if (m_regdat == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not load registration file from %s", Progname,reg_fname) ;
}
printf("Format is %s\n",fmt);
sprintf(fname, "%s/%s/surf/lh.white", sdir, subject) ;
printf("reading surface %s\n", fname) ;
mris_lh_white = MRISread(fname) ;
if (mris_lh_white == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not load lh white surface from %s", Progname,fname) ;
sprintf(fname, "%s/%s/surf/rh.white", sdir, subject) ;
printf("reading surface %s\n", fname) ;
mris_rh_white = MRISread(fname) ;
if (mris_rh_white == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not load rh white surface from %s", Progname,fname) ;
sprintf(fname, "%s/%s/surf/lh.pial", sdir, subject) ;
printf("reading surface %s\n", fname) ;
mris_lh_pial = MRISread(fname) ;
if (mris_lh_pial == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not load lh pial surface from %s", Progname,fname) ;
sprintf(fname, "%s/%s/surf/rh.pial", sdir, subject) ;
printf("reading surface %s\n", fname) ;
mris_rh_pial = MRISread(fname) ;
if (mris_rh_pial == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not load rh pial surface from %s", Progname,fname) ;
sprintf(fname, "%s/%s/mri/aseg.mgz", sdir, subject) ;
printf("reading volume %s\n", fname) ;
mri_aseg = MRIread(fname) ;
if (mri_aseg == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not load aseg volume from %s", Progname,fname) ;
printf("reading movable volume %s\n", in_fname) ;
mri_in = MRIread(in_fname) ;
if (mri_in == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not load input volume from %s", Progname,in_fname) ;
nvox = (int)ceil(256/resolution);
mri_pial = MRIalloc(nvox, nvox, nvox, MRI_UCHAR) ;
MRIsetResolution(mri_pial, resolution, resolution, resolution) ;
mri_pial->xstart = -resolution*mri_pial->width/2.0 ;
mri_pial->xend = resolution*mri_pial->width/2.0 ;
mri_pial->ystart = -resolution*mri_pial->height/2.0 ;
mri_pial->yend = resolution*mri_pial->height/2.0 ;
mri_pial->zstart = -resolution*mri_pial->depth/2.0 ;
mri_pial->zend = resolution*mri_pial->depth/2 ;
mri_pial->c_r = mri_aseg->c_r ; mri_pial->c_a = mri_aseg->c_a ; mri_pial->c_s = mri_aseg->c_s ;
MRIreInitCache(mri_pial) ;
printf("filling interior of lh pial surface...\n") ;
MRISfillInterior(mris_lh_pial, resolution, mri_pial) ;
mri_seg = MRIclone(mri_pial, NULL) ;
mri_tmp = MRIclone(mri_pial, NULL) ;
printf("filling interior of rh pial surface...\n") ;
MRISfillInterior(mris_rh_pial, resolution, mri_tmp) ;
MRIcopyLabel(mri_tmp, mri_pial, 1) ;
MRIclear(mri_tmp) ;
printf("filling interior of lh white matter surface...\n") ;
MRISfillWhiteMatterInterior(mris_lh_white, mri_aseg, mri_seg, resolution,
WM_VAL, SUBCORT_GM_VAL, CSF_VAL);
printf("filling interior of rh white matter surface...\n") ;
MRISfillWhiteMatterInterior(mris_rh_white, mri_aseg, mri_tmp, resolution,
WM_VAL, SUBCORT_GM_VAL, CSF_VAL);
MRIcopyLabel(mri_tmp, mri_seg, WM_VAL) ;
MRIcopyLabel(mri_tmp, mri_seg, SUBCORT_GM_VAL) ;
MRIcopyLabel(mri_tmp, mri_seg, CSF_VAL) ;
MRIfree(&mri_tmp) ;
mri_ribbon = MRInot(mri_seg, NULL) ;
MRIcopyLabel(mri_seg, mri_pial, CSF_VAL) ;
MRIreplaceValuesOnly(mri_pial, mri_pial, CSF_VAL, 0) ;
MRIand(mri_ribbon, mri_pial, mri_ribbon, 1) ;
MRIbinarize(mri_ribbon, mri_ribbon, 1, 0, GM_VAL) ;
MRIcopyLabel(mri_ribbon, mri_seg, GM_VAL) ;
MRIreplaceValuesOnly(mri_seg, mri_seg, CSF_VAL, 0) ;
add_aseg_structures_outside_ribbon(mri_seg, mri_aseg, mri_seg, WM_VAL, SUBCORT_GM_VAL, CSF_VAL) ;
{
MATRIX *m_conformed_to_epi_vox2vox, *m_seg_to_conformed_vox2vox,
*m_seg_to_epi_vox2vox ;
if (m_regdat == NULL) // assume identity transform
m_seg_to_epi_vox2vox = MRIgetVoxelToVoxelXform(mri_seg, mri_in) ;
else
{
m_conformed_to_epi_vox2vox = MRIvoxToVoxFromTkRegMtx(mri_in, mri_aseg, m_regdat);
m_seg_to_conformed_vox2vox = MRIgetVoxelToVoxelXform(mri_seg, mri_aseg) ;
m_seg_to_epi_vox2vox = MatrixMultiply(m_conformed_to_epi_vox2vox, m_seg_to_conformed_vox2vox, NULL) ;
MatrixFree(&m_regdat) ; MatrixFree(&m_conformed_to_epi_vox2vox) ;
MatrixFree(&m_seg_to_conformed_vox2vox);
}
printf("seg to EPI vox2vox matrix:\n") ;
MatrixPrint(Gstdout, m_seg_to_epi_vox2vox) ;
mri_cortex = MRIalloc(mri_in->width, mri_in->height, mri_in->depth, MRI_FLOAT) ;
MRIcopyHeader(mri_in, mri_cortex) ;
mri_subcort_gm = MRIclone(mri_cortex, NULL) ;
mri_wm = MRIclone(mri_cortex, NULL) ;
mri_csf = MRIclone(mri_cortex, NULL) ;
printf("computing partial volume fractions...\n") ;
MRIcomputePartialVolumeFractions(mri_in, m_seg_to_epi_vox2vox, mri_seg, mri_wm, mri_subcort_gm, mri_cortex, mri_csf,
WM_VAL, SUBCORT_GM_VAL, GM_VAL, 0) ;
}
sprintf(fname, "%s.wm.%s", out_stem,fmt) ;
printf("writing wm %% to %s\n", fname) ;
MRIwrite(mri_wm, fname) ;
sprintf(fname, "%s.subcort_gm.%s", out_stem,fmt) ;
printf("writing subcortical gm %% to %s\n", fname) ;
MRIwrite(mri_subcort_gm, fname) ;
sprintf(fname, "%s.cortex.%s", out_stem, fmt) ;
printf("writing cortical gm %% to %s\n", fname) ;
MRIwrite(mri_cortex, fname) ;
sprintf(fname, "%s.csf.%s", out_stem,fmt) ;
printf("writing csf %% to %s\n", fname) ;
MRIwrite(mri_csf, fname) ;
msec = TimerStop(&start) ;
seconds = nint((float)msec/1000.0f) ;
minutes = seconds / 60 ;
seconds = seconds % 60 ;
printf("volume fraction calculation took %d minutes"
" and %d seconds.\n", minutes, seconds) ;
exit(0) ;
return(0) ;
}
/*-------------------------------------------------------------*/
int main(int argc, char *argv[])
{
/* check for and handle version tag */
int nargs = handle_version_option
(argc, argv,
"$Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $",
"$Name: stable5 $");
if (nargs && argc - nargs == 1)
{
exit (0);
}
argc -= nargs;
Progname = argv[0] ;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
parse_commandline(argc, argv);
MRI *mri, *mri2, *mri3, *mri_mask=NULL;
mri3 = MRIread(in_filename);
if ( mri3 == NULL )
{
printf("can't read file %s\nexit!\n", in_filename);
exit(0);
}
mri = MRISeqchangeType(mri3, MRI_UCHAR, 0.0, 0.999, FALSE);
mri2 = MRISeqchangeType(mri3, MRI_UCHAR, 0.0, 0.999, FALSE);
//MRI* mri4 = MRIread("gcutted.mgz");
if (bNeedMasking == 1)
{
printf("reading mask...\n");
mri_mask = MRIread(mask_filename);
if ( mri_mask == NULL )
{
printf("can't read %s, omit -mult option!\n", mask_filename);
print_help();
exit(1);
}
else
{
if ( mri_mask->width != mri->width ||
mri_mask->height != mri->height ||
mri_mask->depth != mri->depth )
{
printf("Two masks are of different size, omit -mult option!\n");
print_help();
exit(1);
}
}
}
int w = mri->width;
int h = mri->height;
int d = mri->depth;
// -- copy of mri matrix
unsigned char ***label;
label = new unsigned char**[d];
for (int i = 0; i < d; i++)
{
label[i] = new unsigned char*[h];
for (int j = 0; j < h; j++)
{
label[i][j] = new unsigned char[w];
for (int k = 0; k < w; k++)
{
label[i][j][k] = 0;
}
}
}
// -- gcut image
int ***im_gcut;
im_gcut = new int**[d];
for (int i = 0; i < d; i++)
{
im_gcut[i] = new int*[h];
for (int j = 0; j < h; j++)
{
im_gcut[i][j] = new int[w];
for (int k = 0; k < w; k++)
{
im_gcut[i][j][k] = 0;
}
}
}
// -- diluted
int ***im_diluteerode;
im_diluteerode = new int**[d];
for (int i = 0; i < d; i++)
{
im_diluteerode[i] = new int*[h];
for (int j = 0; j < h; j++)
{
im_diluteerode[i][j] = new int[w];
for (int k = 0; k < w; k++)
{
im_diluteerode[i][j][k] = 0;
}
}
}
//int w, h, d;
//int x, y, z;
double whitemean;
if (bNeedPreprocessing == 0)
{
// pre-processed: 110 intensity voxels are the WM
if (LCC_function(mri ->slices,
label,
mri->width,
mri->height,
mri->depth,
whitemean) == 1)
{
if ( whitemean < 0 )
{
printf("whitemean < 0 error!\n");
exit(0);
}
}
else
{
whitemean = 110;
printf("use voxels with intensity 110 as WM mask\n");
}
}
else
{
printf("estimating WM mask\n");
whitemean = pre_processing(mri ->slices,
label,
mri->width,
mri->height,
mri->depth);
if ( whitemean < 0 )
{
printf("whitemean < 0 error!\n");
exit(0);
}
}
double threshold = whitemean * _t;
printf("threshold set to: %f*%f=%f\n", whitemean, _t, threshold);
for (int z = 0 ; z < mri->depth ; z++)
{
for (int y = 0 ; y < mri->height ; y++)
{
for (int x = 0 ; x < mri->width ; x++)
{
if ( mri->slices[z][y][x] < threshold + 1 )
{
mri->slices[z][y][x] = 0;
}
}
}//end of for
}
//new code
int ***foregroundseedwt;
int ***backgroundseedwt;
matrix_alloc(&foregroundseedwt, d, h, w);
matrix_alloc(&backgroundseedwt, d, h, w);
double kval = 2.3;
graphcut(mri->slices, label, im_gcut,
foregroundseedwt, backgroundseedwt,
w, h, d, kval, threshold, whitemean);
printf("g-cut done!\npost-processing...\n");
//printf("_test: %f\n", _test);
post_processing(mri2->slices,
mri->slices,
threshold,
im_gcut,
im_diluteerode,
w, h, d);
printf("post-processing done!\n");
if (bNeedMasking == 1)//masking
{
printf("masking...\n");
for (int z = 0 ; z < mri_mask->depth ; z++)
{
for (int y = 0 ; y < mri_mask->height ; y++)
{
for (int x = 0 ; x < mri_mask->width ; x++)
{
if ( mri_mask->slices[z][y][x] == 0 )
{
im_diluteerode[z][y][x] = 0;
}
}
}
}
}
//if the output might have some problem
int numGcut = 0, numMask = 0;
double _ratio = 0;
int error_Hurestic = 0;
if (bNeedMasking == 1)//-110 and masking are both set
{
for (int z = 0 ; z < mri_mask->depth ; z++)
{
for (int y = 0 ; y < mri_mask->height ; y++)
{
for (int x = 0 ; x < mri_mask->width ; x++)
{
if ( im_diluteerode[z][y][x] != 0 )
{
numGcut++;
}
if ( mri_mask->slices[z][y][x] != 0 )
{
numMask++;
}
}
}
}
_ratio = (double)numGcut / numMask;
if (_ratio <= 0.85)
{
error_Hurestic = 1;
}
}
if (error_Hurestic == 1)
{
printf("** Gcutted brain is much smaller than the mask!\n");
printf("** Using the mask as the output instead!\n");
//printf("** Gcutted output is written as: 'error_gcutted_sample'\n");
}
for (int z = 0 ; z < mri->depth ; z++)
{
for (int y = 0 ; y < mri->height ; y++)
{
for (int x = 0 ; x < mri->width ; x++)
{
if (error_Hurestic == 0)
{
if ( im_diluteerode[z][y][x] == 0 )
{
mri2 ->slices[z][y][x] = 0;
}
}
else
{
if ( mri_mask->slices[z][y][x] == 0 )
{
mri2 ->slices[z][y][x] = 0;
}
//if( im_diluteerode[z][y][x] == 0 )
//mri ->slices[z][y][x] = 0;
}
}
}//end of for 2
}//end of for 1
MRIwrite(mri2, out_filename);
// if user supplied a filename to which to write diffs, then write-out
// volume file containing where cuts were made (for debug)
if (diff_filename[0] && (error_Hurestic != 1))
{
MRI *mri_diff = MRISeqchangeType(mri3, MRI_UCHAR, 0.0, 0.999, FALSE);
for (int z = 0 ; z < mri3->depth ; z++)
{
for (int y = 0 ; y < mri3->height ; y++)
{
for (int x = 0 ; x < mri3->width ; x++)
{
if (mri_mask)
{
mri_diff->slices[z][y][x] =
mri2->slices[z][y][x] - mri_mask->slices[z][y][x];
}
else
{
mri_diff->slices[z][y][x] =
mri2->slices[z][y][x] - mri3->slices[z][y][x];
}
}
}//end of for 2
}//end of for 1
MRIwrite(mri_diff, diff_filename);
MRIfree(&mri_diff);
}
if (mri)
{
MRIfree(&mri);
}
if (mri2)
{
MRIfree(&mri2);
}
if (mri3)
{
MRIfree(&mri3);
}
if (mri_mask)
{
MRIfree(&mri_mask);
}
for (int i = 0; i < d; i++)
{
for (int j = 0; j < h; j++)
{
delete[] im_diluteerode[i][j];
delete[] im_gcut[i][j];
delete[] label[i][j];
}
delete[] im_diluteerode[i];
delete[] im_gcut[i];
delete[] label[i];
}
delete[] im_diluteerode;
delete[] im_gcut;
delete[] label;
return 0;
}
/*--------------------------------------------------*/
int main(int argc, char **argv) {
int nargs, err, asegid, c, r, s, annot, hemioffset;
int annotid;
struct utsname uts;
char *cmdline, cwd[2000];
/* rkt: check for and handle version tag */
nargs = handle_version_option (argc, argv, vcid, "$Name: stable5 $");
if (nargs && argc - nargs == 1) exit (0);
argc -= nargs;
cmdline = argv2cmdline(argc,argv);
uname(&uts);
getcwd(cwd,2000);
Progname = argv[0] ;
argc --;
argv++;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
if (argc == 0) usage_exit();
parse_commandline(argc, argv);
check_options();
dump_options(stdout);
printf("\n");
printf("%s\n",vcid);
printf("cwd %s\n",cwd);
printf("cmdline %s\n",cmdline);
printf("sysname %s\n",uts.sysname);
printf("hostname %s\n",uts.nodename);
printf("machine %s\n",uts.machine);
SUBJECTS_DIR = getenv("SUBJECTS_DIR");
if (SUBJECTS_DIR==NULL) {
printf("ERROR: SUBJECTS_DIR not defined in environment\n");
exit(1);
}
printf("SUBJECTS_DIR %s\n",SUBJECTS_DIR);
printf("subject %s\n",subject);
printf("\n");
fflush(stdout);
/* ------ Load subject's lh white surface ------ */
sprintf(tmpstr,"%s/%s/surf/lh.white",SUBJECTS_DIR,subject);
printf("Reading lh white surface \n %s\n",tmpstr);
lhwhite = MRISread(tmpstr);
if (lhwhite == NULL) {
fprintf(stderr,"ERROR: could not read %s\n",tmpstr);
exit(1);
}
printf("Building hash of lh white\n");
lhwhite_hash = MHTfillVertexTableRes(lhwhite, NULL,CURRENT_VERTICES,16);
/* ------ Load lh annotation ------ */
sprintf(annotfile,"%s/%s/label/lh.aparc.annot",SUBJECTS_DIR,subject);
printf("Loading lh annotations from %s\n",annotfile);
err = MRISreadAnnotation(lhwhite, annotfile);
if (err) {
printf("ERROR: MRISreadAnnotation() failed %s\n",annotfile);
exit(1);
}
/* ------ Load subject's rh surface ------ */
sprintf(tmpstr,"%s/%s/surf/rh.white",SUBJECTS_DIR,subject);
printf("Reading rh white surface \n %s\n",tmpstr);
rhwhite = MRISread(tmpstr);
if (rhwhite == NULL) {
fprintf(stderr,"ERROR: could not read %s\n",tmpstr);
exit(1);
}
if (debug) printf("Building hash of rh white\n");
rhwhite_hash = MHTfillVertexTableRes(rhwhite, NULL,CURRENT_VERTICES,16);
/* ------ Load rh annotation ------ */
sprintf(annotfile,"%s/%s/label/rh.aparc.annot",SUBJECTS_DIR,subject);
printf("Loading rh annotations from %s\n",annotfile);
err = MRISreadAnnotation(rhwhite, annotfile);
if (err) {
printf("ERROR: MRISreadAnnotation() failed %s\n",annotfile);
exit(1);
}
if (debug && lhwhite->ct) printf("Have color table for annotation\n");
if (debug) print_annotation_table(stdout);
/* ------ Load ASeg ------ */
sprintf(tmpstr,"%s/%s/mri/aseg.mgz",SUBJECTS_DIR,subject);
if (!fio_FileExistsReadable(tmpstr)) {
sprintf(tmpstr,"%s/%s/mri/aseg.mgh",SUBJECTS_DIR,subject);
if (!fio_FileExistsReadable(tmpstr)) {
sprintf(tmpstr,"%s/%s/mri/aseg/COR-.info",SUBJECTS_DIR,subject);
if (!fio_FileExistsReadable(tmpstr)) {
printf("ERROR: cannot find aseg\n");
exit(1);
} else
sprintf(tmpstr,"%s/%s/mri/aseg/",SUBJECTS_DIR,subject);
}
}
printf("Loading aseg from %s\n",tmpstr);
ASeg = MRIread(tmpstr);
if (ASeg == NULL) {
printf("ERROR: loading aseg %s\n",tmpstr);
exit(1);
}
mritmp = MRIchangeType(ASeg,MRI_INT,0,0,0);
MRIfree(&ASeg);
ASeg = mritmp;
WMSeg = MRIclone(ASeg,NULL);
Vox2RAS = MRIxfmCRS2XYZtkreg(ASeg);
if (debug) {
printf("ASeg Vox2RAS: -----------\n");
MatrixPrint(stdout,Vox2RAS);
printf("-------------------------\n");
}
CRS = MatrixAlloc(4,1,MATRIX_REAL);
CRS->rptr[4][1] = 1;
RAS = MatrixAlloc(4,1,MATRIX_REAL);
RAS->rptr[4][1] = 1;
// Go through each voxel in the aseg
printf("\n");
printf("Labeling WM\n");
for (c=0; c < ASeg->width; c++) {
if (debug) printf("%3d ",c);
if (debug && c%20 ==19) printf("\n");
for (r=0; r < ASeg->height; r++) {
for (s=0; s < ASeg->depth; s++) {
// If it's not labeled as white matter in the aseg, set
// seg value to that from the aseg and skip the rest
asegid = MRIgetVoxVal(ASeg,c,r,s,0);
if (asegid != 2 && asegid != 41) {
MRIsetVoxVal(WMSeg,c,r,s,0,asegid);
continue;
}
// Convert the CRS to RAS
CRS->rptr[1][1] = c;
CRS->rptr[2][1] = r;
CRS->rptr[3][1] = s;
RAS = MatrixMultiply(Vox2RAS,CRS,RAS);
vtx.x = RAS->rptr[1][1];
vtx.y = RAS->rptr[2][1];
vtx.z = RAS->rptr[3][1];
// Get the index of the closest vertex in the
// lh.white, rh.white
lhwvtx = MHTfindClosestVertexNo(lhwhite_hash,lhwhite,&vtx,&dlhw);
rhwvtx = MHTfindClosestVertexNo(rhwhite_hash,rhwhite,&vtx,&drhw);
if ( (lhwvtx < 0) && (rhwvtx < 0) ) {
printf("ERROR: could not map to any surface.\n");
printf("crs = %d %d %d, ras = %6.4f %6.4f %6.4f \n",
c,r,s,vtx.x,vtx.y,vtx.z);
exit(1);
}
if (lhwvtx < 0) dlhw = 1000000000000000.0;
if (rhwvtx < 0) drhw = 1000000000000000.0;
if (dlhw < drhw) {
// Left hemi is closer than the right
annot = lhwhite->vertices[lhwvtx].annotation;
hemioffset = 1000;
if (lhwhite->ct)
CTABfindAnnotation(lhwhite->ct, annot, &annotid);
else
annotid = annotation_to_index(annot);
} else {
// Right hemi is closer than the left
annot = rhwhite->vertices[rhwvtx].annotation;
hemioffset = 2000;
if (rhwhite->ct)
CTABfindAnnotation(lhwhite->ct, annot, &annotid);
else
annotid = annotation_to_index(annot);
}
MRIsetVoxVal(WMSeg,c,r,s,0,annotid+hemioffset);
}
}
}
printf("\nWriting output wmseg to %s\n",WMSegFile);
MRIwrite(WMSeg,WMSegFile);
printf("mri_aparc2wmseg done\n");
return(0);
}
int
main(int argc, char *argv[])
{
char *gca_fname, *in_fname, *out_fname, **av, *xform_fname, fname[STRLEN] ;
MRI *mri_in, *mri_norm = NULL, *mri_tmp, *mri_ctrl = NULL ;
GCA *gca ;
int ac, nargs, nsamples, msec, minutes, seconds;
int i, struct_samples, norm_samples = 0, n, input, ninputs ;
struct timeb start ;
GCA_SAMPLE *gcas, *gcas_norm = NULL, *gcas_struct ;
TRANSFORM *transform = NULL ;
char cmdline[CMD_LINE_LEN], line[STRLEN], *cp, subject[STRLEN], sdir[STRLEN], base_name[STRLEN] ;
FILE *fp ;
make_cmd_version_string
(argc, argv,
"$Id: mri_cal_normalize.c,v 1.2.2.1 2011/08/31 00:32:41 nicks Exp $",
"$Name: stable5 $", cmdline);
/* rkt: check for and handle version tag */
nargs = handle_version_option
(argc, argv,
"$Id: mri_cal_normalize.c,v 1.2.2.1 2011/08/31 00:32:41 nicks Exp $",
"$Name: stable5 $");
if (nargs && argc - nargs == 1)
exit (0);
argc -= nargs;
setRandomSeed(-1L) ;
Progname = argv[0] ;
DiagInit(NULL, NULL, NULL) ;
ErrorInit(NULL, NULL, NULL) ;
ac = argc ;
av = argv ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++)
{
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
if (argc < 6)
ErrorExit
(ERROR_BADPARM,
"usage: %s [<options>] <longitudinal time point file> <in vol> <atlas> <transform file> <out vol> \n",
Progname) ;
in_fname = argv[2] ;
gca_fname = argv[3] ;
xform_fname = argv[4] ;
out_fname = argv[5] ;
transform = TransformRead(xform_fname) ;
if (transform == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read transform from %s", Progname, xform_fname) ;
if (read_ctrl_point_fname)
{
mri_ctrl = MRIread(read_ctrl_point_fname) ;
if (mri_ctrl == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read precomputed control points from %s",
Progname, read_ctrl_point_fname) ;
}
TimerStart(&start) ;
printf("reading atlas from '%s'...\n", gca_fname) ;
fflush(stdout) ;
gca = GCAread(gca_fname) ;
if (gca == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not open GCA %s.\n",Progname, gca_fname) ;
GCAregularizeConditionalDensities(gca, .5) ;
FileNamePath(argv[1], sdir) ;
cp = strrchr(sdir, '/') ;
if (cp)
{
strcpy(base_name, cp+1) ;
*cp = 0 ; // remove last component of path, which is base subject name
}
ninputs = 0 ;
fp = fopen(argv[1], "r") ;
if (fp == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read time point file %s", argv[1]) ;
do
{
cp = fgetl(line, STRLEN-1, fp) ;
if (cp != NULL && strlen(cp) > 0)
{
subjects[ninputs] = (char *)calloc(strlen(cp)+1, sizeof(char)) ;
strcpy(subjects[ninputs], cp) ;
ninputs++ ;
}
} while (cp != NULL && strlen(cp) > 0) ;
fclose(fp) ;
printf("processing %d timepoints in SUBJECTS_DIR %s...\n", ninputs, sdir) ;
for (input = 0 ; input < ninputs ; input++)
{
sprintf(subject, "%s.long.%s", subjects[input], base_name) ;
printf("reading subject %s - %d of %d\n", subject, input+1, ninputs) ;
sprintf(fname, "%s/%s/mri/%s", sdir, subject, in_fname) ;
mri_tmp = MRIread(fname) ;
if (!mri_tmp)
ErrorExit(ERROR_NOFILE, "%s: could not read input MR volume from %s",
Progname, fname) ;
MRImakePositive(mri_tmp, mri_tmp) ;
if (mri_tmp && ctrl_point_fname && !mri_ctrl)
{
mri_ctrl = MRIallocSequence(mri_tmp->width, mri_tmp->height,
mri_tmp->depth,MRI_FLOAT, nregions*2) ; // labels and means
MRIcopyHeader(mri_tmp, mri_ctrl) ;
}
if (input == 0)
{
mri_in =
MRIallocSequence(mri_tmp->width, mri_tmp->height, mri_tmp->depth,
mri_tmp->type, ninputs) ;
if (!mri_in)
ErrorExit(ERROR_NOMEMORY,
"%s: could not allocate input volume %dx%dx%dx%d",
mri_tmp->width,mri_tmp->height,mri_tmp->depth,ninputs) ;
MRIcopyHeader(mri_tmp, mri_in) ;
}
if (mask_fname)
{
int i ;
MRI *mri_mask ;
mri_mask = MRIread(mask_fname) ;
if (!mri_mask)
ErrorExit(ERROR_NOFILE, "%s: could not open mask volume %s.\n",
Progname, mask_fname) ;
for (i = 1 ; i < WM_MIN_VAL ; i++)
MRIreplaceValues(mri_mask, mri_mask, i, 0) ;
MRImask(mri_tmp, mri_mask, mri_tmp, 0, 0) ;
MRIfree(&mri_mask) ;
}
MRIcopyFrame(mri_tmp, mri_in, 0, input) ;
MRIfree(&mri_tmp) ;
}
MRIaddCommandLine(mri_in, cmdline) ;
GCAhistoScaleImageIntensitiesLongitudinal(gca, mri_in, 1) ;
{
int j ;
gcas = GCAfindAllSamples(gca, &nsamples, NULL, 1) ;
printf("using %d sample points...\n", nsamples) ;
GCAcomputeSampleCoords(gca, mri_in, gcas, nsamples, transform) ;
if (sample_fname)
GCAtransformAndWriteSamples
(gca, mri_in, gcas, nsamples, sample_fname, transform) ;
for (j = 0 ; j < 1 ; j++)
{
for (n = 1 ; n <= nregions ; n++)
{
for (norm_samples = i = 0 ; i < NSTRUCTURES ; i++)
{
if (normalization_structures[i] == Gdiag_no)
DiagBreak() ;
printf("finding control points in %s....\n",
cma_label_to_name(normalization_structures[i])) ;
gcas_struct = find_control_points(gca, gcas, nsamples, &struct_samples, n,
normalization_structures[i], mri_in, transform, min_prior,
ctl_point_pct) ;
discard_unlikely_control_points(gca, gcas_struct, struct_samples, mri_in, transform,
cma_label_to_name(normalization_structures[i])) ;
if (mri_ctrl && ctrl_point_fname) // store the samples
copy_ctrl_points_to_volume(gcas_struct, struct_samples, mri_ctrl, n-1) ;
if (i)
{
GCA_SAMPLE *gcas_tmp ;
gcas_tmp = gcas_concatenate(gcas_norm, gcas_struct, norm_samples, struct_samples) ;
free(gcas_norm) ;
norm_samples += struct_samples ;
gcas_norm = gcas_tmp ;
}
else
{
gcas_norm = gcas_struct ; norm_samples = struct_samples ;
}
}
printf("using %d total control points "
"for intensity normalization...\n", norm_samples) ;
if (normalized_transformed_sample_fname)
GCAtransformAndWriteSamples(gca, mri_in, gcas_norm, norm_samples,
normalized_transformed_sample_fname,
transform) ;
mri_norm = GCAnormalizeSamplesAllChannels(mri_in, gca, gcas_norm, file_only ? 0 :norm_samples,
transform, ctl_point_fname, bias_sigma) ;
if (Gdiag & DIAG_WRITE)
{
char fname[STRLEN] ;
sprintf(fname, "norm%d.mgz", n) ;
printf("writing normalized volume to %s...\n", fname) ;
MRIwrite(mri_norm, fname) ;
sprintf(fname, "norm_samples%d.mgz", n) ;
GCAtransformAndWriteSamples(gca, mri_in, gcas_norm, norm_samples,
fname, transform) ;
}
MRIcopy(mri_norm, mri_in) ; /* for next pass through */
MRIfree(&mri_norm) ;
}
}
}
// now do cross-time normalization to bring each timepoint closer to the mean at each location
{
MRI *mri_frame1, *mri_frame2, *mri_tmp ;
double rms_before, rms_after ;
int i ;
mri_tmp = MRIcopy(mri_in, NULL) ;
mri_frame1 = MRIcopyFrame(mri_in, NULL, 0, 0) ;
mri_frame2 = MRIcopyFrame(mri_in, NULL, 1, 0) ;
rms_before = MRIrmsDiff(mri_frame1, mri_frame2) ;
printf("RMS before = %2.2f\n", rms_before) ;
MRIfree(&mri_frame1) ; MRIfree(&mri_frame2) ;
for (i = 50 ; i <= 50 ; i += 25)
{
MRIcopy(mri_tmp, mri_in) ;
normalize_timepoints_with_samples(mri_in, gcas_norm, norm_samples, i) ;
mri_frame1 = MRIcopyFrame(mri_in, NULL, 0, 0) ;
mri_frame2 = MRIcopyFrame(mri_in, NULL, 1, 0) ;
rms_after = MRIrmsDiff(mri_frame1, mri_frame2) ;
MRIfree(&mri_frame1) ; MRIfree(&mri_frame2) ;
printf("RMS after (%d) = %2.2f\n", i, rms_after) ;
}
}
{
MRI *mri_frame1, *mri_frame2 ;
double rms_after ;
int i ;
mri_tmp = MRIcopy(mri_in, NULL) ;
for (i = 10 ; i <= 10 ; i += 10)
{
MRIcopy(mri_tmp, mri_in) ;
normalize_timepoints(mri_in, 2.0, i) ;
mri_frame1 = MRIcopyFrame(mri_in, NULL, 0, 0) ;
mri_frame2 = MRIcopyFrame(mri_in, NULL, 1, 0) ;
rms_after = MRIrmsDiff(mri_frame1, mri_frame2) ;
MRIfree(&mri_frame1) ; MRIfree(&mri_frame2) ;
printf("RMS after intensity cohering = %2.2f\n", rms_after) ;
}
}
for (input = 0 ; input < ninputs ; input++)
{
sprintf(fname, "%s/%s.long.%s/mri/%s", sdir, subjects[input], base_name, out_fname) ;
printf("writing normalized volume to %s...\n", fname) ;
if (MRIwriteFrame(mri_in, fname, input) != NO_ERROR)
ErrorExit(ERROR_BADFILE, "%s: could not write normalized volume to %s",Progname, fname);
}
if (ctrl_point_fname)
{
printf("writing control points to %s\n", ctrl_point_fname) ;
MRIwrite(mri_ctrl, ctrl_point_fname) ;
MRIfree(&mri_ctrl) ;
}
MRIfree(&mri_in) ;
printf("freeing GCA...") ;
if (gca)
GCAfree(&gca) ;
printf("done.\n") ;
msec = TimerStop(&start) ;
seconds = nint((float)msec/1000.0f) ;
minutes = seconds / 60 ;
seconds = seconds % 60 ;
printf("normalization took %d minutes and %d seconds.\n",
minutes, seconds) ;
if (diag_fp)
fclose(diag_fp) ;
exit(0) ;
return(0) ;
}
int
main(int argc, char *argv[])
{
char **av, in_surf_fname[STRLEN], *in_patch_fname, *out_patch_fname,
fname[STRLEN], path[STRLEN], *cp, hemi[10] ;
int ac, nargs ;
MRI_SURFACE *mris ;
MRI *mri_vertices ;
/* rkt: check for and handle version tag */
nargs = handle_version_option
(argc, argv,
"$Id: mris_flatten.c,v 1.42 2016/12/10 22:57:46 fischl Exp $",
"$Name: $");
if (nargs && argc - nargs == 1)
exit (0);
argc -= nargs;
Gdiag |= DIAG_SHOW ;
Progname = argv[0] ;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
Gdiag |= (DIAG_SHOW | DIAG_WRITE) ;
memset(&parms, 0, sizeof(parms)) ;
parms.dt = .1 ;
parms.projection = PROJECT_PLANE ;
parms.tol = 0.2 ;
parms.n_averages = 1024 ;
parms.l_dist = 1.0 ;
parms.l_nlarea = 1.0 ;
parms.niterations = 40 ;
parms.area_coef_scale = 1.0 ;
parms.dt_increase = 1.01 /* DT_INCREASE */;
parms.dt_decrease = 0.98 /* DT_DECREASE*/ ;
parms.error_ratio = 1.03 /*ERROR_RATIO */;
parms.integration_type = INTEGRATE_LINE_MINIMIZE ;
parms.momentum = 0.9 ;
parms.desired_rms_height = -1.0 ;
parms.base_name[0] = 0 ;
parms.nbhd_size = 7 ; /* out to 7-connected neighbors */
parms.max_nbrs = 12 ; /* 12 at each distance */
ac = argc ;
av = argv ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++)
{
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
if (argc < 3)
print_help() ;
parms.base_dt = base_dt_scale * parms.dt ;
in_patch_fname = argv[1] ;
out_patch_fname = argv[2] ;
FileNamePath(in_patch_fname, path) ;
cp = strrchr(in_patch_fname, '/') ;
if (!cp)
cp = in_patch_fname ;
cp = strchr(cp, '.') ;
if (cp)
{
strncpy(hemi, cp-2, 2) ;
hemi[2] = 0 ;
}
else
strcpy(hemi, "lh") ;
if (one_surf_flag)
sprintf(in_surf_fname, "%s", in_patch_fname) ;
else
sprintf(in_surf_fname, "%s/%s.%s", path, hemi, original_surf_name) ;
if (parms.base_name[0] == 0)
{
FileNameOnly(out_patch_fname, fname) ;
cp = strchr(fname, '.') ;
if (cp)
strcpy(parms.base_name, cp+1) ;
else
strcpy(parms.base_name, "flattened") ;
}
mris = MRISread(in_surf_fname) ;
if (!mris)
ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",
Progname, in_surf_fname) ;
if (sphere_flag)
{
MRIScenter(mris, mris) ;
mris->radius = MRISaverageRadius(mris) ;
MRISstoreMetricProperties(mris) ;
MRISsaveVertexPositions(mris, ORIGINAL_VERTICES) ;
}
if (Gdiag_no >= 0)
{
int n ;
printf("vertex %d has %d nbrs before patch:\n",
Gdiag_no, mris->vertices[Gdiag_no].vnum) ;
for (n = 0 ; n < mris->vertices[Gdiag_no].vnum ; n++)
printf("\t%d\n", mris->vertices[Gdiag_no].v[n]) ;
}
if (one_surf_flag) /* only have the 1 surface - no patch file */
{
mris->patch = 1 ;
mris->status = MRIS_PATCH ;
if (!FEQUAL(rescale,1))
{
MRISscaleBrain(mris, mris, rescale) ;
MRIScomputeMetricProperties(mris) ;
}
MRISstoreMetricProperties(mris) ;
MRISsaveVertexPositions(mris, ORIGINAL_VERTICES) ;
}
else
{
MRISresetNeighborhoodSize(mris, mris->vertices[0].nsize) ; // set back to max
if (label_fname) // read in a label instead of a patch
{
LABEL *area ;
area = LabelRead(NULL, label_fname) ;
if (area == NULL)
ErrorExit(ERROR_BADPARM, "%s: could not read label file %s",
Progname, label_fname) ;
LabelDilate(area, mris, dilate_label, CURRENT_VERTICES) ;
MRISclearMarks(mris) ;
LabelMark(area, mris) ;
MRISripUnmarked(mris) ;
MRISripFaces(mris);
mris->patch = 1 ;
mris->status = MRIS_CUT ;
LabelFree(&area) ;
printf("%d valid vertices (%2.1f %% of total)\n",
MRISvalidVertices(mris),
100.0*MRISvalidVertices(mris)/mris->nvertices) ;
}
else
{
if (MRISreadPatch(mris, in_patch_fname) != NO_ERROR)
ErrorExit(ERROR_BADPARM, "%s: could not read patch file %s",
Progname, in_patch_fname) ;
if (dilate)
{
printf("dilating patch %d times\n", dilate) ;
MRISdilateRipped(mris, dilate) ;
printf("%d valid vertices (%2.1f %% of total)\n",
MRISvalidVertices(mris), 100.0*MRISvalidVertices(mris)/mris->nvertices) ;
}
}
MRISremoveRipped(mris) ;
MRISupdateSurface(mris) ;
#if 0
mris->nsize = 1 ; // before recalculation of 2 and 3-nbrs
{
int vno ;
VERTEX *v ;
for (vno= 0 ; vno < mris->nvertices ; vno++)
{
v = &mris->vertices[vno] ;
v->vtotal = v->vnum ;
v->nsize = 1 ;
}
}
MRISsetNeighborhoodSize(mris, nbrs) ;
#endif
}
if (Gdiag_no >= 0)
printf("vno %d is %sin patch\n", Gdiag_no,
mris->vertices[Gdiag_no].ripflag ? "NOT " : "") ;
if (Gdiag_no >= 0 && mris->vertices[Gdiag_no].ripflag == 0)
{
int n ;
printf("vertex %d has %d nbrs after patch:\n",
Gdiag_no, mris->vertices[Gdiag_no].vnum) ;
for (n = 0 ; n < mris->vertices[Gdiag_no].vnum ; n++)
printf("\t%d\n", mris->vertices[Gdiag_no].v[n]) ;
}
fprintf(stderr, "reading original vertex positions...\n") ;
if (!FZERO(disturb))
mrisDisturbVertices(mris, disturb) ;
if (parms.niterations > 0)
{
MRISresetNeighborhoodSize(mris, nbrs) ;
if (!FZERO(parms.l_unfold) || !FZERO(parms.l_expand))
{
static INTEGRATION_PARMS p2 ;
sprintf(in_surf_fname, "%s/%s.%s", path, hemi, original_surf_name) ;
if (stricmp(original_unfold_surf_name,"none") == 0)
{
printf("using current position of patch as initial position\n") ;
MRISstoreMetricProperties(mris) ; /* use current positions */
}
else if (!sphere_flag && !one_surf_flag)
MRISreadOriginalProperties(mris, original_unfold_surf_name) ;
*(&p2) = *(&parms) ;
p2.l_dist = 0 ;
p2.niterations = 100 ;
p2.nbhd_size = p2.max_nbrs = 1 ;
p2.n_averages = 0 ;
p2.write_iterations = parms.write_iterations > 0 ? 25 : 0 ;
p2.tol = -1 ;
p2.dt = 0.5 ;
p2.l_area = 0.0 ;
p2.l_spring = 0.9 ;
p2.l_convex = 0.9 ;
p2.momentum = 0 ;
p2.integration_type = INTEGRATE_MOMENTUM ;
MRISrestoreVertexPositions(mris, ORIGINAL_VERTICES) ;
#if 0
p2.flags |= IPFLAG_NO_SELF_INT_TEST ;
printf("expanding surface....\n") ;
MRISexpandSurface(mris, 4.0, &p2) ; // push it away from fissure
#endif
p2.niterations = 100 ;
MRISunfold(mris, &p2, 1) ;
p2.niterations = 300 ;
p2.l_unfold *= 0.25 ;
MRISunfold(mris, &p2, 1) ;
p2.l_unfold *= 0.25 ;
MRISunfold(mris, &p2, 1) ;
#if 0
printf("smoothing unfolded surface..\n");
p2.niterations = 200 ;
p2.l_unfold = 0 ; // just smooth it
MRISunfold(mris, &p2, max_passes) ;
#endif
parms.start_t = p2.start_t ;
parms.l_unfold = parms.l_convex = parms.l_boundary = parms.l_expand=0 ;
MRIfree(&parms.mri_dist) ;
}
sprintf(in_surf_fname, "%s/%s.%s", path, hemi, original_surf_name) ;
if (!sphere_flag && !one_surf_flag)
MRISreadOriginalProperties(mris, original_surf_name) ;
if (randomly_flatten)
MRISflattenPatchRandomly(mris) ;
else
MRISflattenPatch(mris) ;
/* optimize metric properties of flat map */
fprintf(stderr,"minimizing metric distortion induced by projection...\n");
MRISscaleBrain(mris, mris, scale) ;
MRIScomputeMetricProperties(mris) ;
MRISunfold(mris, &parms, max_passes) ;
MRIScenter(mris, mris) ;
fprintf(stderr, "writing flattened patch to %s\n", out_patch_fname) ;
MRISwritePatch(mris, out_patch_fname) ;
}
if (plane_flag || sphere_flag)
{
char fname[STRLEN] ;
FILE *fp ;
#if 0
sprintf(fname, "%s.%s.out",
mris->hemisphere == RIGHT_HEMISPHERE ? "rh" : "lh",
parms.base_name);
#else
sprintf(fname, "flatten.log") ;
#endif
fp = fopen(fname, "a") ;
if (plane_flag)
MRIScomputeAnalyticDistanceError(mris, MRIS_PLANE, fp) ;
else if (sphere_flag)
MRIScomputeAnalyticDistanceError(mris, MRIS_SPHERE, fp) ;
fclose(fp) ;
}
if (mri_overlay)
{
MRI *mri_flattened ;
char fname[STRLEN] ;
// if it is NxNx1x1 reshape it to be Nx1x1xN
if ( mri_overlay->width == mri_overlay->height &&
mri_overlay->depth == 1 &&
mri_overlay->nframes == 1)
{
MRI *mri_tmp ;
printf("reshaping to move 2nd dimension to time\n") ;
mri_tmp = mri_reshape( mri_overlay, mri_overlay->width, 1, 1, mri_overlay->height);
MRIfree( &mri_overlay );
mri_overlay = mri_tmp;
}
// put in some special code that knows about icosahedra
if (mris->nvertices == 163842 || // ic7
mris->nvertices == 40962 || // ic6
mris->nvertices == 10242 || // ic5
mris->nvertices == 2562) // ic4
{
int nvals, start_index, end_index ;
MRI *mri_tmp ;
printf("cross-hemispheric correlation matrix detected, reshaping...\n") ;
nvals = mri_overlay->width * mri_overlay->height * mri_overlay->depth ;
if (nvals == 2*mris->nvertices) // it's a corr matrix for both hemis
{
if (mris->hemisphere == LEFT_HEMISPHERE || mris->hemisphere == RIGHT_HEMISPHERE)
{
if (mris->hemisphere == LEFT_HEMISPHERE)
{
start_index = 0 ;
end_index = mris->nvertices-1 ;
}
else
{
start_index = mris->nvertices ;
end_index = 2*mris->nvertices-1 ;
}
mri_tmp = MRIextract(mri_overlay, NULL, start_index, 0, 0, mris->nvertices, 1, 1) ;
MRIfree(&mri_overlay) ;
mri_overlay = mri_tmp;
}
else // both hemis
{
}
}
}
printf("resampling overlay (%d x %d x %d x %d) into flattened coordinates..\n",
mri_overlay->width, mri_overlay->height, mri_overlay->depth, mri_overlay->nframes) ;
if (synth_name)
{
LABEL *area_lh, *area_rh ;
char fname[STRLEN], path[STRLEN], fname_no_path[STRLEN] ;
int vno, n, vno2, n2 ;
MRIsetValues(mri_overlay, 0) ;
FileNameOnly(synth_name, fname_no_path) ;
FileNamePath(synth_name, path) ;
sprintf(fname, "%s/lh.%s", path, fname_no_path) ;
area_lh = LabelRead(NULL, fname) ;
if (area_lh == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read label from %s",
Progname,fname) ;
sprintf(fname, "%s/rh.%s", path, fname_no_path) ;
area_rh = LabelRead(NULL, fname) ;
if (area_rh == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read label from %s",
Progname,fname) ;
#if 0
for (n = 0 ; n < area_lh->n_points ; n++)
{
vno = area_lh->lv[n].vno ;
MRIsetVoxVal(mri_overlay, vno, 0, 0, vno, 1) ;
printf("synthesizing map with vno %d: (%2.1f, %2.1f)\n", vno, mris->vertices[vno].x, mris->vertices[vno].y) ;
break ;
}
#else
for (n = 0 ; n < area_lh->n_points ; n++)
{
vno = area_lh->lv[n].vno ;
if (vno >= 0)
{
for (n2 = 0 ; n2 < area_lh->n_points ; n2++)
{
vno2 = area_lh->lv[n2].vno ;
if (vno2 >= 0)
MRIsetVoxVal(mri_overlay, vno, 0, 0, vno2, 1) ;
}
for (n2 = 0 ; n2 < area_rh->n_points ; n2++)
{
vno2 = area_rh->lv[n2].vno ;
if (vno2 >= 0)
MRIsetVoxVal(mri_overlay, vno, 0, 0, mris->nvertices+vno2, 1) ;
}
}
}
#endif
}
mri_flattened = MRIflattenOverlay(mris, mri_overlay, NULL, 1.0, label_overlay, &mri_vertices) ;
printf("writing flattened overlay to %s\n", out_patch_fname) ;
MRIwrite(mri_flattened, out_patch_fname) ;
MRIfree(&mri_flattened) ;
FileNameRemoveExtension(out_patch_fname, fname) ;
strcat(fname, ".vnos.mgz") ;
printf("writing flattened vertex #s to %s\n", fname) ;
MRIwrite(mri_vertices, fname) ;
MRIfree(&mri_vertices) ;
}
#if 0
sprintf(fname, "%s.area_error", out_fname) ;
printf("writing area errors to %s\n", fname) ;
MRISwriteAreaError(mris, fname) ;
sprintf(fname, "%s.angle_error", out_fname) ;
printf("writing angle errors to %s\n", fname) ;
MRISwriteAngleError(mris, fname) ;
MRISfree(&mris) ;
#endif
exit(0) ;
return(0) ; /* for ansi */
}
int main(int argc, char *argv[]) {
char *inner_mris_fname,*outer_mris_fname,*input_mri_pref,*output_mri_pref;
MRI *mri=0,*mri_src=0;
MRI_SURFACE *inner_mris=0,*outer_mris=0;
int nargs;
LABEL *area = NULL ;
/* rkt: check for and handle version tag */
nargs = handle_version_option
(argc, argv,
"$Id: mri_ribbon.c,v 1.15 2011/03/02 00:04:24 nicks Exp $",
"$Name: stable5 $");
if (nargs && argc - nargs == 1)
exit (0);
argc -= nargs;
Progname=argv[0];
if (argc > 1)
while (*argv[1] == '-')
{
int nargs = 0 ;
switch (toupper(argv[1][1]))
{
case 'L':
printf("cropping ribbon to label file %s\n", argv[2]) ;
nargs = 1 ;
area = LabelRead(NULL, argv[2]) ;
if (area == NULL)
ErrorExit(ERROR_NOFILE,
"%s: could not read label file %s\n",
argv[2]) ;
break ;
default:
break ;
}
argc -= (nargs+1) ;
if (argc == 1) break;
argv += (nargs+1) ;
}
/* Set command-line parameters */
if (argc!=5) {
printf("Usage: mri_ribbon [-l fname.label] \\ \n"
" inner_surface_fname \\ \n"
" outer_surface_fname \\ \n"
" input_volume_pref \\ \n"
" output_volume_pref\n");
exit(1);
}
inner_mris_fname=argv[1];
outer_mris_fname=argv[2];
input_mri_pref=argv[3];
output_mri_pref=argv[4];
/* Read surface information from inner surface file */
printf("Reading surface file %s.\n",inner_mris_fname);
inner_mris=MRISread(inner_mris_fname);
if (!inner_mris) {
printf("Could not read surface file %s.\n",inner_mris_fname);
exit(1);
}
/* Read surface information from outer surface file */
printf("Reading surface file %s.\n",outer_mris_fname);
outer_mris=MRISread(outer_mris_fname);
if (!outer_mris) {
printf("Could not read surface file %s.\n",outer_mris_fname);
exit(1);
}
/* Read example volume from file */
printf("Reading MRI volume directory %s.\n",input_mri_pref);
mri_src=MRIread(input_mri_pref);
if (!mri_src) {
printf("Could not read MRI volume directory %s.\n",input_mri_pref);
exit(1);
}
/* Extract ribbon */
printf("Extracting ribbon.\n");
mri=MRISribbon(inner_mris,outer_mris,mri_src,NULL);
if (area)
MRIcropVolumeToLabel(mri, mri, area, inner_mris, outer_mris) ;
/* Save MRI volume to directory */
printf("Writing volume file %s.\n",output_mri_pref);
MRIwrite(mri,output_mri_pref);
MRIfree(&mri);
MRIfree(&mri_src);
MRISfree(&inner_mris);
MRISfree(&outer_mris);
return 0;
}
int main(int argc, char *argv[]) {
MRIS *mris;
char *in_orig_fname=NULL, *in_seg_fname=NULL,*out_fname=NULL;
MRI *mri_orig=NULL,*mri_seg=NULL,*mri_out=NULL;
int nargs,n;
char fname[512];
Progname=argv[0];
fprintf(stderr,"\n");
MRI_TOPOLOGY_PARMSdefault(&parms);
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
if (parms.tesselation_mode==-1)
parms.tesselation_mode=parms.connectivity;
if (argc<4) {
fprintf(stderr, "\nUsage: %s options input_orig_file input_segmented_file output_folder\n", Progname);
exit(1);
};
in_orig_fname=argv[argc-3];
in_seg_fname = argv[argc-2];
out_fname = argv[argc-1];
fprintf(stderr,"************************************************************"
"\nThe input orig volume is %s"
"\nThe input segmented volume is %s"
"\nThe output volume is %s"
"\nIf this is incorrect, please exit quickly the program (Ctl-C)\n",in_orig_fname,in_seg_fname,out_fname);
for (n=0;n<parms.nlabels;n++)
fprintf(stderr,"label = %d: %s \n",parms.labels[n],cma_label_to_name(parms.labels[n]));
if (parms.using_gca_maps)
fprintf(stderr,"mixing parameters: alpha=%1.3f , beta=%1.3f \n",parms.alpha,parms.beta);
else {
parms.beta=1.0f;
parms.alpha=1.0f;
}
fprintf(stderr,"connectivity = %d\n",parms.connectivity);
mri_orig=MRIread(in_orig_fname);
if (!mri_orig && parms.using_gca_maps)
Error("orig volume: orig volume could not be read\n");
mri_seg=MRIread(in_seg_fname);
if (!mri_seg)
Error("segmented volume: segmented volume could not be read\n");
//check euler characteristic of initial surface
if (parms.initial_surface_file) {
int i,j,k,val,euler,pnvertices, pnfaces, pnedges;
MRI *mri_tmp;
mri_tmp=MRIclone(mri_seg,NULL);
for (k=0;k<mri_seg->depth;k++)
for (j=0;j<mri_seg->height;j++)
for (i=0;i<mri_seg->width;i++)
for (n=0;n<parms.nlabels;n++) {
val=MRIgetVoxVal(mri_seg,i,j,k, 0);
if (val==parms.labels[n]) {
MRIsetVoxVal(mri_tmp,i,j,k,0,1);
break;
}
}
mris=MRIScreateSurfaceFromVolume(mri_tmp,1,parms.connectivity);
euler=MRIScomputeEulerNumber(mris,&pnvertices,&pnfaces,&pnedges);
fprintf(stderr,"\ninitial euler characteristic = %d, %d vertices, %d faces, %d edges"
,euler,pnvertices,pnfaces,pnedges);
MRISwrite(mris,parms.initial_surface_file);
MRISfree(&mris);
MRIfree(&mri_tmp);
}
mri_out=MRIcorrectTopology(mri_orig,mri_seg,NULL,&parms);
if (parms.nlabels == 1) {
MRI *mri_tmp ;
// turn off all voxels that are going to be on in the output
MRImask(mri_seg, mri_out, mri_seg, 1, 0) ;
/* whatever ones are left are now incorrect and should be labeled
something else
*/
resegment_erased_voxels(mri_orig, mri_seg, mri_seg, parms.labels[0]) ;
MRIreplaceValues(mri_out, mri_out, 1, parms.labels[0]) ;
mri_tmp = MRIcopy(mri_seg, NULL) ;
MRIcopyLabel(mri_out, mri_tmp, parms.labels[0]) ;
MRIfree(&mri_out) ;
mri_out = mri_tmp ;
// check_volume(mri_save, mri_out, parms.labels[0]) ;
}
MRIwrite(mri_out,out_fname);
////TEMPORARY VALIDATION STUFF //////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////////////////////////////////////////
#if 0
//validation of the algo
{
FILE *f;
MRIS *mristb[20],*mrisr;
int n,i,j,k,depth,height,width,count,count2;
int tab[20]={4,43,51,12,52,13,54,18,53,17,49,10,50,11};//,6,7,10,11,12,13,17,18,43,44,45,46,49,50,51,52,53,54};
MRI *mri_val=MRIclone(parms.mri_seg,NULL);
parms.nlabels=1;
depth=parms.mri_seg->depth;
height=parms.mri_seg->height;
width=parms.mri_seg->width;
for (n=0;n<14;n++) {
MRIfree(&parms.mri_output);
MRIfree(&parms.mri_bin);
MRIfree(&parms.mri_dist);
MRIfree(&parms.mri_fcost);
MRIfree(&parms.mri_bcost);
MRIfree(&parms.mri_fprior);
MRIfree(&parms.mri_bprior);
MRIfree(&parms.mri_labeled);
segmentationFree(&parms.F_Bseg);
segmentationFree(&parms.F_Rseg);
segmentationFree(&parms.B_Bseg);
segmentationFree(&parms.B_Rseg);
CCSfree(&parms.F_Bccs);
CCSfree(&parms.F_Rccs);
CCSfree(&parms.B_Bccs);
CCSfree(&parms.B_Rccs);
parms.labels[0]=tab[n];
MRIcorrectTopology(parms.mri_orig,parms.mri_seg,&parms.mri_output,mris
,parms.labels,parms.nblabels,parms.f_c,parms);
MRISwrite(*mris,"./tmp");
mristb[n]=MRISread("./tmp");
#if 0
count=0;
count2=0;
for (k=0;k<depth;k++)
for (j=0;j<height;j++)
for (i=0;i<width;i++) {
if (MRIvox(parms.mri_seg,i,j,k)==parms.labels[0])
count2++;
if (MRIvox(parms.mri_output,i,j,k)==1) {
MRIvox(mri_val,i,j,k)++;
if (MRIvox(parms.mri_seg,i,j,k)!=parms.labels[0])
count++;
} else if (MRIvox(parms.mri_seg,i,j,k)==parms.labels[0])
count++;
}
fprintf(stderr,"\n yeh %d %d %f \n",count,count2,100.*count/count2);
sprintf(fname,"./label%d",tab[n]);
f=fopen(fname,"a+");
fprintf(f,"\n %d %d %f ",count,count2,(float)100.*count/count2);
fclose(f);
#endif
#if 0
sprintf(fname,"./surf%d",n);
MRISwrite(mristb[n],fname);
MRISsmoothSurface2(mristb[n],5,0.5,0);
MRISsmoothSurface2(mristb[n],5,0.25,2);
MRISsmoothSurface2(mristb[n],10,0.05,5);
sprintf(fname,"./surfsmooth%d",n);
mristb[n]->type=MRIS_TRIANGULAR_SURFACE;//MRIS_BINARY_QUADRANGLE_FILE;
MRISwrite(mristb[n],fname);
MRISsetNeighborhoodSize(mristb[n],3) ;
MRIScomputeMetricProperties(mristb[n]) ;
MRIScomputeSecondFundamentalForm(mristb[n]) ;
MRISuseMeanCurvature(mristb[n]);
MRISaverageCurvatures(mristb[n],2) ;
MRISnormalizeCurvature(mristb[n], NORM_MEAN) ;
sprintf(fname,"./curv%d",n);
MRISwriteCurvature(mristb[n],fname);
#endif
}
#if 0
mrisr=MRISconcatenateQuadSurfaces(n,mristb);
mrisr->type=MRIS_TRIANGULAR_SURFACE;
MRISwrite(mrisr,"./lh.ZURFACE");
// for(k=0;k<mrisr->nvertices;k++)
// mrisr->vertices[k].curv=0.3;
//MRISnormalizeCurvature(mrisr, NORM_MEAN) ;
MRISwriteCurvature(mrisr,"./ZURFACE_CURVATURE");
for (k=0;k<mrisr->nvertices;k++)
mrisr->vertices[k].curv=mrisr->vertices[k].val;
MRISwriteCurvature(mrisr,"./ZURFACE_VAL");
#endif
n=0;
count=0;
for (k=0;k<depth;k++)
for (j=0;j<height;j++)
for (i=0;i<width;i++) {
if (MRIgetVoxVal(mri_val,i,j,k,0)>=1) {
n++;
if (MRIsetVoxVal(mri_val,i,j,k,0)>1)
count++;
}
}
// sprintf(fname,"./labeltotal");
/// f=fopen(fname,"a+");
//fprintf(f,"\n %s %d %d %f ",in_seg_fname,count,n,(float)100.*count/n);
//fclose(f);
#if 0
MRIwrite(mri_val,"/tmp/tmp");
#endif
fprintf(stderr,"\n WE HAVE %d %d %f \n",count,n,100.*count/n);
}
#endif
//////////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////////
if (parms.final_surface_file) {
int euler,pnvertices, pnfaces, pnedges;
mris=MRIScreateSurfaceFromVolume(mri_out,1,parms.connectivity);
euler=MRIScomputeEulerNumber(mris,&pnvertices,&pnfaces,&pnedges);
fprintf(stderr,"\nfinal euler characteristic = %d, %d vertices, %d faces, %d edges"
,euler,pnvertices,pnfaces,pnedges);
sprintf(fname,"%s",parms.final_surface_file);
MRISwrite(mris,fname);
#if 0
MRISsmoothSurface(mris,7,0.2);
strcat(fname,"_smooth");
MRISwrite(mris,fname);
if (parms.fit) {
sprintf(fname,parms.surfname);
strcat(fname,"_fit");
MRISmatchSurfaceToLabel(parms.mris,parms.mri_output,1,NULL,NULL,parms.f_c);
MRISwrite(parms.mris,fname);
}
#endif
MRISfree(&mris);
}
if (mri_out)
MRIfree(&mri_out);
if (mri_orig)
MRIfree(&mri_orig);
if (mri_seg)
MRIfree(&mri_seg);
fprintf(stderr,"\n");
return NO_ERROR;
}
/* ------------------------------------------------------------------ */
static int parse_commandline(int argc, char **argv) {
int i, nargc , nargsused;
char **pargv, *option ;
char tmpstr[1000];
if (argc < 1) usage_exit();
nargc = argc;
pargv = argv;
while (nargc > 0) {
option = pargv[0];
if (debug) printf("%d %s\n",nargc,option);
nargc -= 1;
pargv += 1;
nargsused = 0;
if (!strcasecmp(option, "--help")) print_help() ;
else if (!strcasecmp(option, "--version")) print_version() ;
else if (!strcasecmp(option, "--debug")) debug = 1;
else if (!strcasecmp(option, "--abs")) DoAbs = 1;
else if (!strcasecmp(option, "--nogmnnorm")) gmnnorm = 0;
else if (!strcasecmp(option, "--rescale")) rescale=1;
else if (!strcasecmp(option, "--norescale")) rescale=0;
else if (!strcasecmp(option, "--no-output")) NoOutput = 1;
else if (!strcasecmp(option, "--fft")) UseFFT = 1;
else if (!strcasecmp(option, "--offset")) AddOffset=1;
else if (!strcasecmp(option, "--offset-mid")){
AddOffset = 1;
OffsetFrame = -1;
}
else if (!strcmp(option, "--hsc")) {
if (nargc < 2) argnerr(option,2);
sscanf(pargv[0],"%lf",&HSCMin);
sscanf(pargv[1],"%lf",&HSCMax);
DoHSC = 1;
nargsused = 2;
}
else if (!strcmp(option, "--sum2")) {
if (nargc < 1) argnerr(option,1);
sum2file = pargv[0];
pdfname = "delta";
//NoOutput = 1;
nframes = 1;
nargsused = 1;
}
else if (!strcmp(option, "--hsynth")) {
// eres mask DoTnorm out
if (nargc < 3) argnerr(option,3);
mri = MRIread(pargv[0]);
mask = MRIread(pargv[1]);
sscanf(pargv[2],"%d",&DoTNorm);
mri2 = fMRIhsynth(mri, mask, DoTNorm);
MRIwrite(mri2,pargv[3]);
exit(0);
nargsused = 2;
}
else if (!strcmp(option, "--vol") || !strcmp(option, "--o")) {
if (nargc < 1) argnerr(option,1);
volid = pargv[0];
nargsused = 1;
if (nth_is_arg(nargc, pargv, 1)) {
volfmt = pargv[1];
nargsused ++;
volfmtid = checkfmt(volfmt);
}
}
else if (!strcmp(option, "--temp") || !strcmp(option, "--template")) {
if(DoCurv){
printf("ERROR: cannot use --temp and --curv\n");
exit(1);
}
if(nargc < 1) argnerr(option,1);
tempid = pargv[0];
nargsused = 1;
if (nth_is_arg(nargc, pargv, 1)) {
tempfmt = pargv[1];
nargsused ++;
tempfmtid = checkfmt(tempfmt);
} else tempfmtid = getfmtid(tempid);
} else if (!strcmp(option, "--curv")) {
if(tempid != NULL){
printf("ERROR: cannot use --temp and --curv\n");
exit(1);
}
if(nargc < 2) argnerr(option,2);
subject = pargv[0];
hemi = pargv[1];
DoCurv = 1;
nargsused = 2;
sprintf(tmpstr,"%s/%s/surf/%s.thickness",getenv("SUBJECTS_DIR"),subject,hemi);
tempid = strcpyalloc(tmpstr);
} else if ( !strcmp(option, "--dim") ) {
if (nargc < 4) argnerr(option,4);
for (i=0;i<4;i++) sscanf(pargv[i],"%d",&dim[i]);
nargsused = 4;
dimSpeced = 1;
}
else if ( !strcmp(option, "--nframes") ) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%d",&nframes);
nargsused = 1;
}
else if ( !strcmp(option, "--TR") || !strcmp(option, "--tr") ) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%lf",&TR);
nargsused = 1;
}
else if ( !strcmp(option, "--res") ) {
if (nargc < 4) argnerr(option,4);
for (i=0;i<4;i++) sscanf(pargv[i],"%f",&res[i]);
nargsused = 4;
resSpeced = 1;
}
else if ( !strcmp(option, "--vox-size") ) {
if (nargc < 3) argnerr(option,3);
for (i=0;i<3;i++) sscanf(pargv[i],"%f",&res[i]);
nargsused = 4;
resSpeced = 1;
NewVoxSizeSpeced = 1;
}
else if ( !strcmp(option, "--c_ras") ) {
if (nargc < 3) argnerr(option,3);
for (i=0;i<3;i++) sscanf(pargv[i],"%f",&cras[i]);
nargsused = 3;
}
else if ( !strcmp(option, "--p0") ) {
if (nargc < 3) argnerr(option,3);
for (i=0;i<3;i++) sscanf(pargv[i],"%f",&p0[i]);
usep0 = 1;
nargsused = 3;
}
else if ( !strcmp(option, "--cdircos") ) {
if (nargc < 3) argnerr(option,3);
for (i=0;i<3;i++) sscanf(pargv[i],"%f",&cdircos[i]);
nargsused = 3;
} else if ( !strcmp(option, "--rdircos") ) {
if (nargc < 3) argnerr(option,3);
for (i=0;i<3;i++) sscanf(pargv[i],"%f",&rdircos[i]);
nargsused = 3;
} else if ( !strcmp(option, "--sdircos") ) {
if (nargc < 3) argnerr(option,3);
for (i=0;i<3;i++) sscanf(pargv[i],"%f",&sdircos[i]);
nargsused = 3;
} else if ( !strcmp(option, "--fwhm") ) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%f",&fwhm);
gstd = fwhm/sqrt(log(256.0));
nargsused = 1;
} else if (!strcmp(option, "--precision")) {
if (nargc < 1) argnerr(option,1);
precision = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--seed")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%ld",&seed);
nargsused = 1;
} else if (!strcmp(option, "--seedfile")) {
if (nargc < 1) argnerr(option,1);
seedfile = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--pdf")) {
if (nargc < 1) argnerr(option,1);
pdfname = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--bb")) {
if (nargc < 6) argnerr(option,6);
sscanf(pargv[0],"%d",&boundingbox.x);
sscanf(pargv[1],"%d",&boundingbox.y);
sscanf(pargv[2],"%d",&boundingbox.z);
sscanf(pargv[3],"%d",&boundingbox.dx);
sscanf(pargv[4],"%d",&boundingbox.dy);
sscanf(pargv[5],"%d",&boundingbox.dz);
pdfname = "boundingbox";
nargsused = 6;
}
else if (!strcasecmp(option, "--checker"))
pdfname = "checker";
else if (!strcmp(option, "--dof-num")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%d",&numdof);
nargsused = 1;
} else if (!strcmp(option, "--val-a")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%lf",&ValueA);
nargsused = 1;
} else if (!strcmp(option, "--val-b")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%lf",&ValueB);
nargsused = 1;
} else if (!strcmp(option, "--radius")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%lf",&voxradius);
nargsused = 1;
} else if (!strcmp(option, "--dof-den") || !strcmp(option, "--dof")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%d",&dendof);
nargsused = 1;
} else if (!strcmp(option, "--gmean")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%lf",&gausmean);
nargsused = 1;
} else if (!strcmp(option, "--gstd")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%lf",&gausstd);
nargsused = 1;
} else if (!strcmp(option, "--delta-crsf")) {
if (nargc < 4) argnerr(option,4);
sscanf(pargv[0],"%d",&delta_crsf[0]);
sscanf(pargv[1],"%d",&delta_crsf[1]);
sscanf(pargv[2],"%d",&delta_crsf[2]);
sscanf(pargv[3],"%d",&delta_crsf[3]);
delta_crsf_speced = 1;
nargsused = 4;
} else if (!strcmp(option, "--delta-val")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%lf",&delta_value);
nargsused = 1;
} else if (!strcmp(option, "--delta-val-off")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%lf",&delta_off_value);
nargsused = 1;
} else if (!strcmp(option, "--spike")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%d",&SpikeTP);
nargsused = 1;
} else {
fprintf(stderr,"ERROR: Option %s unknown\n",option);
if (singledash(option))
fprintf(stderr," Did you really mean -%s ?\n",option);
exit(-1);
}
nargc -= nargsused;
pargv += nargsused;
}
return(0);
}
int
main(int argc, char *argv[])
{
char **av, *in_fname;
int ac, nargs, i, j, x, y, z, width, height, depth;
MRI *mri_flash[MAX_IMAGES], *mri_label, *mri_mask;
int index;
int msec, minutes, seconds, nvolumes, nvolumes_total ;
struct timeb start ;
float max_val, min_val, value;
float *LDAweight = NULL;
float **LDAmeans = NULL; /* Centroid for each considered class */
float *classSize =NULL; /* relative size of each class */
MATRIX **SWs; /* Within class scatter-matrix for each considered class */
MATRIX *AdjMatrix; /* Adjacency matrix of all classes */
FILE *fp;
int num_classes;
double cnr;
/* rkt: check for and handle version tag */
nargs = handle_version_option (argc, argv, "$Id: mri_ms_compute_CNR.c,v 1.10 2011/03/02 00:04:55 nicks Exp $", "$Name: $");
if (nargs && argc - nargs == 1)
exit (0);
argc -= nargs;
Progname = argv[0] ;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
TimerStart(&start) ;
ac = argc ;
av = argv ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++)
{
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
if (argc < 2)
usage_exit(1) ;
printf("command line parsing finished\n");
if (label_fname == NULL)
{
printf("Use -label option to specify file for segmentation \n");
usage_exit(0);
}
if (have_weight == 1 && weight_fname == NULL)
{
printf("Use -weight option to specify file for input LDA weights \n") ;
usage_exit(0);
}
if (have_weight == 1 && synth_fname == NULL)
{
printf("Use -synth option to specify file for output synthesized volume \n") ;
usage_exit(0);
}
if (ldaflag)
{
MINLABEL = MIN(class1, class2);
MAXLABEL = MAX(class1, class2);
}
num_classes = MAXLABEL - MINLABEL + 1;
printf("Total of %d classes considered in LDA training\n", num_classes);
if (num_classes <= 1)
{
printf("Need to specify at least two classes to evaluate CNR\n");
usage_exit(0);
}
//////////////////////////////////////////////////////////////////////////////////
/*** Read in the input multi-echo volumes ***/
nvolumes = 0 ;
for (i = 1 ; i < argc; i++)
{
in_fname = argv[i] ;
printf("reading %s...\n", in_fname) ;
mri_flash[nvolumes] = MRIread(in_fname) ;
if (mri_flash[nvolumes] == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read volume %s",
Progname, in_fname) ;
/* conform will convert all data to UCHAR, which will reduce data resolution*/
printf("%s read in. \n", in_fname) ;
if (conform)
{
MRI *mri_tmp ;
printf("embedding and interpolating volume\n") ;
mri_tmp = MRIconform(mri_flash[nvolumes]) ;
mri_flash[nvolumes] = mri_tmp ;
}
/* Change all volumes to float type for convenience */
if (mri_flash[nvolumes]->type != MRI_FLOAT)
{
printf("Volume %d type is %d\n", nvolumes+1, mri_flash[nvolumes]->type);
MRI *mri_tmp;
printf("Change data to float type \n");
mri_tmp = MRIchangeType(mri_flash[nvolumes], MRI_FLOAT, 0, 1.0, 1);
MRIfree(&mri_flash[nvolumes]);
mri_flash[nvolumes] = mri_tmp; //swap
}
nvolumes++ ;
}
printf("All data read in\n");
///////////////////////////////////////////////////////////////////////////
nvolumes_total = nvolumes ; /* all volumes read in */
for (i = 0 ; i < nvolumes ; i++)
{
for (j = i+1 ; j < nvolumes ; j++)
{
if ((mri_flash[i]->width != mri_flash[j]->width) ||
(mri_flash[i]->height != mri_flash[j]->height) ||
(mri_flash[i]->depth != mri_flash[j]->depth))
ErrorExit(ERROR_BADPARM, "%s:\nvolumes %d (type %d) and %d (type %d) don't match (%d x %d x %d) vs (%d x %d x %d)\n",
Progname, i, mri_flash[i]->type, j, mri_flash[j]->type, mri_flash[i]->width,
mri_flash[i]->height, mri_flash[i]->depth,
mri_flash[j]->width, mri_flash[j]->height, mri_flash[j]->depth) ;
}
}
width = mri_flash[0]->width;
height = mri_flash[0]->height;
depth = mri_flash[0]->depth;
if (label_fname != NULL)
{
mri_label = MRIread(label_fname);
if (!mri_label)
ErrorExit(ERROR_NOFILE, "%s: could not read input volume %s\n",
Progname, label_fname);
if ((mri_label->width != mri_flash[0]->width) ||
(mri_label->height != mri_flash[0]->height) ||
(mri_label->depth != mri_flash[0]->depth))
ErrorExit(ERROR_BADPARM, "%s: label volume size doesn't match data volumes\n", Progname);
/* if(mri_label->type != MRI_UCHAR)
ErrorExit(ERROR_BADPARM, "%s: label volume is not UCHAR type \n", Progname); */
}
if (mask_fname != NULL)
{
mri_mask = MRIread(mask_fname);
if (!mri_mask)
ErrorExit(ERROR_NOFILE, "%s: could not read input volume %s\n",
Progname, mask_fname);
if ((mri_mask->width != mri_flash[0]->width) ||
(mri_mask->height != mri_flash[0]->height) ||
(mri_mask->depth != mri_flash[0]->depth))
ErrorExit(ERROR_BADPARM, "%s: mask volume size doesn't macth data volumes\n", Progname);
if (mri_mask->type != MRI_UCHAR)
ErrorExit(ERROR_BADPARM, "%s: mask volume is not UCHAR type \n", Progname);
}
else
{
mri_mask = MRIalloc(mri_flash[0]->width, mri_flash[0]->height, mri_flash[0]->depth, MRI_UCHAR);
MRIcopyHeader(mri_flash[0], mri_mask);
/* Simply set mask to be 1 everywhere */
for (z=0; z < depth; z++)
for (y=0; y< height; y++)
for (x=0; x < width; x++)
{
MRIvox(mri_mask, x, y,z) = 1;
}
}
if (debug_flag && window_flag)
{
/* Limit LDA to a local window */
printf("Local window size = %d\n", window_size);
window_size /= 2;
for (z=0; z < depth; z++)
for (y=0; y< height; y++)
for (x=0; x < width; x++)
{
if (MRIvox(mri_mask, x, y,z) == 0) continue;
if (z < (Gz - window_size) || z >(Gz + window_size)
|| y <(Gy - window_size) || y > (Gy + window_size)
|| x < (Gx - window_size) || x > (Gx + window_size))
MRIvox(mri_mask, x, y,z) = 0;
}
}
LDAweight = (float *)calloc(nvolumes_total, sizeof(float));
/* Allocate memory */
LDAmeans = (float **)malloc(num_classes*sizeof(float *));
SWs = (MATRIX **)malloc(num_classes*sizeof(MATRIX *));
classSize = (float *)malloc(num_classes*sizeof(float));
for (i=0; i< num_classes; i++)
{
LDAmeans[i] = (float *)malloc(nvolumes_total*sizeof(float));
SWs[i] = (MATRIX *)MatrixAlloc(nvolumes_total, nvolumes_total, MATRIX_REAL);
if (SWs[i] == NULL || LDAmeans[i] == NULL)
ErrorExit(ERROR_BADPARM, "%s: unable to allocate required memory \n", Progname);
}
if (ldaflag)
{
AdjMatrix = (MATRIX *)MatrixAlloc(num_classes, num_classes, MATRIX_REAL);
/* The diagnoal entries of AdjMatrix is set to zero initially */
for (i=1; i <= num_classes;i++)
for (j=i; j <= num_classes; j++)
{
AdjMatrix->rptr[i][j] = 0.0;
AdjMatrix->rptr[j][i] = 0.0;
}
AdjMatrix->rptr[class1-MINLABEL +1][class2-MINLABEL+1] = 1.0;
AdjMatrix->rptr[class1-MINLABEL +1][class1-MINLABEL+1] = 1.0;
AdjMatrix->rptr[class2-MINLABEL +1][class2-MINLABEL+1] = 1.0;
AdjMatrix->rptr[class2-MINLABEL +1][class1-MINLABEL+1] = 1.0;
}
else if (MINLABEL <=2 && MAXLABEL >= 76)
{
printf("Manually set adjacent matrix \n");
AdjMatrix = (MATRIX *)MatrixAlloc(num_classes, num_classes, MATRIX_REAL);
/* The diagnoal entries of AdjMatrix is set to zero initially */
for (i=1; i <= num_classes;i++)
for (j=i; j <= num_classes; j++)
{
AdjMatrix->rptr[i][j] = 0.0;
AdjMatrix->rptr[j][i] = 0.0;
}
for (index = 0; index < CNR_pairs; index++)
{
i = ilist[index] - MINLABEL;
j = jlist[index] - MINLABEL;
AdjMatrix->rptr[i+1][j+1] = 1.0;
AdjMatrix->rptr[j+1][i+1] = 1.0;
}
/* left-hemisphere */
/*
AdjMatrix->rptr[2+1-MINLABEL][17+1-MINLABEL] = 1.0;
AdjMatrix->rptr[17+1-MINLABEL][18+1-MINLABEL] = 1.0;
AdjMatrix->rptr[3+1-MINLABEL][17+1-MINLABEL] = 1.0;
AdjMatrix->rptr[5+1-MINLABEL][17+1-MINLABEL] = 1.0;
AdjMatrix->rptr[4+1-MINLABEL][17+1-MINLABEL] = 1.0;
AdjMatrix->rptr[18+1-MINLABEL][2+1-MINLABEL] = 1.0;
AdjMatrix->rptr[18+1-MINLABEL][3+1-MINLABEL] = 1.0;
AdjMatrix->rptr[18+1-MINLABEL][5+1-MINLABEL] = 1.0;
AdjMatrix->rptr[18+1-MINLABEL][4+1-MINLABEL] = 1.0;
AdjMatrix->rptr[10+1-MINLABEL][11+1-MINLABEL] = 1.0;
AdjMatrix->rptr[10+1-MINLABEL][4+1-MINLABEL] = 1.0;
AdjMatrix->rptr[10+1-MINLABEL][12+1-MINLABEL] = 1.0;
AdjMatrix->rptr[10+1-MINLABEL][2+1-MINLABEL] = 1.0;
AdjMatrix->rptr[2+1-MINLABEL][3+1-MINLABEL] = 1.0;
*/
/* right-hemisphere */
/*
AdjMatrix->rptr[53+1-MINLABEL][41+1-MINLABEL] = 1.0;
AdjMatrix->rptr[53+1-MINLABEL][54+1-MINLABEL] = 1.0;
AdjMatrix->rptr[53+1-MINLABEL][42+1-MINLABEL] = 1.0;
AdjMatrix->rptr[53+1-MINLABEL][44+1-MINLABEL] = 1.0;
AdjMatrix->rptr[53+1-MINLABEL][43+1-MINLABEL] = 1.0;
AdjMatrix->rptr[54+1-MINLABEL][41+1-MINLABEL] = 1.0;
AdjMatrix->rptr[54+1-MINLABEL][42+1-MINLABEL] = 1.0;
AdjMatrix->rptr[54+1-MINLABEL][44+1-MINLABEL] = 1.0;
AdjMatrix->rptr[54+1-MINLABEL][43+1-MINLABEL] = 1.0;
AdjMatrix->rptr[49+1-MINLABEL][50+1-MINLABEL] = 1.0;
AdjMatrix->rptr[49+1-MINLABEL][43+1-MINLABEL] = 1.0;
AdjMatrix->rptr[49+1-MINLABEL][51+1-MINLABEL] = 1.0;
AdjMatrix->rptr[49+1-MINLABEL][41+1-MINLABEL] = 1.0;
AdjMatrix->rptr[41+1-MINLABEL][42+1-MINLABEL] = 1.0;
for(i=1; i < num_classes;i++)
for(j=i+1; j <= num_classes; j++){
if(AdjMatrix->rptr[i][j] > 0.5)
AdjMatrix->rptr[j][i] = AdjMatrix->rptr[i][j];
else
AdjMatrix->rptr[i][j] = AdjMatrix->rptr[j][i];
}
*/
/* AdjMatrix->rptr[2+1-MINLABEL][3+1-MINLABEL] = 1.0;
AdjMatrix->rptr[2+1-MINLABEL][10+1-MINLABEL] = 1.0;
AdjMatrix->rptr[2+1-MINLABEL][11+1-MINLABEL] = 1.0;
AdjMatrix->rptr[2+1-MINLABEL][12+1-MINLABEL] = 1.0;
AdjMatrix->rptr[2+1-MINLABEL][13+1-MINLABEL] = 1.0;
AdjMatrix->rptr[2+1-MINLABEL][17+1-MINLABEL] = 1.0;
AdjMatrix->rptr[2+1-MINLABEL][18+1-MINLABEL] = 1.0;
AdjMatrix->rptr[3+1-MINLABEL][12+1-MINLABEL] = 1.0;
AdjMatrix->rptr[3+1-MINLABEL][17+1-MINLABEL] = 1.0;
AdjMatrix->rptr[3+1-MINLABEL][18+1-MINLABEL] = 1.0;
AdjMatrix->rptr[4+1-MINLABEL][10+1-MINLABEL] = 1.0;
AdjMatrix->rptr[4+1-MINLABEL][11+1-MINLABEL] = 1.0;
AdjMatrix->rptr[10+1-MINLABEL][11+1-MINLABEL] = 1.0;
AdjMatrix->rptr[10+1-MINLABEL][13+1-MINLABEL] = 1.0;
AdjMatrix->rptr[12+1-MINLABEL][13+1-MINLABEL] = 1.0;
AdjMatrix->rptr[12+1-MINLABEL][26+1-MINLABEL] = 1.0;
AdjMatrix->rptr[17+1-MINLABEL][18+1-MINLABEL] = 1.0;
*/
/* right-hemisphere */
/* AdjMatrix->rptr[41+1-MINLABEL][42+1-MINLABEL] = 1.0;
AdjMatrix->rptr[41+1-MINLABEL][49+1-MINLABEL] = 1.0;
AdjMatrix->rptr[41+1-MINLABEL][50+1-MINLABEL] = 1.0;
AdjMatrix->rptr[41+1-MINLABEL][51+1-MINLABEL] = 1.0;
AdjMatrix->rptr[41+1-MINLABEL][52+1-MINLABEL] = 1.0;
AdjMatrix->rptr[41+1-MINLABEL][53+1-MINLABEL] = 1.0;
AdjMatrix->rptr[41+1-MINLABEL][54+1-MINLABEL] = 1.0;
AdjMatrix->rptr[42+1-MINLABEL][51+1-MINLABEL] = 1.0;
AdjMatrix->rptr[42+1-MINLABEL][53+1-MINLABEL] = 1.0;
AdjMatrix->rptr[42+1-MINLABEL][54+1-MINLABEL] = 1.0;
AdjMatrix->rptr[43+1-MINLABEL][49+1-MINLABEL] = 1.0;
AdjMatrix->rptr[43+1-MINLABEL][50+1-MINLABEL] = 1.0;
AdjMatrix->rptr[49+1-MINLABEL][50+1-MINLABEL] = 1.0;
AdjMatrix->rptr[49+1-MINLABEL][52+1-MINLABEL] = 1.0;
AdjMatrix->rptr[51+1-MINLABEL][52+1-MINLABEL] = 1.0;
AdjMatrix->rptr[51+1-MINLABEL][58+1-MINLABEL] = 1.0;
AdjMatrix->rptr[53+1-MINLABEL][54+1-MINLABEL] = 1.0;
*/
}
else
AdjMatrix = ComputeAdjMatrix(mri_label, mri_mask, MINLABEL, MAXLABEL);
/* AdjMatrix may need manual adjusted to avoid meaningless comparisons
* such as computing CNR between left WM and right WM
*/
for (i=1; i <= num_classes;i++)
for (j=1; j <= num_classes; j++)
{
if (j==i) continue;
/* the diagonal term will indicate whether the class is useful or not */
AdjMatrix->rptr[i][i] += AdjMatrix->rptr[i][j] + AdjMatrix->rptr[j][i];
}
printf("Compute individual class statistics\n");
/* Compute class means and covariance matrix */
/* Note that here SWs will be covaraince matrix, not scatter matrix */
for (i=0; i < num_classes; i++)
{
if (AdjMatrix->rptr[i+1][i+1] < 0.5) continue;
computeClassStats(LDAmeans[i], SWs[i], &classSize[i], mri_flash, mri_label, mri_mask, nvolumes_total, MINLABEL + i);
}
printf("class statistics computed \n");
if (fname != NULL)
fp = fopen(fname, "w");
else
fp = 0;
printf("compute pair-wise CNR/Mahalanobis distances \n");
if (ldaflag)
{
for (i=0; i <num_classes-1;i++)
for (j=i+1; j < num_classes; j++)
{
if (AdjMatrix->rptr[i+1][j+1] < 0.5) continue;
cnr = computePairCNR(LDAmeans[i], LDAmeans[j], SWs[i], SWs[j], classSize[i], classSize[j], nvolumes_total, LDAweight, 1);
if (fp)
fprintf(fp, "%9.4f ", (float)cnr);
printf("CNR of class %d and class %d is %g\n", i+MINLABEL, j+MINLABEL, cnr);
}
if (fp)
{
fprintf(fp, "\n");
fclose(fp);
}
}
else
{
for (index = 0; index < CNR_pairs; index++)
{
i = ilist[index] - MINLABEL;
j = jlist[index] - MINLABEL;
if (AdjMatrix->rptr[i+1][j+1] < 0.5) continue;
if (i== (2-MINLABEL) && j == (3-MINLABEL) && nvolumes_total > 1)
cnr = computePairCNR(LDAmeans[i], LDAmeans[j], SWs[i], SWs[j], classSize[i], classSize[j], nvolumes_total, LDAweight, 1);
else
cnr = computePairCNR(LDAmeans[i], LDAmeans[j], SWs[i], SWs[j], classSize[i], classSize[j], nvolumes_total, 0, 0);
if (fp)
fprintf(fp, "%9.4f ", (float)cnr);
printf("CNR of class %d and class %d is %g\n", i+MINLABEL, j+MINLABEL, cnr);
}
if (fp)
{
fprintf(fp, "\n");
fclose(fp);
}
}
/* output weights for optimize CNR for class 2 and class 3 */
if (weight_fname != NULL)
{
output_weights_to_file(LDAweight, weight_fname, nvolumes_total);
}
free(classSize);
for (i=0; i< num_classes; i++)
{
free(LDAmeans[i]);
MatrixFree(&SWs[i]);
}
free(LDAmeans);
free(SWs);
MatrixFree(&AdjMatrix);
if (nvolumes_total > 1 && ((MINLABEL <=2 && MAXLABEL >= 3) || ldaflag))
{
if (ldaflag)
{
printf("LDA weights for %d-%d are: \n", class1, class2);
}
else
{
printf("LDA weights for 2-3 are: \n");
}
for (i=0; i < nvolumes_total; i++)
{
printf("%g ", LDAweight[i]);
}
printf("\n");
if (synth_fname != NULL)
{
/* linear projection of input volumes to a 1D volume */
min_val = 10000.0;
max_val = -10000.0;
for (z=0; z < depth; z++)
for (y=0; y< height; y++)
for (x=0; x < width; x++)
{
if (whole_volume == 0 && MRIvox(mri_mask, x, y, z) == 0) continue;
value = 0.0;
for (i=0; i < nvolumes_total; i++)
{
value += MRIFvox(mri_flash[i], x, y, z)*LDAweight[i];
}
if (max_val < value) max_val = value;
if (min_val > value) min_val = value;
/* Borrow mri_flash[0] to store the float values first */
MRIFvox(mri_flash[0], x, y, z) = value;
}
printf("max_val = %g, min_val = %g \n", max_val, min_val);
/* Scale output to [0, 255] */
for (z=0; z < depth; z++)
for (y=0; y< height; y++)
for (x=0; x < width; x++)
{
if (whole_volume == 0 && MRIvox(mri_mask, x, y, z) == 0) continue;
value = (MRIFvox(mri_flash[0], x, y, z) - min_val)*255.0/(max_val - min_val) + 0.5; /* +0.5 for round-off */
if (value > 255.0) value = 255.0;
if (value < 0) value = 0;
/* Borrow mri_flash[0] to store the float values first */
MRIvox(mri_mask, x, y, z) = (BUFTYPE) value;
}
/* Output synthesized volume */
MRIwrite(mri_mask, synth_fname);
}
}
free(LDAweight);
msec = TimerStop(&start) ;
seconds = nint((float)msec/1000.0f) ;
minutes = seconds / 60 ;
seconds = seconds % 60 ;
printf("LDA took %d minutes and %d seconds.\n", minutes, seconds) ;
MRIfree(&mri_mask);
MRIfree(&mri_label);
for (i=0; i < nvolumes_total; i++)
{
MRIfree(&mri_flash[i]);
}
exit(0);
}
int
main(int argc, char *argv[]) {
char **av, *in_fname;
int ac, nargs, i, j, x, y, z, width, height, depth;
MRI *mri_flash[MAX_IMAGES], *mri_label, *mri_mask, *mri_tmp;
int msec, minutes, seconds, nvolumes, nvolumes_total ;
struct timeb start ;
float max_val, min_val, value;
float *LDAmean1, *LDAmean2, *LDAweight;
int label;
double sum_white, sum_gray;
int count_white, count_gray;
/* rkt: check for and handle version tag */
nargs = handle_version_option (argc, argv, "$Id: mri_ms_LDA.c,v 1.4 2011/03/02 00:04:23 nicks Exp $", "$Name: $");
if (nargs && argc - nargs == 1)
exit (0);
argc -= nargs;
Progname = argv[0] ;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
TimerStart(&start) ;
ac = argc ;
av = argv ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
if (argc < 2)
usage_exit(1) ;
printf("command line parsing finished\n");
if (have_weight == 0 && ldaflag == 0) {
printf("Use -lda option to specify two class labels to optimize CNR on \n");
usage_exit(0);
}
if (have_weight == 0 && label_fname == NULL) {
printf("Use -label option to specify file for segmentation \n");
usage_exit(0);
}
if (have_weight == 1 && weight_fname == NULL) {
printf("Use -weight option to specify file for input LDA weights \n") ;
usage_exit(0);
}
if (have_weight == 1 && synth_fname == NULL) {
printf("Use -synth option to specify file for output synthesized volume \n") ;
usage_exit(0);
}
//////////////////////////////////////////////////////////////////////////////////
/*** Read in the input multi-echo volumes ***/
nvolumes = 0 ;
for (i = 1 ; i < argc; i++) {
in_fname = argv[i] ;
printf("reading %s...\n", in_fname) ;
mri_flash[nvolumes] = MRIread(in_fname) ;
if (mri_flash[nvolumes] == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read volume %s",
Progname, in_fname) ;
/* conform will convert all data to UCHAR, which will reduce data resolution*/
printf("%s read in. \n", in_fname) ;
if (conform) {
printf("embedding and interpolating volume\n") ;
mri_tmp = MRIconform(mri_flash[nvolumes]) ;
MRIfree(&mri_flash[nvolumes]);
mri_flash[nvolumes] = mri_tmp ;
}
/* Change all volumes to float type for convenience */
if (mri_flash[nvolumes]->type != MRI_FLOAT) {
printf("Volume %d type is %d\n", nvolumes+1, mri_flash[nvolumes]->type);
printf("Change data to float type \n");
mri_tmp = MRIchangeType(mri_flash[nvolumes], MRI_FLOAT, 0, 1.0, 1);
MRIfree(&mri_flash[nvolumes]);
mri_flash[nvolumes] = mri_tmp; //swap
}
nvolumes++ ;
}
printf("All data read in\n");
///////////////////////////////////////////////////////////////////////////
nvolumes_total = nvolumes ; /* all volumes read in */
for (i = 0 ; i < nvolumes ; i++) {
for (j = i+1 ; j < nvolumes ; j++) {
if ((mri_flash[i]->width != mri_flash[j]->width) ||
(mri_flash[i]->height != mri_flash[j]->height) ||
(mri_flash[i]->depth != mri_flash[j]->depth))
ErrorExit(ERROR_BADPARM, "%s:\nvolumes %d (type %d) and %d (type %d) don't match (%d x %d x %d) vs (%d x %d x %d)\n",
Progname, i, mri_flash[i]->type, j, mri_flash[j]->type, mri_flash[i]->width,
mri_flash[i]->height, mri_flash[i]->depth,
mri_flash[j]->width, mri_flash[j]->height, mri_flash[j]->depth) ;
}
}
width = mri_flash[0]->width;
height = mri_flash[0]->height;
depth = mri_flash[0]->depth;
if (label_fname != NULL) {
mri_label = MRIread(label_fname);
if (!mri_label)
ErrorExit(ERROR_NOFILE, "%s: could not read input volume %s\n",
Progname, label_fname);
if ((mri_label->width != mri_flash[0]->width) ||
(mri_label->height != mri_flash[0]->height) ||
(mri_label->depth != mri_flash[0]->depth))
ErrorExit(ERROR_BADPARM, "%s: label volume size doesn't match data volumes\n", Progname);
/* if(mri_label->type != MRI_UCHAR)
ErrorExit(ERROR_BADPARM, "%s: label volume is not UCHAR type \n", Progname); */
}
if (mask_fname != NULL) {
mri_mask = MRIread(mask_fname);
if (!mri_mask)
ErrorExit(ERROR_NOFILE, "%s: could not read input volume %s\n",
Progname, mask_fname);
if ((mri_mask->width != mri_flash[0]->width) ||
(mri_mask->height != mri_flash[0]->height) ||
(mri_mask->depth != mri_flash[0]->depth))
ErrorExit(ERROR_BADPARM, "%s: mask volume size doesn't macth data volumes\n", Progname);
if (mri_mask->type != MRI_UCHAR)
ErrorExit(ERROR_BADPARM, "%s: mask volume is not UCHAR type \n", Progname);
} else {
if (have_weight == 1)
noise_threshold = - 1e20;
printf("Threshold input vol1 at %g to create mask \n", noise_threshold);
printf("this threshold is useful to process skull-stripped data \n");
mri_mask = MRIalloc(mri_flash[0]->width, mri_flash[0]->height, mri_flash[0]->depth, MRI_UCHAR);
MRIcopyHeader(mri_flash[0], mri_mask);
/* Simply set mask to be 1 everywhere */
for (z=0; z < depth; z++)
for (y=0; y< height; y++)
for (x=0; x < width; x++) {
if ((float)MRIgetVoxVal(mri_flash[0], x, y,z,0) < noise_threshold)
MRIvox(mri_mask, x, y,z) = 0;
else
MRIvox(mri_mask, x, y,z) = 1;
}
}
/* Normalize input volumes */
if (normflag) {
printf("Normalize input volumes to zero mean, variance 1\n");
for (i=0; i <nvolumes_total; i++) {
mri_flash[i] = MRInormalizeXH(mri_flash[i], mri_flash[i], mri_mask);
}
printf("Normalization done.\n");
}
if (0) {
printf("Using both hemi-sphere by changing rh-labels\n");
for (z=0; z < depth; z++)
for (y=0; y< height; y++)
for (x=0; x < width; x++) {
label = (int)MRIgetVoxVal(mri_label, x, y,z,0);
if (label == 41) /* white matter */
MRIsetVoxVal(mri_label, x, y, z, 0, 2);
else if (label == 42) /* gm */
MRIsetVoxVal(mri_label, x, y, z, 0, 3);
}
}
if (debug_flag && window_flag) {
/* Limit LDA to a local window */
printf("Local window size = %d\n", window_size);
window_size /= 2;
for (z=0; z < depth; z++)
for (y=0; y< height; y++)
for (x=0; x < width; x++) {
if (MRIvox(mri_mask, x, y,z) == 0) continue;
if (z < (Gz - window_size) || z >(Gz + window_size)
|| y <(Gy - window_size) || y > (Gy + window_size)
|| x < (Gx - window_size) || x > (Gx + window_size))
MRIvox(mri_mask, x, y,z) = 0;
}
}
LDAmean1 = (float *)malloc(nvolumes_total*sizeof(float));
LDAmean2 = (float *)malloc(nvolumes_total*sizeof(float));
LDAweight = (float *)malloc(nvolumes_total*sizeof(float));
if (have_weight) {
printf("Read in LDA weights from weight-file\n");
input_weights_to_file(LDAweight, weight_fname, nvolumes_total);
} else { /* compute LDA weights */
printf("Compute LDA weights to maximize CNR for region %d and region %d\n", class1, class2);
/* Compute class means */
update_LDAmeans(mri_flash, mri_label, mri_mask, LDAmean1, LDAmean2, nvolumes_total, class1, class2);
printf("class means computed \n");
/* Compute Fisher's LDA weights */
computeLDAweights(LDAweight, mri_flash, mri_label, mri_mask, LDAmean1, LDAmean2, nvolumes_total, class1, class2);
if (weight_fname != NULL) {
output_weights_to_file(LDAweight, weight_fname, nvolumes_total);
}
}
printf("LDA weights are: \n");
for (i=0; i < nvolumes_total; i++) {
printf("%g ", LDAweight[i]);
}
printf("\n");
if (synth_fname != NULL) {
/* linear projection of input volumes to a 1D volume */
min_val = 10000.0;
max_val = -10000.0;
for (z=0; z < depth; z++)
for (y=0; y< height; y++)
for (x=0; x < width; x++) {
if (whole_volume == 0 && MRIvox(mri_mask, x, y, z) == 0) continue;
value = 0.0;
for (i=0; i < nvolumes_total; i++) {
value += MRIFvox(mri_flash[i], x, y, z)*LDAweight[i];
}
// if(value < 0) value = 0;
if (max_val < value) max_val = value;
if (min_val > value) min_val = value;
/* Borrow mri_flash[0] to store the float values first */
MRIFvox(mri_flash[0], x, y, z) = value;
}
printf("max_val = %g, min_val = %g \n", max_val, min_val);
/* Check to make sure class1 has higher intensity than class2 */
if (have_weight == 0) {
sum_white =0;
count_white = 0;
sum_gray = 0;
count_gray = 0;
for (z=0; z < depth; z++) {
if (count_white > 300 && count_gray > 300) break;
for (y=0; y< height; y++) {
for (x=0; x < width; x++) {
if ((int)MRIgetVoxVal(mri_label, x, y,z,0) == class1) {
sum_white += MRIFvox(mri_flash[0], x, y, z);
count_white += 1;
} else if ((int)MRIgetVoxVal(mri_label, x, y,z,0) == class2) {
sum_gray += MRIFvox(mri_flash[0], x, y, z);
count_gray += 1;
}
}
}
}
if (count_white > 1 && count_gray > 1) {
if (sum_white *count_gray < sum_gray*count_white) {
for (z=0; z < depth; z++)
for (y=0; y< height; y++)
for (x=0; x < width; x++) {
if (whole_volume == 0 && MRIvox(mri_mask, x, y, z) == 0) continue;
value = MRIFvox(mri_flash[0], x, y, z);
MRIFvox(mri_flash[0], x, y, z) = max_val - value;
}
max_val = max_val - min_val;
min_val = 0;
}
}
}
/* The following is copied to be consistent with mri_synthesize */
/* Don't know why add min_val, minus should make more sense */
for (z=0; z < depth; z++)
for (y=0; y< height; y++)
for (x=0; x < width; x++) {
if (whole_volume == 0 && MRIvox(mri_mask, x, y, z) == 0) {
MRIFvox(mri_flash[0], x, y, z) = 0; /*background always set to 0 */
continue;
}
/* Borrow mri_flash[0] to store the float values first */
if (shift_value > 0) {
value = MRIFvox(mri_flash[0], x, y, z) + shift_value;
if (value < 0) value = 0;
MRIFvox(mri_flash[0], x, y, z) = value;
} else if (mask_fname != NULL)
MRIFvox(mri_flash[0], x, y, z) -= min_val;
}
MRIfree(&mri_mask);
if (mri_flash[0]->type == out_type) {
mri_mask = MRIcopy(mri_flash[0], mri_mask);
} else {
mri_mask = MRIchangeType(mri_flash[0], out_type, 0.1, 0.99, 0);
}
/* Scale output to [0, 255] */
if (0) {
for (z=0; z < depth; z++)
for (y=0; y< height; y++)
for (x=0; x < width; x++) {
if (whole_volume == 0 && MRIvox(mri_mask, x, y, z) == 0) continue;
value = (MRIFvox(mri_flash[0], x, y, z) - min_val)*255.0/(max_val - min_val) + 0.5; /* +0.5 for round-off */
if (value > 255.0) value = 255.0;
if (value < 0) value = 0;
/* Borrow mri_flash[0] to store the float values first */
MRIvox(mri_mask, x, y, z) = (BUFTYPE) value;
}
}
/* Output synthesized volume */
MRIwrite(mri_mask, synth_fname);
}
free(LDAmean1);
free(LDAmean2);
free(LDAweight);
msec = TimerStop(&start) ;
seconds = nint((float)msec/1000.0f) ;
minutes = seconds / 60 ;
seconds = seconds % 60 ;
printf("LDA took %d minutes and %d seconds.\n", minutes, seconds) ;
MRIfree(&mri_mask);
if (label_fname)
MRIfree(&mri_label);
for (i=0; i < nvolumes_total; i++) {
MRIfree(&mri_flash[i]);
}
exit(0);
}
int main(int argc, char *argv[]) {
char **av;
MRI *mri_T1, *mri_tmp, *mri_ctrl, *mri_in, *mri_out;
MRI *mri_snr, *mri_bias;
MRI *mri_mask1 = NULL;
MRI *mri_mask2 = NULL;
int ac, nargs;
int width, height, depth, x, y, z;
int mask1_set = 0;
int mask2_set = 0;
int i, j, k, cx, cy, cz, count;
LTA *lta = 0;
int transform_type;
double mean, std, value, src, bias, norm;
// HISTOGRAM *h;
// float bin_size;
// int nbins, bin_no;
double mean1, std1, mean2, std2, count1, count2, slope, offset;
VOL_GEOM vgtmp;
LT *lt = NULL;
MATRIX *m_tmp = NULL;
Progname = argv[0];
nargs = handle_version_option
(argc, argv,
"$Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $",
"$Name: stable5 $");
if (nargs && argc - nargs == 1)
exit (0);
argc -= nargs ;
ac = argc ;
av = argv ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
if (argc != 3)
usage(1);
if (tp1_ctrl_fname == NULL || tp1_T1_fname == NULL) {
printf("Use options to specify ctrl volume and T1 volume for tp1\n");
usage(1);
}
mri_in = MRIread(argv[1]) ;
if (!mri_in)
ErrorExit(ERROR_BADPARM, "%s: could not read input volume %s",
Progname, argv[1]) ;
mri_T1 = MRIread(tp1_T1_fname) ;
if (!mri_T1)
ErrorExit(ERROR_BADPARM, "%s: could not read T1 volume for tp1 %s",
Progname, tp1_T1_fname) ;
mri_ctrl = MRIread(tp1_ctrl_fname) ;
if (!mri_ctrl)
ErrorExit(ERROR_BADPARM,
"%s: could not read control points volume for tp1 %s",
Progname, tp1_ctrl_fname) ;
if ((mri_in->width != mri_T1->width) ||
(mri_in->height != mri_T1->height) ||
(mri_in->depth != mri_T1->depth) ||
(mri_in->width != mri_ctrl->width) ||
(mri_in->height != mri_ctrl->height) ||
(mri_in->depth != mri_ctrl->depth)
) ErrorExit
(ERROR_BADPARM,
"%s: three input volumes have different sizes \n", Progname);
if (mask1_fname) {
mri_mask1 = MRIread(mask1_fname) ;
if (!mri_mask1)
ErrorExit(ERROR_BADPARM,
"%s, could not read mask volume for tp1 %s",
Progname, mask1_fname);
mask1_set = 1;
if ((mri_mask1->width != mri_in->width) ||
(mri_mask1->height != mri_in->height) ||
(mri_mask1->depth != mri_in->depth))
ErrorExit
(ERROR_BADPARM,
"%s: mask volumes have different sizes than other volumes \n",
Progname);
}
if (mask2_fname) {
mri_mask2 = MRIread(mask2_fname) ;
if (!mri_mask2)
ErrorExit
(ERROR_BADPARM,
"%s, could not read mask volume for tp2 %s",
Progname, mask2_fname);
mask2_set = 1;
if ((mri_mask2->width != mri_T1->width) ||
(mri_mask2->height != mri_T1->height) ||
(mri_mask2->depth != mri_T1->depth)
)
ErrorExit
(ERROR_BADPARM,
"%s: mask volumes have different sizes than other volumes \n",
Progname);
}
width = mri_in->width ;
height = mri_in->height ;
depth = mri_in->depth ;
//nbins = 200;
//h = HISTOalloc(nbins);
mri_out = MRIclone(mri_in, NULL) ;
/* Read LTA transform and apply it to mri_ctrl */
if (xform_fname != NULL) {
// read transform
transform_type = TransformFileNameType(xform_fname);
if (transform_type == MNI_TRANSFORM_TYPE ||
transform_type == TRANSFORM_ARRAY_TYPE ||
transform_type == REGISTER_DAT ||
transform_type == FSLREG_TYPE
) {
printf("Reading transform ...\n");
lta = LTAreadEx(xform_fname) ;
if (!lta)
ErrorExit(ERROR_NOFILE, "%s: could not read transform file %s",
Progname, xform_fname) ;
if (transform_type == FSLREG_TYPE) {
if (lta_src == 0 || lta_dst == 0) {
fprintf
(stderr,
"ERROR: fslmat does not have information "
"on the src and dst volumes\n");
fprintf
(stderr,
"ERROR: you must give options '-lta_src' and "
"'-lta_dst' to specify the src and dst volume infos\n");
}
LTAmodifySrcDstGeom
(lta, lta_src, lta_dst); // add src and dst information
LTAchangeType(lta, LINEAR_VOX_TO_VOX); //this is necessary
}
if (lta->xforms[0].src.valid == 0) {
if (lta_src == 0) {
fprintf
(stderr,
"The transform does not have the valid src volume info.\n");
fprintf
(stderr,
"Either you give src volume info by option -lta_src or\n");
fprintf(stderr, "make the transform to have the valid src info.\n");
ErrorExit(ERROR_BAD_PARM, "Bailing out...\n");
} else {
LTAmodifySrcDstGeom(lta, lta_src, NULL); // add src information
// getVolGeom(lta_src, <->src);
}
}
if (lta->xforms[0].dst.valid == 0) {
if (lta_dst == 0) {
fprintf
(stderr,
"The transform does not have the valid dst volume info.\n");
fprintf
(stderr,
"Either you give src volume info by option -lta_dst or\n");
fprintf
(stderr,
"make the transform to have the valid dst info.\n");
fprintf
(stderr,
"If the dst was average_305, then you can set\n");
fprintf
(stderr,
"environmental variable USE_AVERAGE305 true\n");
fprintf
(stderr,
"without giving the dst volume for RAS-to-RAS transform.\n");
ErrorExit(ERROR_BAD_PARM, "Bailing out...\n");
} else {
LTAmodifySrcDstGeom(lta, NULL, lta_dst); // add dst information
}
}
} else {
ErrorExit
(ERROR_BADPARM,
"transform is not of MNI, nor Register.dat, nor FSLMAT type");
}
if (invert) {
m_tmp = lta->xforms[0].m_L ;
lta->xforms[0].m_L = MatrixInverse(lta->xforms[0].m_L, NULL) ;
MatrixFree(&m_tmp) ;
lt = <a->xforms[0];
if (lt->dst.valid == 0 || lt->src.valid == 0) {
fprintf
(stderr,
"WARNING:***********************************************\n");
fprintf
(stderr,
"WARNING: dst volume infor is invalid. "
"Most likely produce wrong inverse.\n");
fprintf
(stderr,
"WARNING:***********************************************\n");
}
copyVolGeom(<->dst, &vgtmp);
copyVolGeom(<->src, <->dst);
copyVolGeom(&vgtmp, <->src);
}
// LTAchangeType(lta, LINEAR_VOX_TO_VOX);
/* apply lta to the ctrl volume */
mri_tmp = MRIalloc(mri_ctrl->width,
mri_ctrl->height,
mri_ctrl->depth,
mri_ctrl->type) ;
MRIcopyHeader(mri_in, mri_tmp) ;
// this function doesn't do NEAREST at all!!
// I found the bug, in LTAtransformInterp()
mri_tmp = LTAtransformInterp(mri_ctrl, mri_tmp, lta, SAMPLE_NEAREST);
MRIfree(&mri_ctrl);
mri_ctrl = mri_tmp;
if (mask1_fname != NULL && mask2_fname == NULL) {
printf("map mask for tp1 to get mask for tp2 ...\n");
mri_mask2 = MRIalloc(mri_in->width,
mri_in->height,
mri_in->depth,
mri_mask1->type) ;
MRIcopyHeader(mri_in, mri_mask2) ;
mri_mask2 = LTAtransformInterp(mri_mask1,
mri_mask2,
lta,
SAMPLE_NEAREST);
mask2_set = 1;
if (debug_flag)
MRIwrite(mri_mask2, "mri_mask2.mgz");
} else if (mask2_fname != NULL && mask1_fname == NULL) {
printf("map mask for tp2 to get mask for tp1 ...\n");
//need to invert lta first
m_tmp = lta->xforms[0].m_L ;
lta->xforms[0].m_L = MatrixInverse(lta->xforms[0].m_L, NULL) ;
MatrixFree(&m_tmp) ;
lt = <a->xforms[0];
copyVolGeom(<->dst, &vgtmp);
copyVolGeom(<->src, <->dst);
copyVolGeom(&vgtmp, <->src);
mri_mask1 = MRIalloc(mri_T1->width,
mri_T1->height,
mri_T1->depth,
mri_mask2->type) ;
MRIcopyHeader(mri_T1, mri_mask1) ;
mri_mask1 = LTAtransformInterp(mri_mask2,
mri_mask1,
lta,
SAMPLE_NEAREST);
mask1_set = 1;
if (debug_flag)
MRIwrite(mri_mask1, "mri_mask1.mgz");
}
if (lta_src)
MRIfree(<a_src);
if (lta_dst)
MRIfree(<a_dst);
if (lta)
LTAfree(<a);
} /* if (xform_fname != NULL) */
if (debug_flag) {
// MRIwrite(mri_snr, "snr.mgz");
MRIwrite(mri_ctrl, "ctrl.mgz");
}
if (mask1_set == 0) {
//create mask1
mri_mask1 = MRIalloc(mri_T1->width,
mri_T1->height,
mri_T1->depth,
MRI_UCHAR) ;
for (z=0; z < depth; z++)
for (y=0; y< height; y++)
for (x=0; x < width; x++) {
if (MRIgetVoxVal(mri_T1, x, y, z, 0) < noise_threshold) {
MRIvox(mri_mask1,x,y,z) = 0;
} else
MRIvox(mri_mask1,x,y,z) = 1;
}
}
if (mask2_set == 0) {
//create mask2
mri_mask2 = MRIalloc(mri_in->width,
mri_in->height,
mri_in->depth,
MRI_UCHAR) ;
for (z=0; z < depth; z++)
for (y=0; y< height; y++)
for (x=0; x < width; x++) {
if (MRIgetVoxVal(mri_in, x, y, z, 0) < noise_threshold) {
MRIvox(mri_mask2,x,y,z) = 0;
} else
MRIvox(mri_mask2,x,y,z) = 1;
}
}
#if 0
/* compute the mean and std of T1 volume */
/* Using only high SNR points */
mri_snr = MRIalloc(mri_T1->width, mri_T1->height, mri_T1->depth, MRI_FLOAT) ;
MRIcopyHeader(mri_T1, mri_snr) ;
h->bin_size = bin_size = 0.5;
for (bin_no = 0; bin_no < nbins; bin_no++)
h->bins[bin_no] = (bin_no)*bin_size;
for (z=0; z < depth; z++)
for (y=0; y< height; y++)
for (x=0; x < width; x++) {
if (MRIgetVoxVal(mri_T1, x, y, z, 0) < noise_threshold) {
MRIFvox(mri_snr,x,y,z) = 0;
continue;
}
mean = 0;
std = 0;
count = 0;
for (i=-1; i<=1; i++)
for (j=-1; j<=1; j++)
for (k=-1;k<=1;k++) {
cx = x+i;
cy = y+j, cz = z+k;
if (cx < 0 ||
cx >= width ||
cy < 0 ||
cy >= height ||
cz < 0 ||
cz >= depth) continue;
count++;
value = MRIgetVoxVal(mri_T1, cx, cy, cz, 0);
mean += value;
std += value*value;
}
mean /= (count + 1e-30);
std /= (count + 1e-30);
std = std - mean *mean;
if (std <= 0)
std = 0;
value = mean/sqrt(std);
MRIFvox(mri_snr,x,y,z) = value;
bin_no = nint((float)value/(float)bin_size);
if (bin_no >= nbins) bin_no = nbins - 1;
h->counts[bin_no]++;
}
for (num = 0.0f, b = h->nbins - 1; b >= 1; b --) {
num += h->counts[b];
if (num > 20000) /* this may make me only use WM points,
is it good to use only WM to compute
scale of intensity?? */
break;
}
printf("using SNR threshold %2.3f at bin %d\n", h->bins[b], b);
mean1 = 0;
std1 = 0;
count1 = 0;
for (z=0; z < depth; z++)
for (y=0; y< height; y++)
for (x=0; x < width; x++) {
if (MRIgetVoxVal(mri_T1, x, y, z, 0) < noise_threshold) {
continue;
}
value = MRIFvox(mri_snr,x,y,z);
if (value < h->bins[b]) continue;
value = MRIgetVoxVal(mri_T1, x, y, z, 0);
count1++;
mean1 += value;
std1 += value*value;
}
MRIfree(&mri_snr);
#else
printf("compute mean and std of tp1 volume within masked area...\n");
mean1 = 0;
std1 = 0;
count1 = 0;
for (z=0; z < depth; z++)
for (y=0; y< height; y++)
for (x=0; x < width; x++) {
if (MRIgetVoxVal(mri_mask1, x, y, z, 0) <= 1e-30) {
continue;
}
value = MRIgetVoxVal(mri_T1, x, y, z, 0);
count1++;
mean1 += value;
std1 += value*value;
}
#endif
mean1 /= (count1 + 1e-30);
std1 /= (count1 + 1e-30);
std1 = std1 - mean1*mean1;
if (std1 <= 0)
printf("warning: negative std for T1 volume. \n");
else
printf("mean and variance for tp1 volume are %g and %g\n", mean1, std1);
printf("now compute SNR and stats for input volume ... \n");
mri_snr = MRIalloc(mri_in->width, mri_in->height, mri_in->depth, MRI_FLOAT) ;
MRIcopyHeader(mri_in, mri_snr) ;
//HISTOclear(h,h);
//h->bin_size = bin_size = 0.5;
//for (bin_no = 0; bin_no < nbins; bin_no++)
// h->bins[bin_no] = (bin_no)*bin_size;
for (z=0; z < depth; z++)
for (y=0; y< height; y++)
for (x=0; x < width; x++) {
if (MRIgetVoxVal(mri_in, x, y, z, 0) < noise_threshold) {
MRIFvox(mri_snr,x,y,z) = 0;
continue;
}
mean = 0;
std = 0;
count = 0;
for (i=-1; i<=1; i++)
for (j=-1; j<=1; j++)
for (k=-1;k<=1;k++) {
cx = x+i;
cy = y+j, cz = z+k;
if (cx < 0 ||
cx >= width ||
cy < 0 ||
cy >= height ||
cz < 0 ||
cz >= depth) continue;
count++;
value = MRIgetVoxVal(mri_in, cx, cy, cz, 0);
mean += value;
std += value*value;
}
mean /= (count + 1e-30);
std /= (count + 1e-30);
std = std - mean *mean;
if (std <= 0)
std = 0;
value = mean/sqrt(std);
MRIFvox(mri_snr,x,y,z) = value;
//bin_no = nint((float)value/(float)bin_size);
//if (bin_no >= nbins) bin_no = nbins - 1;
//h->counts[bin_no]++;
}
#if 0
for (num = 0.0f, b = h->nbins - 1; b >= 1; b --) {
num += h->counts[b];
if (num > 20000) /* this may make me only use WM points, is it good to
use only WM to compute scale of intensity?? */
break;
}
printf("using SNR threshold %2.3f at bin %d\n", h->bins[b], b);
mean2 = 0;
std2 = 0;
count2 = 0;
for (z=0; z < depth; z++)
for (y=0; y< height; y++)
for (x=0; x < width; x++) {
if (MRIgetVoxVal(mri_in, x, y, z, 0) < noise_threshold) {
continue;
}
value = MRIFvox(mri_snr,x,y,z);
if (value >= h->bins[b]) {
count2++;
mean2 += value;
std2 += value*value;
}
}
#else
printf("compute mean and std of tp2 volume within masked area\n");
/* somehow mri_watershed seems to leave some unzero voxels around
image border, so I will skip image boundaries
no, that's not a problem of most recent mri_watershed;
something wrong previously */
mean2 = 0;
std2 = 0;
count2 = 0;
for (z=0; z < depth; z++)
for (y=0; y< height; y++)
for (x=0; x < width; x++) {
if (MRIgetVoxVal(mri_mask2, x, y, z, 0) <= 1e-30) {
continue;
}
value = MRIgetVoxVal(mri_in, x, y, z, 0);
count2++;
mean2 += value;
std2 += value*value;
}
#endif
mean2 /= (count2 + 1e-30);
std2 /= (count2 + 1e-30);
std2 = std2 - mean2*mean2;
if (std2 <= 0)
printf("warning: negative std for input volume. \n");
else
printf("mean and variance for input tp2 volume are %g and %g\n",
mean2, std2);
//compute intensity scale
slope = sqrt(std1/std2);
offset = mean1 - slope*mean2;
printf("scale input volume by %g x + %g\n", slope, offset);
// first change mri_in to FLOAT type
mri_tmp = MRIchangeType(mri_in, MRI_FLOAT, 0, 1.0, 1);
MRIfree(&mri_in);
mri_in = mri_tmp;
for (z=0; z < depth; z++)
for (y=0; y< height; y++)
for (x=0; x < width; x++) {
value = MRIFvox(mri_in, x, y, z);
MRIFvox(mri_in, x, y, z) = value*slope + offset;
}
// printf("compute SNR map of tp2 volume\n"); //already done above
// mri_snr = MRIalloc(mri_ctrl->width,
// mri_ctrl->height, mri_ctrl->depth, MRI_FLOAT) ;
for (z=0; z < depth; z++)
for (y=0; y< height; y++)
for (x=0; x < width; x++) {
if (MRIgetVoxVal(mri_in, x, y, z, 0) < noise_threshold) {
// MRIFvox(mri_snr,x,y,z) = 0;
continue;
}
value = MRIFvox(mri_snr,x,y,z);
if (value < 20) MRIvox(mri_ctrl, x, y, z) = 0;
else if (MRIvox(mri_ctrl, x, y, z) > 0) {
MRIvox(mri_ctrl, x, y, z) = 1;
}
}
if (debug_flag) {
MRIwrite(mri_snr, "snr.mgz");
// MRIwrite(mri_ctrl, "ctrl.mgz");
}
// SNR >= 20 seems a good threshold
// Now use ctrl points to normalize tp2
printf("normalize tp2...\n");
mri_bias = MRIbuildBiasImage(mri_in, mri_ctrl, NULL, bias_sigma) ;
for (z = 0 ; z < depth ; z++) {
for (y = 0 ; y < height ; y++) {
for (x = 0 ; x < width ; x++) {
src = MRIgetVoxVal(mri_in, x, y, z, 0) ;
bias = MRIgetVoxVal(mri_bias, x, y, z, 0) ;
if (!bias) /* should never happen */
norm = (float)src ;
else
norm = (float)src * 110.0 / (float)bias ;
if (norm > 255.0f && mri_out->type == MRI_UCHAR)
norm = 255.0f ;
else if (norm < 0.0f && mri_out->type == MRI_UCHAR)
norm = 0.0f ;
MRIsetVoxVal(mri_out, x, y, z, 0, norm) ;
}
}
}
printf("writing normalized volume to %s...\n", argv[2]) ;
MRIwrite(mri_out, argv[2]);
MRIfree(&mri_in);
MRIfree(&mri_bias);
MRIfree(&mri_out);
MRIfree(&mri_T1);
MRIfree(&mri_ctrl);
MRIfree(&mri_snr);
//HISTOfree(&h);
exit(0);
} /* end main() */
int
main(int argc, char *argv[]) {
char **av, *in_vol, *out_vol;
int ac, nargs;
MRI *mri_in, *mri_out, *mri_tmp ;
LTA *lta = 0;
MATRIX *i_to_r_src = 0; /* src geometry of the input LTA */
MATRIX *V_to_V = 0; /* Final voxel-to-voxel transform */
MATRIX *r_to_i_dst = 0; /* dst geometry of the input LTA */
MATRIX *m_tmp = 0;
MATRIX *i_to_r_reg = 0; /* i_to_r of the volume after registration */
MATRIX *r_to_i_out = 0; /* r_to_i of the final output volume */
VOL_GEOM vgm_in;
int x, y, z;
double maxV, minV, value;
int transform_type;
// MATRIX *i_to_r, *r_to_i;
HISTOGRAM *h, *hsmooth ;
float fmin, fmax, val, peak, smooth_peak;
int i, nbins, bin;
/* rkt: check for and handle version tag */
nargs = handle_version_option (argc, argv, "$Id: mri_transform_to_COR.c,v 1.3 2011/03/02 00:04:25 nicks Exp $", "$Name: stable5 $");
if (nargs && argc - nargs == 1)
usage_exit (0);
argc -= nargs;
Progname = argv[0] ;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
ac = argc ;
av = argv ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
if (argc < 3)
usage_exit(0) ;
in_vol = argv[1] ;
out_vol = argv[2] ;
printf("reading volume from %s...\n", in_vol) ;
mri_in = MRIread(in_vol) ;
if (!mri_in)
ErrorExit(ERROR_NOFILE, "%s: could not read MRI volume %s", Progname,
in_vol) ;
/* Convert mri_in to float type */
/* double would be more accurate */
if (mri_in->type != MRI_FLOAT) {
printf("Input volume type is %d\n", mri_in->type);
printf("Change input volume to float type for convenience and accuracy");
mri_tmp = MRIchangeType(mri_in, MRI_FLOAT, 0, 1.0, 1);
MRIfree(&mri_in);
mri_in = mri_tmp; //swap
}
/* Get input volume geometry, which is needed to compute i_to_r
* and r_to_i of input volume. Note that i_to_r and r_to_i assumed
* a certain prespecified c_r, c_a, c_s
*/
getVolGeom(mri_in, &vgm_in);
maxV = -10000.0;
minV = 10000.0;
for (z=0; z < mri_in->depth; z++)
for (y=0; y< mri_in->height; y++)
for (x=0; x < mri_in->width; x++) {
if (MRIFvox(mri_in, x, y, z) > maxV )
maxV = MRIFvox(mri_in, x, y,z) ;
if (MRIFvox(mri_in, x, y, z) < minV )
minV = MRIFvox(mri_in, x, y,z) ;
}
printf("Input volume has max = %g, min =%g\n", maxV, minV);
printf("Scale input volume by %g \n", scale);
maxV = -10000.0;
minV = 10000.0;
for (z=0; z < mri_in->depth; z++)
for (y=0; y< mri_in->height; y++)
for (x=0; x < mri_in->width; x++) {
MRIFvox(mri_in, x, y, z) *= scale;
if (MRIFvox(mri_in, x, y, z) > maxV )
maxV = MRIFvox(mri_in, x, y,z) ;
if (MRIFvox(mri_in, x, y, z) < minV )
minV = MRIFvox(mri_in, x, y,z) ;
}
printf("Input volume after scaling has max = %g, min =%g\n", maxV, minV);
/* Try to compute the Voxel_to_Voxel transform from the input volume
* and the registration target/reference volume!
* If no registration is involved, vox_to_vox is simply identity
*/
/* Things become more complicated when allowing inverse transform */
if (transform_flag) {
printf("INFO: Applying transformation from file %s...\n",
transform_fname);
transform_type = TransformFileNameType(transform_fname);
/* Read in LTA transform file name */
if (transform_type == MNI_TRANSFORM_TYPE ||
transform_type == TRANSFORM_ARRAY_TYPE ||
transform_type == REGISTER_DAT ||
transform_type == FSLREG_TYPE
) {
printf("Reading transform ...\n");
lta = LTAreadEx(transform_fname) ;
if (!lta)
ErrorExit(ERROR_NOFILE, "%s: could not read transform file %s",
Progname, transform_fname) ;
if (transform_type == FSLREG_TYPE) {
if (lta_src == 0 || lta_dst == 0) {
fprintf(stderr, "ERROR: fslmat does not have information on the src and dst volumes\n");
fprintf(stderr, "ERROR: you must give options '-src' and '-dst' to specify the src and dst volume infos for the registration\n");
}
LTAmodifySrcDstGeom(lta, lta_src, lta_dst); // add src and dst information
//The following is necessary to interpret FSLMAT correctly!!!
LTAchangeType(lta, LINEAR_VOX_TO_VOX);
}
if (lta->xforms[0].src.valid == 0) {
if (lta_src == 0) {
fprintf(stderr, "The transform does not have the valid src volume info.\n");
fprintf(stderr, "Either you give src volume info by option -src or\n");
fprintf(stderr, "make the transform to have the valid src info.\n");
ErrorExit(ERROR_BAD_PARM, "Bailing out...\n");
} else {
LTAmodifySrcDstGeom(lta, lta_src, NULL); // add src information
}
}
if (lta->xforms[0].dst.valid == 0) {
if (lta_dst == 0) {
fprintf(stderr, "The transform does not have the valid dst volume info.\n");
fprintf(stderr, "Either you give src volume info by option -dst or\n");
fprintf(stderr, "make the transform to have the valid dst info.\n");
fprintf(stderr, "If the dst was average_305, then you can set\n");
fprintf(stderr, "environmental variable USE_AVERAGE305 true\n");
fprintf(stderr, "instead.\n");
ErrorExit(ERROR_BAD_PARM, "Bailing out...\n");
} else {
LTAmodifySrcDstGeom(lta, NULL, lta_dst); // add dst information
}
}
// The following procedure aims to apply an LTA computed from COR format to a volume in non-COR format, or vice versa, as long as they share the same RAS
// first change to LINEAR RAS_TO_RAS using old info
if (lta->type != LINEAR_RAS_TO_RAS) {
LTAchangeType(lta, LINEAR_RAS_TO_RAS);
}
// now possiblly reset the src and dst
if (lta_src != NULL) {
//always trust the user
LTAmodifySrcDstGeom(lta, lta_src, NULL);
}
if (lta_dst != NULL) {
//always trust the user
LTAmodifySrcDstGeom(lta, NULL, lta_dst);
}
if (lta->type == LINEAR_RAS_TO_RAS) {
/* Convert it to VOX_TO_VOX */
/* VOXELsrc_to_VOXELdst = R2Vdst*R2Rlta*V2Rsrc */
/* Note whether the input should be identical to src or dst here depends
* on whether the LTA here is the direct or inverse transform
*/
i_to_r_src = vg_i_to_r(<a->xforms[0].src);
r_to_i_dst = vg_r_to_i(<a->xforms[0].dst);
if (!r_to_i_dst || !i_to_r_src)
ErrorExit(ERROR_BADFILE, "%s: failed to extract volume geometries from input LTA file",Progname);
m_tmp = MatrixMultiply(lta->xforms[0].m_L, i_to_r_src, NULL);
V_to_V = MatrixMultiply(r_to_i_dst, m_tmp, NULL);
MatrixFree(&m_tmp);
MatrixFree(&i_to_r_src);
MatrixFree(&r_to_i_dst);
}
} else {
fprintf(stderr, "unknown transform type in file %s\n",
transform_fname);
exit(1);
}
if (invert_flag) {
/* Geometry of input volume should match that of the dst of the LTA */
if (MYvg_isEqual(<a->xforms[0].dst, &vgm_in) == 0) {
ErrorExit(ERROR_BADFILE, "%s: dst volume of lta doesn't match that of input volume",Progname);
}
i_to_r_reg = vg_i_to_r(<a->xforms[0].src);
if (!i_to_r_reg)
ErrorExit(ERROR_BADFILE, "%s: failed to extract i_to_r of registered volume from LTA",Progname);
m_tmp = MatrixInverse(V_to_V, NULL);
if (!m_tmp)
ErrorExit(ERROR_BADPARM, "%s: transform is singular!", Progname);
MatrixFree(&V_to_V);
V_to_V = m_tmp;
} else {
/* Geometry of input volume should match that of the src of the LTA */
if (MYvg_isEqual(<a->xforms[0].src, &vgm_in) == 0) {
ErrorExit(ERROR_BADFILE, "%s: src volume of lta doesn't match that of input volume",Progname);
}
i_to_r_reg = vg_i_to_r(<a->xforms[0].dst);
if (!i_to_r_reg)
ErrorExit(ERROR_BADFILE, "%s: failed to extract i_to_r of registered volume from LTA",Progname);
}
} else {
/* No registration transform need be applied */
V_to_V = MatrixIdentity(4, NULL);
i_to_r_reg = extract_i_to_r(mri_in);
if (!i_to_r_reg)
ErrorExit(ERROR_BADFILE, "%s: failed to extract i_to_r from input volume",Progname);
}
/* Now need to find the vox-to-vox transformation between registered volume
* (or input volume itself if no registration involved) and the output
* volume, either in COR format or as the out-like volume
*/
/* Given a volume with a certain i_to_r, we need to compute the necessary
* vox-to-voxel transform to change its i_to_r to like another volume.
* The vox-to-vox is equal to R2V(r_to_i)_likevol*i_to_r_current_vol.
*/
if (out_like_fname) {
mri_tmp = MRIread(out_like_fname) ;
if (!mri_tmp)
ErrorExit(ERROR_NOFILE, "%s: could not read template volume from %s",out_like_fname) ;
/* out_type = mri_tmp->type; */
/* specify the out-type to float initially so as not to lose accuracy
* during reslicing, will change type to correct type later.
*/
mri_out = MRIalloc(mri_tmp->width, mri_tmp->height, mri_tmp->depth, MRI_FLOAT) ;
MRIcopyHeader(mri_tmp, mri_out) ;
MRIfree(&mri_tmp);
} else /* assume output is in COR format */
{
mri_out = MRIalloc(256, 256, 256, MRI_FLOAT) ;
/* out_type = MRI_UCHAR; */
/* Who says MRIlinearTransformInterp will change the header??
* I don't think so!
*/
//E/ set xyzc_ras to coronal ones.. - these'll get zorched
//by MRIlinearTransformInterp() - copy again later - is there
//any use in having them here now? yes, so we can pass mri_out
//to the ras2vox fns.
mri_out->imnr0 = 1; /* what's this? */
mri_out->imnr1 = 256; /* what's this? */
mri_out->thick = 1.0;
mri_out->ps = 1.0; /* what's this? */
mri_out->xsize = mri_out->ysize = mri_out->zsize = 1.0;
mri_out->xstart = mri_out->ystart = mri_out->zstart = -128.0;
mri_out->xend = mri_out->yend = mri_out->zend = 128.0;
mri_out->x_r =-1;
mri_out->y_r = 0;
mri_out->z_r = 0;
mri_out->x_a = 0;
mri_out->y_a = 0;
mri_out->z_a = 1;
mri_out->x_s = 0;
mri_out->y_s =-1;
mri_out->z_s = 0;
/* In this case, the RAS itself is not fully determined, i.e., c_ras.
* It's quite arbitrary, different values just change the final
* sitting of the volume inside the RAS system.
*/
/* NO! The C_RAS has to be set correctly, depending which target
* volume the previous Vox_to_Vox transformation assumes!
* When a registration is involved, the target volume is either
* the src of LTA (direct) or the dst (inverse transform). When
* just change format, the target volume is the input itself!!
*/
if (transform_flag) {
if (invert_flag) {
mri_out->c_r = lta->xforms[0].src.c_r;
mri_out->c_a = lta->xforms[0].src.c_a;
mri_out->c_s = lta->xforms[0].src.c_s;
} else {
mri_out->c_r = lta->xforms[0].dst.c_r;
mri_out->c_a = lta->xforms[0].dst.c_a;
mri_out->c_s = lta->xforms[0].dst.c_s;
}
} else {
mri_out->c_r = mri_in->c_r;
mri_out->c_a = mri_in->c_a;
mri_out->c_s = mri_in->c_s;
}
mri_out->ras_good_flag=1; /* What does this flag mean ? */
/* since output is just transformed input */
MRIcopyPulseParameters(mri_in, mri_out) ;
}
/* Compute the final input-to-output VOX_to_VOX transformation matrix */
r_to_i_out = extract_r_to_i(mri_out);
m_tmp = MatrixMultiply(r_to_i_out, i_to_r_reg, NULL);
V_to_V = MatrixMultiply(m_tmp, V_to_V, V_to_V);
MatrixFree(&m_tmp);
printf("InterpMethod = %d\n", InterpMethod);
/* Modify the MyMRIlinearTr... if I want to implement my cubic-B-spline
* interpolation method. Otherwise, unnecessary
*/
/* mri_out = MyMRIlinearTransformInterp(mri_in, mri_out, V_to_V, InterpMethod); */
if (InterpMethod == SAMPLE_BSPLINE)
mri_out = MRIlinearTransformInterpBSpline(mri_in, mri_out, V_to_V,
SplineDegree);
else
mri_out = MRIlinearTransformInterp(mri_in, mri_out, V_to_V, InterpMethod);
maxV = -10000.0;
minV = 10000.0;
for (z=0; z < mri_out->depth; z++)
for (y=0; y< mri_out->height; y++)
for (x=0; x < mri_out->width; x++) {
if (MRIFvox(mri_out, x, y, z) > maxV )
maxV = MRIFvox(mri_out, x, y,z) ;
if (MRIFvox(mri_out, x, y, z) < minV )
minV = MRIFvox(mri_out, x, y,z) ;
}
if (autoscale) {
noscale = 1;
/* compute histogram of output volume */
fmin = minV;
fmax = maxV;
if (fmin < 0) fmin = 0;
nbins = 256 ;
h = HISTOalloc(nbins) ;
hsmooth = HISTOcopy(h, NULL) ;
HISTOclear(h, h) ;
h->bin_size = (fmax-fmin)/255.0 ;
for (i = 0 ; i < nbins ; i++)
h->bins[i] = (i+1)*h->bin_size ;
for (z=0; z < mri_out->depth; z++)
for (y=0; y< mri_out->height; y++)
for (x=0; x < mri_out->width; x++) {
val = MRIFvox(mri_out, x, y, z);
if (val <= 0) continue;
bin = nint((val - fmin)/h->bin_size);
if (bin >= h->nbins)
bin = h->nbins-1;
else if (bin < 0)
bin = 0;
h->counts[bin] += 1.0;
}
HISTOfillHoles(h) ;
HISTOsmooth(h, hsmooth, 5) ;
peak =
hsmooth->bins[HISTOfindHighestPeakInRegion(h, 1, h->nbins)] ;
// smooth_peak =
// hsmooth->bins[HISTOfindHighestPeakInRegion(hsmooth, 1, hsmooth->nbins)] ;
smooth_peak =
hsmooth->bins[HISTOfindLastPeak(hsmooth, 5, 0.8)] ;
/*
bin = nint((smooth_peak - fmin)/hsmooth->bin_size) ;
printf("Highest peak has count = %d\n", (int)hsmooth->counts[bin]);
bin = nint((420 - fmin)/hsmooth->bin_size) ;
printf("bin at 420 has count = %d\n", (int)hsmooth->counts[bin]);
*/
scale = 110.0/smooth_peak;
printf("peak of output volume is %g, smooth-peak is %g, multiply by %g to scale it to 110\n", peak, smooth_peak, scale);
for (z=0; z < mri_out->depth; z++)
for (y=0; y< mri_out->height; y++)
for (x=0; x < mri_out->width; x++) {
val = MRIFvox(mri_out, x, y, z);
MRIFvox(mri_out, x, y, z) = val*scale;
}
}
printf("Output volume (before type-conversion) has max = %g, min =%g\n", maxV, minV);
/* Finally change type to desired */
if (mri_out->type != out_type) {
printf("Change output volume to type %d\n", out_type);
/* I need to modify the MIRchangeType function to make sure
* it does roundoff instead of simple truncation!
*/
/* Note if the last flag is set to 1, then it won't do scaling
and small float numbers will become zero after convert to
BYTE
*/
if (out_type == 0 && noscale == 1) {
//convert data to UCHAR
mri_tmp = MRIalloc(mri_out->width, mri_out->height, mri_out->depth, out_type) ;
MRIcopyHeader(mri_out, mri_tmp);
for (z=0; z < mri_out->depth; z++)
for (y=0; y< mri_out->height; y++)
for (x=0; x < mri_out->width; x++) {
value = floor(MRIgetVoxVal(mri_out, x, y, z, 0) + 0.5);
if (value < 0 ) value = 0;
if (value > 255) value = 255;
MRIvox(mri_tmp,x,y,z) = (unsigned char)value;
}
} else
mri_tmp = MRIchangeType(mri_out, out_type, thred_low, thred_high, noscale);
MRIfree(&mri_out);
mri_out = mri_tmp; //swap
}
MRIwrite(mri_out, out_vol) ;
MRIfree(&mri_in);
MRIfree(&mri_out);
if (lta_src)
MRIfree(<a_src);
if (lta_dst)
MRIfree(<a_dst);
MatrixFree(&V_to_V);
if (!r_to_i_out)
MatrixFree(&r_to_i_out);
if (!i_to_r_reg)
MatrixFree(&i_to_r_reg);
return(0) ; /* for ansi */
}
int
main(int argc, char *argv[])
{
char **av, fname[STRLEN], *out_fname, *subject_name, *cp, *tp1_name, *tp2_name ;
char s1_name[STRLEN], s2_name[STRLEN], *sname ;
int ac, nargs, i, n, options, max_index ;
int msec, minutes, seconds, nsubjects, input ;
struct timeb start ;
MRI *mri_seg, *mri_tmp, *mri_in ;
TRANSFORM *transform ;
// int counts ;
int t;
RANDOM_FOREST *rf = NULL ;
GCA *gca = NULL ;
Progname = argv[0] ;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
TimerStart(&start) ;
parms.width = parms.height = parms.depth = DEFAULT_VOLUME_SIZE ;
parms.ntrees = 10 ;
parms.max_depth = 10 ;
parms.wsize = 1 ;
parms.training_size = 100 ;
parms.training_fraction = .5 ;
parms.feature_fraction = 1 ;
/* rkt: check for and handle version tag */
nargs = handle_version_option
(argc, argv,
"$Id: mri_rf_long_train.c,v 1.5 2012/06/15 12:22:28 fischl Exp $",
"$Name: $");
if (nargs && argc - nargs == 1)
exit (0);
argc -= nargs;
// parse command line args
ac = argc ;
av = argv ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++)
{
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
if (!strlen(subjects_dir)) /* hasn't been set on command line */
{
cp = getenv("SUBJECTS_DIR") ;
if (!cp)
ErrorExit(ERROR_BADPARM, "%s: SUBJECTS_DIR not defined in environment",
Progname);
strcpy(subjects_dir, cp) ;
}
if (argc < 3)
usage_exit(1) ;
// options parsed. subjects, tp1 and tp2 and rf name remaining
out_fname = argv[argc-1] ;
nsubjects = (argc-2)/3 ;
for (options = i = 0 ; i < nsubjects ; i++)
{
if (argv[i+1][0] == '-')
{
nsubjects-- ;
options++ ;
}
}
printf("training on %d subject and writing results to %s\n",
nsubjects, out_fname) ;
// rf_inputs can be T1, PD, ...per subject
if (parms.nvols == 0)
parms.nvols = ninputs ;
/* gca reads same # of inputs as we read
from command line - not the case if we are mapping to flash */
n = 0 ;
//////////////////////////////////////////////////////////////////
// set up gca direction cosines, width, height, depth defaults
gca = GCAread(gca_name) ;
if (gca == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read GCA from %s", Progname, gca_name) ;
/////////////////////////////////////////////////////////////////////////
// weird way options and subject name are mixed here
/////////////////////////////////////////////////////////
// first calculate mean
////////////////////////////////////////////////////////
// going through the subject one at a time
max_index = nsubjects+options ;
nargs = 0 ;
mri_in = NULL ;
#ifdef HAVE_OPENMP
subject_name = NULL ; sname = NULL ; t = 0 ;
// counts = 0 ; would be private
input = 0 ;
transform = NULL ;
tp1_name = tp2_name = NULL ;
mri_tmp = mri_seg = NULL ;
#pragma omp parallel for firstprivate(tp1_name, tp2_name, mri_in,mri_tmp, input, xform_name, transform, subjects_dir, force_inputs, conform, Progname, mri_seg, subject_name, s1_name, s2_name, sname, t, fname) shared(mri_inputs, transforms, mri_segs,argv) schedule(static,1)
#endif
for (i = 0 ; i < max_index ; i++)
{
subject_name = argv[3*i+1] ;
tp1_name = argv[3*i+2] ;
tp2_name = argv[3*i+3] ;
sprintf(s1_name, "%s_%s.long.%s_base", subject_name, tp1_name, subject_name) ;
sprintf(s2_name, "%s_%s.long.%s_base", subject_name, tp2_name, subject_name) ;
//////////////////////////////////////////////////////////////
printf("***************************************"
"************************************\n");
printf("processing subject %s, %d of %d (%s and %s)...\n", subject_name,i+1-nargs,
nsubjects, s1_name,s2_name);
for (t = 0 ; t < 2 ; t++)
{
sname = t == 0 ? s1_name : s2_name;
// reading this subject segmentation
sprintf(fname, "%s/%s/mri/%s", subjects_dir, sname, seg_dir) ;
if (Gdiag & DIAG_SHOW && DIAG_VERBOSE_ON)
fprintf(stderr, "Reading segmentation from %s...\n", fname) ;
mri_seg = MRIread(fname) ;
if (!mri_seg)
ErrorExit(ERROR_NOFILE, "%s: could not read segmentation file %s",
Progname, fname) ;
if ((mri_seg->type != MRI_UCHAR) && (make_uchar != 0))
{
MRI *mri_tmp ;
mri_tmp = MRIchangeType(mri_seg, MRI_UCHAR, 0, 1,1);
MRIfree(&mri_seg) ;
mri_seg = mri_tmp ;
}
if (wmsa_fname)
{
MRI *mri_wmsa ;
sprintf(fname, "%s/%s/mri/%s", subjects_dir, sname, wmsa_fname) ;
printf("reading WMSA labels from %s...\n", fname) ;
mri_wmsa = MRIread(fname) ;
if (mri_wmsa == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read WMSA file %s", fname) ;
MRIbinarize(mri_wmsa, mri_wmsa, 1, 0, WM_hypointensities) ;
MRIcopyLabel(mri_wmsa, mri_seg, WM_hypointensities) ;
lateralize_hypointensities(mri_seg) ;
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON )
{
char s[STRLEN] ;
sprintf(s, "%s/%s/mri/seg_%s",
subjects_dir, subject_name, wmsa_fname) ;
MRIwrite(mri_seg, s) ;
}
}
if (binarize)
{
int j ;
for (j = 0 ; j < 256 ; j++)
{
if (j == binarize_in)
MRIreplaceValues(mri_seg, mri_seg, j, binarize_out) ;
else
MRIreplaceValues(mri_seg, mri_seg, j, 0) ;
}
}
if (insert_fname)
{
MRI *mri_insert ;
sprintf(fname, "%s/%s/mri/%s",
subjects_dir, subject_name, insert_fname) ;
mri_insert = MRIread(fname) ;
if (mri_insert == NULL)
ErrorExit(ERROR_NOFILE,
"%s: could not read volume from %s for insertion",
Progname, insert_fname) ;
MRIbinarize(mri_insert, mri_insert, 1, 0, insert_label) ;
MRIcopyLabel(mri_insert, mri_seg, insert_label) ;
MRIfree(&mri_insert) ;
}
replaceLabels(mri_seg) ;
MRIeraseBorderPlanes(mri_seg, 1) ;
////////////////////////////////////////////////////////////
if (DIAG_VERBOSE_ON)
fprintf(stderr,
"Gather all input volumes for the subject %s.\n",
subject_name);
// inputs must be coregistered
// note that inputs are T1, PD, ... per subject (same TE, TR, FA)
for (input = 0 ; input < ninputs ; input++)
{
//////////// set the gca type //////////////////////////////
// is this T1/PD training?
// how can we allow flash data training ???????
// currently checks the TE, TR, FA to be the same for all inputs
// thus we cannot allow flash data training.
////////////////////////////////////////////////////////////
sprintf(fname, "%s/%s/mri/%s", subjects_dir, sname,input_names[input]);
if (DIAG_VERBOSE_ON)
printf("reading co-registered input from %s...\n", fname) ;
fprintf(stderr, " reading input %d: %s\n", input, fname);
mri_tmp = MRIread(fname) ;
if (!mri_tmp)
ErrorExit
(ERROR_NOFILE,
"%s: could not read image from file %s", Progname, fname) ;
// input check 1
if (getSliceDirection(mri_tmp) != MRI_CORONAL)
{
ErrorExit
(ERROR_BADPARM,
"%s: must be in coronal direction, but it is not\n",
fname);
}
// input check 2
if (conform &&
(mri_tmp->xsize != 1 || mri_tmp->ysize != 1 || mri_tmp->zsize != 1))
{
ErrorExit
(ERROR_BADPARM,
"%s: must have 1mm voxel size, but have (%f, %f, %f)\n",
fname, mri_tmp->xsize, mri_tmp->ysize, mri_tmp->ysize);
}
// input check 3 is removed. now we can handle c_(ras) != 0 case
// input check 4
if (i == 0)
{
TRs[input] = mri_tmp->tr ;
FAs[input] = mri_tmp->flip_angle ;
TEs[input] = mri_tmp->te ;
}
else if ((force_inputs == 0) &&
(!FEQUAL(TRs[input],mri_tmp->tr) ||
!FEQUAL(FAs[input],mri_tmp->flip_angle) ||
!FEQUAL(TEs[input], mri_tmp->te)))
ErrorExit
(ERROR_BADPARM,
"%s: subject %s input volume %s: sequence parameters "
"(%2.1f, %2.1f, %2.1f)"
"don't match other inputs (%2.1f, %2.1f, %2.1f)",
Progname, subject_name, fname,
mri_tmp->tr, DEGREES(mri_tmp->flip_angle), mri_tmp->te,
TRs[input], DEGREES(FAs[input]), TEs[input]) ;
// first time do the following
if (input == 0)
{
int nframes = ninputs ;
///////////////////////////////////////////////////////////
mri_in = MRIallocSequence(mri_tmp->width, mri_tmp->height, mri_tmp->depth,
mri_tmp->type, nframes) ;
if (!mri_in)
ErrorExit
(ERROR_NOMEMORY,
"%s: could not allocate input volume %dx%dx%dx%d",
mri_tmp->width, mri_tmp->height, mri_tmp->depth,nframes) ;
MRIcopyHeader(mri_tmp, mri_in) ;
}
// -mask option ////////////////////////////////////////////
if (mask_fname)
{
MRI *mri_mask ;
sprintf(fname, "%s/%s/mri/%s",
subjects_dir, subject_name, mask_fname);
printf("reading volume %s for masking...\n", fname) ;
mri_mask = MRIread(fname) ;
if (!mri_mask)
ErrorExit(ERROR_NOFILE, "%s: could not open mask volume %s.\n",
Progname, fname) ;
MRImask(mri_tmp, mri_mask, mri_tmp, 0, 0) ;
MRIfree(&mri_mask) ;
}
MRIcopyFrame(mri_tmp, mri_in, 0, input) ;
MRIfree(&mri_tmp) ;
}// end of inputs per subject
/////////////////////////////////////////////////////////
// xform_name is given, then we can use the consistent c_(r,a,s) for gca
/////////////////////////////////////////////////////////
if (xform_name)
{
// we read talairach.xfm which is a RAS-to-RAS
sprintf(fname, "%s/%s/mri/transforms/%s", subjects_dir, sname, xform_name) ;
if (Gdiag & DIAG_SHOW && DIAG_VERBOSE_ON)
printf("INFO: reading transform file %s...\n", fname);
if (!FileExists(fname))
{
fprintf(stderr,"ERROR: cannot find transform file %s\n",fname);
exit(1);
}
transform = TransformRead(fname);
if (!transform)
ErrorExit(ERROR_NOFILE, "%s: could not read transform from file %s",
Progname, fname);
// modify_transform(transform, mri_in, gca);
// Here we do 2 things
// 1. modify gca direction cosines to
// that of the transform destination (both linear and non-linear)
// 2. if ras-to-ras transform,
// then change it to vox-to-vox transform (linear case)
// modify transform to store inverse also
TransformInvert(transform, mri_in) ;
}
else
{
// GCAreinit(mri_in, gca);
// just use the input value, since dst = src volume
transform = TransformAlloc(LINEAR_VOXEL_TO_VOXEL, NULL) ;
}
/////////////////////////////////////////////////////////
if (do_sanity_check)
{
// conduct a sanity check of particular labels, most importantly
// hippocampus, that such labels do not exist in talairach coords
// where they are known not to belong (indicating a bad manual edit)
int errs = check(mri_seg, subjects_dir, subject_name);
if (errs)
{
printf(
"ERROR: mri_ca_train: possible bad training data! subject:\n"
"\t%s/%s\n\n", subjects_dir, subject_name);
fflush(stdout) ;
sanity_check_badsubj_count++;
}
}
mri_segs[i][t] = mri_seg ;
mri_inputs[i][t] = mri_in ;
transforms[i][t] = transform ;
}
}
rf = train_rforest(mri_inputs, mri_segs, transforms, nsubjects, gca, &parms, wm_thresh,wmsa_whalf, 2) ;
printf("writing random forest to %s\n", out_fname) ;
if (RFwrite(rf, out_fname) != NO_ERROR)
ErrorExit
(ERROR_BADFILE, "%s: could not write rf to %s", Progname, out_fname) ;
msec = TimerStop(&start) ;
seconds = nint((float)msec/1000.0f) ;
minutes = seconds / 60 ;
seconds = seconds % 60 ;
printf("classifier array training took %d minutes and %d seconds.\n", minutes, seconds) ;
exit(0) ;
return(0) ;
}
