int
main(int argc, char *argv[])
{
char **av, *output_fname ;
int ac, nargs, msec, mode=-1 ;
LABEL *area = NULL ;
MRI_SURFACE *mris ;
struct timeb then ;
MRI *mri_dist ;
/* rkt: check for and handle version tag */
nargs = handle_version_option
(argc, argv,
"$Id: mris_distance_transform.c,v 1.5 2013/04/12 20:59:17 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) ;
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() ;
TimerStart(&then) ;
mris = MRISread(argv[1]) ;
if (mris == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read surface %s",
Progname, argv[1]) ;
if (vol)
{
/*
mri_template = MRIread(argv[2]) ;
if (!mri_template)
ErrorExit(ERROR_NOFILE, "%s: could not read MRI volume from %s\n", Progname, argv[2]) ;
*/
}
else
{
area = LabelRead(NULL, argv[2]) ;
if (area == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read label %s",
Progname, argv[2]) ;
if (anterior_dist > 0)
LabelCropAnterior(area, anterior_dist) ;
if (posterior_dist > 0)
LabelCropPosterior(area, posterior_dist) ;
}
if (stricmp(argv[3], "signed") == 0)
mode = DTRANS_MODE_SIGNED ;
else if (stricmp(argv[3], "unsigned") == 0)
mode = DTRANS_MODE_UNSIGNED ;
else if (stricmp(argv[3], "outside") == 0)
mode = DTRANS_MODE_OUTSIDE ;
else
{
print_usage() ;
ErrorExit(ERROR_BADPARM, "unrecognized mode choice %s\n", argv[3]) ;
}
output_fname = argv[4] ;
MRIScomputeMetricProperties(mris) ;
if (vol)
{
mri_dist = MRIScomputeDistanceToSurface(mris, NULL, 0.25) ;
MRIwrite(mri_dist, argv[4]) ;
}
else
{
MRIScomputeSecondFundamentalForm(mris) ;
if (normalize > 0)
{
normalize = sqrt(mris->total_area) ;
printf("normalizing surface distances by sqrt(%2.1f) = %2.1f\n", mris->total_area,normalize) ;
}
if (divide > 1)
{
int i ;
char fname[STRLEN], ext[STRLEN], base_name[STRLEN] ;
LABEL *area_division ;
FileNameExtension(output_fname, ext) ;
FileNameRemoveExtension(output_fname, base_name) ;
LabelMark(area, mris) ;
MRIScopyMarksToAnnotation(mris) ;
MRISsaveVertexPositions(mris, TMP_VERTICES) ;
if (MRISreadVertexPositions(mris, divide_surf_name) != NO_ERROR)
ErrorExit(ERROR_BADPARM, "%s: could not read vertex coords from %s", Progname, divide_surf_name) ;
MRIScomputeSecondFundamentalForm(mris) ;
MRISdivideAnnotationUnit(mris, 1, divide) ;
MRISrestoreVertexPositions(mris, TMP_VERTICES) ;
MRIScomputeSecondFundamentalForm(mris) ;
// MRISdivideAnnotationUnit sets the marked to be in [0,divide-1], make it [1,divide]
// make sure they are oriented along original a/p direction
#define MAX_UNITS 100
{
double cx[MAX_UNITS], cy[MAX_UNITS], cz[MAX_UNITS], min_a ;
int index, num[MAX_UNITS], new_index[MAX_UNITS], j, min_i ;
VERTEX *v ;
memset(num, 0, sizeof(num[0])*divide) ;
memset(cx, 0, sizeof(cx[0])*divide) ;
memset(cy, 0, sizeof(cy[0])*divide) ;
memset(cz, 0, sizeof(cz[0])*divide) ;
for (i = 0 ; i < area->n_points ; i++)
{
if (area->lv[i].vno < 0 || area->lv[i].deleted > 0)
continue ;
v = &mris->vertices[area->lv[i].vno] ;
v->marked++ ;
index = v->marked ;
cx[index] += v->x ;
cy[index] += v->y ;
cz[index] += v->z ;
num[index]++ ;
}
memset(new_index, 0, sizeof(new_index[0])*divide) ;
for (i = 1 ; i <= divide ; i++)
cy[i] /= num[i] ;
// order them from posterior to anterior
for (j = 1 ; j <= divide ; j++)
{
min_a = 1e10 ; min_i = 0 ;
for (i = 1 ; i <= divide ; i++)
{
if (cy[i] < min_a)
{
min_a = cy[i] ;
min_i = i ;
}
}
cy[min_i] = 1e10 ; // make it biggest so it won't be considered again
new_index[j] = min_i ;
}
for (i = 0 ; i < area->n_points ; i++)
{
if (area->lv[i].vno < 0 || area->lv[i].deleted > 0)
continue ;
v = &mris->vertices[area->lv[i].vno] ;
v->marked = new_index[v->marked] ;
}
}
for (i = 1 ; i <= divide ; i++)
{
area_division = LabelFromMarkValue(mris, i) ;
printf("performing distance transform on division %d with %d vertices\n",
i, area_division->n_points) ;
if (output_label)
{
sprintf(fname, "%s%d.label", base_name, i) ;
printf("writing %dth subdivision to %s\n", i, fname) ;
LabelWrite(area_division, fname);
}
MRISdistanceTransform(mris, area_division, mode) ;
sprintf(fname, "%s%d.%s", base_name, i, ext) ;
if (normalize > 0)
MRISmulVal(mris, 1.0/normalize) ;
MRISwriteValues(mris, fname) ;
}
}
else
{
MRISdistanceTransform(mris, area, mode) ;
if (normalize > 0)
MRISmulVal(mris, 1.0/normalize) ;
MRISwriteValues(mris, output_fname) ;
}
}
msec = TimerStop(&then) ;
fprintf(stderr,"distance transform took %2.1f minutes\n", (float)msec/(60*1000.0f));
exit(0) ;
return(0) ; /* for ansi */
}
/* ----------------------------------------------------------
Name: regio_read_register()
Reads a registration file.
subject -- name of subject as found in the data base
inplaneres -- in-plane resolution
betplaneres -- between-plane resolution
intensity -- for the register program
R - matrix to convert from xyz in COR space to xyz in Volume space,
ie, xyzVol = R*xyzCOR
float2int - if the regfile has a line after the matrix, the string
is passed to float2int_code(), the result of which is passed
back as float2int. If there is no extra line, FLT2INT_TKREG
is returned (indicating that the regfile was created by
tkregister).
-------------------------------------------------------------*/
int regio_read_register(char *regfile, char **subject, float *inplaneres,
float *betplaneres, float *intensity, MATRIX **R,
int *float2int)
{
FILE *fp;
char tmp[1000];
int r,c,n;
float val;
if (!stricmp(FileNameExtension(regfile, tmp), "LTA"))
{
LTA *lta ;
printf("regio_read_register: loading lta\n");
lta = LTAread(regfile) ;
if(lta == NULL) return(1) ;
if(lta->subject[0]==0) strcpy(lta->subject, "subject-unknown");
*subject = (char *) calloc(strlen(lta->subject)+2,sizeof(char));
strcpy(*subject, lta->subject) ;
*intensity = lta->fscale ;
*float2int = FLT2INT_ROUND ;
*inplaneres = lta->xforms[0].src.xsize ;
*betplaneres = lta->xforms[0].src.zsize ;
*R = TransformLTA2RegDat(lta);
LTAfree(<a) ;
return(0) ;
}
fp = fopen(regfile,"r");
if (fp==NULL)
{
perror("regio_read_register()");
fprintf(stderr,"Could not open %s\n",regfile);
return(1);
}
/* subject name */
n = fscanf(fp,"%s",tmp);
if (n != 1)
{
perror("regio_read_register()");
fprintf(stderr,"Error reading subject from %s\n",regfile);
fclose(fp);
return(1);
}
*subject = (char *) calloc(strlen(tmp)+2,sizeof(char));
sprintf(*subject,"%s",tmp);
/* in-plane resolution */
n = fscanf(fp,"%f",inplaneres);
if (n != 1)
{
perror("regio_read_register()");
fprintf(stderr,"Error reading inplaneres from %s\n",regfile);
fclose(fp);
return(1);
}
/* between-plane resolution */
n = fscanf(fp,"%f",betplaneres);
if (n != 1)
{
perror("regio_read_register()");
fprintf(stderr,"Error reading betplaneres from %s\n",regfile);
fclose(fp);
return(1);
}
/* intensity*/
n = fscanf(fp,"%f",intensity);
if (n != 1)
{
perror("regio_read_register()");
fprintf(stderr,"Error reading intensity from %s\n",regfile);
fclose(fp);
return(1);
}
*R = MatrixAlloc(4,4,MATRIX_REAL);
if (*R == NULL)
{
fprintf(stderr,"regio_read_register(): could not alloc R\n");
fclose(fp);
return(1);
}
/* registration matrix */
for (r=0;r<4;r++)
{
for (c=0;c<4;c++)
{
n = fscanf(fp,"%f",&val);
if (n != 1)
{
perror("regio_read_register()");
fprintf(stderr,"Error reading R[%d][%d] from %s\n",r,c,regfile);
fclose(fp);
return(1);
}
(*R)->rptr[r+1][c+1] = val;
}
}
/* Get the float2int method string */
n = fscanf(fp,"%s",&tmp[0]);
fclose(fp);
if (n == EOF)
*float2int = FLT2INT_TKREG;
else
{
*float2int = float2int_code(tmp);
if ( *float2int == -1 )
{
printf("ERROR: regio_read_register(): float2int method %s from file %s,"
" match not found\n",tmp,regfile);
return(1);
}
}
return(0);
}
int
main(int argc, char *argv[]) {
char **av, *surf_fname, *profile_fname, *seg_fname ;
int ac, nargs ;
MRI_SURFACE *mris, *mris_ico = NULL ;
// LABEL *label = NULL ;
MRI *mri_profiles ;
CLUSTER *ct ;
setRandomSeed(10L) ;
/* rkt: check for and handle version tag */
nargs = handle_version_option (argc, argv, "$Id: mris_cluster_profiles.c,v 1.4 2011/03/02 00:04:34 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 < 4)
usage_exit() ;
profile_fname = argv[1] ;
surf_fname = argv[2] ;
seg_fname = argv[3] ;
mris = MRISread(surf_fname) ;
if (!mris)
ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",
Progname, surf_fname) ;
MRISsetNeighborhoodSize(mris, 2) ;
if (MRISreadAnnotation(mris, "ad_aparc") != NO_ERROR) {
if (MRISreadAnnotation(mris, "aparc") != NO_ERROR)
ErrorExit(ERROR_NOFILE, "%s: could not read annotation file ad_aparc", Progname) ;
}
printf("reading intensity profile volume from %s...\n", profile_fname) ;
mri_profiles = MRIread(profile_fname) ;
if (!mri_profiles)
ErrorExit(ERROR_NOFILE, "%s: could not read intensity volume %s",
Progname, profile_fname) ;
rip_vertices_out_of_fov(mris, mri_profiles) ;
rip_bad_vertices(mris, mri_profiles) ;
MRISclearAnnotations(mris) ;
#if 0
if (nlabels > 0) {
int l ;
char label_name[STRLEN] ;
LABEL *ltotal = NULL ;
for (l = 0 ; l < nlabels ; l++) {
sprintf(label_name, "%s/%s/label/%s.%s.label", sdir, sname, hemi,label_names[l]) ;
label = LabelRead(NULL, label_name) ;
if (!label)
ErrorExit(ERROR_NOFILE, "%s: could not read label file %s...\n", Progname,
label_name) ;
if (num_erode > 0) {
printf("eroding label %d times, npoints went from %d ", num_erode,label->n_points) ;
LabelErode(label, mris, num_erode) ;
printf("to %d ", label->n_points) ;
}
ltotal = LabelCombine(label, ltotal) ;
}
if (nlabels == 0)
ltotal = LabelInFOV(mris, mri, MIN_BORDER_DIST) ;
LabelRipRestOfSurfaceWithThreshold(ltotal, mris, thresh) ;
}
#endif
if (navgs > 0) {
printf("smoothing profiles %d times\n", navgs) ;
MRISsmoothFrames(mris, mri_profiles, navgs) ;
}
if (ico_fname) {
mris_ico = MRISread(ico_fname) ;
if (mris_ico == NULL)
ErrorExit(ERROR_BADPARM, "%s: could not read icosahedron from %s...\n", Progname, ico_fname) ;
}
ct = MRIScluster(mris, mri_profiles, cluster_type, k, start_fname, mris_ico) ;
printf("writing cortical intensity clusters to %s...\n", seg_fname) ;
MRISwriteAnnotation(mris, seg_fname) ;
{
int vno ;
VERTEX *v ;
int c, i ;
char fname[STRLEN], ext[STRLEN] ;
// write average profiles into mri_profiles and write it out
for (vno = 0 ; vno < mris->nvertices ; vno++) {
v = &mris->vertices[vno] ;
if (v->ripflag)
continue ;
c = v->curv ;
if (c < 0)
continue ;
for (i = 0 ; i < mri_profiles->nframes ; i++)
MRIsetVoxVal(mri_profiles, vno, 0, 0, i, VECTOR_ELT(ct[c].v_mean,i+1)) ;
}
FileNameExtension(seg_fname, ext) ;
FileNameRemoveExtension(seg_fname, fname) ;
strcat(fname, "_cluster_avg.mgz") ;
printf("writing average cluster profiles to %s...\n", fname) ;
MRIwrite(mri_profiles, fname) ;
}
MRIfree(&mri_profiles) ;
exit(0) ;
return(0) ; /* for ansi */
}
int
main(int argc, char *argv[]) {
MRI_SURFACE *mris ;
char **av, *in_label_fname, *out_label_fname, *surf_fname, ext[STRLEN] ; ;
int ac, nargs ;
LABEL *label, *label_out ;
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 < 4)
usage_exit() ;
in_label_fname = argv[1] ;
surf_fname = argv[2] ;
out_label_fname = argv[3] ;
printf("reading label from %s...\n", in_label_fname) ;
if (!strcmp(FileNameExtension(in_label_fname, ext), "mgz"))
{
MRI *mri = MRIread(in_label_fname) ;
printf("creating label from volumetric inputs with voxval = %d\n", voxval) ;
if (mri == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read input volume from %s", Progname, in_label_fname);
label = LabelfromASeg(mri, voxval) ;
MRIfree(&mri) ;
}
else
{
label = LabelRead(NULL, in_label_fname) ;
if (!label)
ErrorExit(ERROR_NOFILE, "%s: could not read label file %s", Progname, in_label_fname) ;
}
printf("reading surface from %s...\n", surf_fname) ;
mris = MRISread(surf_fname) ;
if (!mris)
ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",Progname, surf_fname) ;
MRISsaveVertexPositions(mris, ORIGINAL_VERTICES) ;
#if 0
LabelFillUnassignedVertices(mris, label) ;
#else
label_out = LabelFillHoles(label, mris, ORIGINAL_VERTICES) ;
#endif
printf("writing sampled label to %s...\n", out_label_fname) ;
LabelWrite(label_out, out_label_fname) ;
MRISfree(&mris) ;
LabelFree(&label) ;
exit(0) ;
return(0) ; /* for ansi */
}
