int
main(int argc, char *argv[])
{
char **av, fname[STRLEN], *cp ;
int ac, nargs ;
char *subject, *out_fname, *hemi, *ohemi ;
int msec, minutes, seconds ;
struct timeb start ;
MRI *mri, *mri_features, *mri_ribbon, *mri_aseg, *mri_aparc ;
MRI_SURFACE *mris, *mris_contra ;
LABEL *cortex ;
/* rkt: check for and handle version tag */
nargs = handle_version_option (argc, argv, "$Id: mri_extract_fcd_features.c,v 1.1 2016/06/15 17:51:09 fischl 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 < 4)
usage_exit(1) ;
subject = argv[1] ;
hemi = argv[2] ;
if (strcmp(hemi, "lh") == 0)
ohemi = "rh" ;
else
ohemi = "lh" ;
out_fname = argv[3] ;
printf("reading data for subject %s and writing output to %s\n", subject, out_fname) ;
if (!strlen(sdir))
{
cp = getenv("SUBJECTS_DIR") ;
if (!cp)
ErrorExit(ERROR_BADPARM,
"%s: SUBJECTS_DIR not defined in environment.\n", Progname) ;
strcpy(sdir, cp) ;
}
sprintf(fname, "%s/%s/surf/%s.%s", sdir, subject, hemi, white_name) ;
printf("reading %s\n", fname) ;
mris = MRISread(fname) ;
if (mris == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read surface from %s\n", Progname, fname) ;
MRISsaveVertexPositions(mris, WHITE_VERTICES) ;
sprintf(fname, "%s/%s/surf/%s.%s", sdir, subject, ohemi, white_name) ;
printf("reading %s\n", fname) ;
mris_contra = MRISread(fname) ;
if (mris_contra == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read surface from %s\n", Progname, fname) ;
MRISsaveVertexPositions(mris_contra, WHITE_VERTICES) ;
sprintf(fname, "%s/%s/mri/%s", sdir, subject, ribbon_name) ;
printf("reading %s\n", fname) ;
mri_ribbon = MRIread(fname) ;
if (mri_ribbon == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read ribbon from %s\n", Progname, fname) ;
sprintf(fname, "%s/%s/mri/%s", sdir, subject, aparc_name) ;
printf("reading %s\n", fname) ;
mri_aparc = MRIread(fname) ;
if (mri_aparc == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read ribbon from %s\n", Progname, fname) ;
sprintf(fname, "%s/%s/mri/%s", sdir, subject, aseg_name) ;
printf("reading %s\n", fname) ;
mri_aseg = MRIread(fname) ;
if (mri_aseg == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read aseg from %s\n", Progname, fname) ;
sprintf(fname, "%s/%s/surf/%s.%s", sdir, subject, hemi, pial_name) ;
if (MRISreadPialCoordinates(mris, fname) != NO_ERROR)
ErrorExit(ERROR_NOFILE, "%s: could not read pial coordinates from %s\n", Progname, fname) ;
sprintf(fname, "%s/%s/surf/%s.%s", sdir, subject, hemi, sphere_name) ;
if (MRISreadCanonicalCoordinates(mris, fname) != NO_ERROR)
ErrorExit(ERROR_NOFILE, "%s: could not read left/right spherical coordinates from %s\n", Progname, fname) ;
sprintf(fname, "%s/%s/surf/%s.%s", sdir, subject, ohemi, pial_name) ;
if (MRISreadPialCoordinates(mris_contra, fname) != NO_ERROR)
ErrorExit(ERROR_NOFILE, "%s: could not read pial coordinates from %s\n", Progname, fname) ;
sprintf(fname, "%s/%s/label/%s.%s", sdir, subject, hemi, cortex_label) ;
cortex = LabelRead(NULL, fname) ;
if (cortex == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read cortical label from %s\n", Progname, fname) ;
LabelRipRestOfSurface(cortex, mris) ;
LabelFree(&cortex) ;
sprintf(fname, "%s/%s/surf/%s.%s", sdir, subject, ohemi, sphere_name) ;
if (MRISreadCanonicalCoordinates(mris_contra, fname) != NO_ERROR)
ErrorExit(ERROR_NOFILE, "%s: could not read left/right spherical coordinates from %s\n", Progname, fname) ;
sprintf(fname, "%s/%s/mri/%s", sdir, subject, vol_name) ;
printf("reading %s\n", fname) ;
mri = MRIread(fname) ;
if (mri == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read volume from %s\n", Progname, fname) ;
if (0)
mri_features = MRIcomputeSurfaceDistanceProbabilities(mris, mri_ribbon, mri, mri_aseg) ;
else
{
MRI *mri_ohemi_features, *mri_ohemi_mapped_to_hemi_features ;
mri_features = MRIcomputeSurfaceDistanceIntensities(mris, mri_ribbon, mri_aparc, mri, mri_aseg, whalf) ;
mri_ohemi_features = MRIcomputeSurfaceDistanceIntensities(mris_contra, mri_ribbon, mri_aparc, mri, mri_aseg, whalf) ;
mri_ohemi_mapped_to_hemi_features = MRISmapToSurface(mris_contra, mris, mri_ohemi_features, NULL) ; // map contra feature to this surface
// MRIwrite(mri_ohemi_mapped_to_hemi_features, "test.mgz") ;
MRIsubtract(mri_features, mri_ohemi_mapped_to_hemi_features, mri_features) ;
}
if (navgs > 0)
{
MRI *mri_tmp ;
mri_tmp = MRISsmoothMRI(mris, mri_features, navgs, NULL, NULL);
MRIfree(&mri_features) ;
mri_features = mri_tmp ;
}
printf("writing output to %s\n", out_fname) ;
if (Gdiag_no >= 0)
printf("feature(%d) = %f\n", Gdiag_no, MRIgetVoxVal(mri_features, Gdiag_no, 0, 0, 0)) ;
MRIwrite(mri_features, out_fname) ;
msec = TimerStop(&start) ;
seconds = nint((float)msec/1000.0f) ;
minutes = seconds / 60 ;
seconds = seconds % 60 ;
fprintf(stderr, "feature extraction took %d minutes and %d seconds.\n", minutes, seconds) ;
exit(0) ;
return(0) ;
}
FCD_DATA *
FCDloadData(char *sdir, char *subject)
{
FCD_DATA *fcd ;
char fname[STRLEN] ;
MRI *mri_interior, *mri_dist, *mri_int_lh, *mri_int_rh, *mri_pvals ;
fcd = (FCD_DATA *)calloc(1, sizeof(FCD_DATA)) ;
sprintf(fname, "%s/%s/surf/lh.white", sdir, subject) ;
fcd->mris_lh = MRISread(fname) ;
if (fcd->mris_lh == NULL)
{
ErrorExit(ERROR_NOFILE, "FCDloadData: couldn't load %s", fname) ;
}
MRISsaveVertexPositions(fcd->mris_lh, WHITE_VERTICES) ;
if (MRISreadPialCoordinates(fcd->mris_lh, "pial") != NO_ERROR)
{
ErrorExit(ERROR_NOFILE, "FCDloadData: couldn't load lh pial vertices") ;
}
sprintf(fname, "%s/%s/surf/lh.pial", sdir, subject) ;
fcd->mris_lh_pial = MRISread(fname) ;
if (fcd->mris_lh_pial == NULL)
{
ErrorExit(ERROR_NOFILE, "FCDloadData: couldn't load %s", fname) ;
}
sprintf(fname, "%s/%s/surf/lh.sphere.d1.left_right", sdir, subject) ;
fcd->mris_lh_sphere_d1 = MRISread(fname) ;
if (fcd->mris_lh_sphere_d1 == NULL)
{
ErrorExit(ERROR_NOFILE, "FCDloadData: couldn't load %s", fname) ;
}
exec_progress_callback(1, 12, 0, 1) ;
sprintf(fname, "%s/%s/surf/rh.white", sdir, subject) ;
fcd->mris_rh = MRISread(fname) ;
if (fcd->mris_rh == NULL)
{
ErrorExit(ERROR_NOFILE, "FCDloadData: couldn't load %s", fname) ;
}
MRISsaveVertexPositions(fcd->mris_rh, WHITE_VERTICES) ;
if (MRISreadPialCoordinates(fcd->mris_rh, "pial") != NO_ERROR)
{
ErrorExit(ERROR_NOFILE, "FCDloadData: couldn't load rh pial vertices") ;
}
sprintf(fname, "%s/%s/surf/rh.pial", sdir, subject) ;
fcd->mris_rh_pial = MRISread(fname) ;
if (fcd->mris_rh_pial == NULL)
{
ErrorExit(ERROR_NOFILE, "FCDloadData: couldn't load %s", fname) ;
}
sprintf(fname, "%s/%s/surf/rh.sphere.d1.left_right", sdir, subject) ;
fcd->mris_rh_sphere_d1 = MRISread(fname) ;
if (fcd->mris_rh_sphere_d1 == NULL)
{
ErrorExit(ERROR_NOFILE, "FCDloadData: couldn't load %s", fname) ;
}
exec_progress_callback(2, 12, 0, 1) ;
sprintf(fname, "%s/%s/mri/aseg.mgz", sdir, subject) ;
fcd->mri_aseg = MRIread(fname) ;
if (fcd->mri_aseg == NULL)
{
ErrorExit(ERROR_NOFILE, "FCDloadData: couldn't load %s", fname) ;
}
exec_progress_callback(3, 12, 0, 1) ;
sprintf(fname, "%s/%s/mri/aparc+aseg.mgz", sdir, subject) ;
fcd->mri_aparc = MRIread(fname) ;
if (fcd->mri_aparc == NULL)
{
ErrorExit(ERROR_NOFILE, "FCDloadData: couldn't load %s", fname) ;
}
exec_progress_callback(4, 12, 0, 1) ;
fcd->mri_flair = NULL;
sprintf(fname, "%s/%s/mri/flair.reg.norm.mgz", sdir, subject) ;
if ( ! FileExists(fname))
{
sprintf(fname, "%s/%s/mri/FLAIR.mgz", sdir, subject) ;
if ( ! FileExists(fname))
{
sprintf(fname, "%s/%s/mri/FLAIRax.mgz", sdir, subject) ;
if ( ! FileExists(fname))
{
sprintf(fname, "%s/%s/mri/FLAIRcor.mgz", sdir, subject) ;
if ( ! FileExists(fname))
{
sprintf(fname, " ");
}
}
}
}
if (strlen(fname) > 1)
{
fcd->mri_flair = MRIread(fname) ;
if (fcd->mri_flair == NULL)
{
ErrorExit(ERROR_NOFILE, "FCDloadData: couldn't load $s", fname) ;
}
}
fcd->mri_t2 = NULL;
sprintf(fname, "%s/%s/mri/T2.mgz", sdir, subject) ;
if ( ! FileExists(fname))
{
sprintf(fname, "%s/%s/mri/T2ax.mgz", sdir, subject) ;
if ( ! FileExists(fname))
{
sprintf(fname, "%s/%s/mri/T2cor.mgz", sdir, subject) ;
if ( ! FileExists(fname))
{
sprintf(fname, " ");
}
}
}
if (strlen(fname) > 1)
{
fcd->mri_t2 = MRIread(fname) ;
if (fcd->mri_t2 == NULL)
{
ErrorExit(ERROR_NOFILE, "FCDloadData: couldn't load $s", fname) ;
}
}
exec_progress_callback(5, 12, 0, 1) ;
sprintf(fname, "%s/%s/mri/norm.mgz", sdir, subject) ;
fcd->mri_norm = MRIread(fname) ;
if (fcd->mri_norm == NULL)
{
ErrorExit(ERROR_NOFILE, "FCDloadData: couldn't load %s", fname) ;
}
fcd->mri_thickness_increase =
MRIcloneDifferentType(fcd->mri_aseg, MRI_FLOAT) ;
fcd->mri_thickness_decrease =
MRIcloneDifferentType(fcd->mri_aseg, MRI_FLOAT) ;
fcd->mri_thickness_difference = MRIadd(fcd->mri_thickness_increase, fcd->mri_thickness_decrease, NULL);
exec_progress_callback(6, 12, 0, 1) ;
sprintf(fname, "%s/%s/surf/lh.rh.thickness.smooth0.mgz", sdir, subject) ;
fcd->rh_thickness_on_lh = MRIread(fname) ;
if (fcd->mri_aseg == NULL)
{
ErrorExit(ERROR_NOFILE, "FCDloadData: couldn't load %s", fname) ;
}
exec_progress_callback(7, 12, 0, 1) ;
sprintf(fname, "%s/%s/surf/rh.thickness.mgz", sdir, subject) ;
fcd->rh_thickness_on_rh = MRIread(fname) ;
if (fcd->rh_thickness_on_rh == NULL)
{
ErrorExit(ERROR_NOFILE, "FCDloadData: couldn't load %s", fname) ;
}
exec_progress_callback(8, 12, 0, 1) ;
sprintf(fname, "%s/%s/surf/lh.thickness.mgz", sdir, subject) ;
fcd->lh_thickness_on_lh = MRIread(fname) ;
if (fcd->lh_thickness_on_lh == NULL)
{
ErrorExit(ERROR_NOFILE, "FCDloadData: couldn't load %s", fname) ;
}
exec_progress_callback(9, 12, 0, 1) ;
sprintf(fname, "%s/%s/surf/rh.lh.thickness.smooth0.mgz", sdir, subject) ;
if ( ! FileExists(fname))
{
sprintf(fname, "%s/%s/surf/rh.lh.thickness.mgz", sdir, subject) ;
if (fcd->lh_thickness_on_rh == NULL)
{
ErrorExit(ERROR_NOFILE, "FCDloadData: couldn't load %s", fname) ;
}
}
fcd->lh_thickness_on_rh = MRIread(fname) ;
exec_progress_callback(10, 12, 0, 1) ;
mri_int_lh = MRIclone(fcd->mri_norm, NULL) ;
mri_int_rh = MRIclone(fcd->mri_norm, NULL) ;
mri_interior = MRIclone(fcd->mri_norm, NULL) ;
mri_dist = MRIcloneDifferentType(mri_interior, MRI_FLOAT) ;
MRISrestoreVertexPositions(fcd->mris_lh, PIAL_VERTICES) ;
MRISrestoreVertexPositions(fcd->mris_rh, PIAL_VERTICES) ;
MRISfillInterior(fcd->mris_lh, mri_interior->xsize, mri_int_lh) ;
MRISfillInterior(fcd->mris_rh, mri_interior->xsize, mri_int_rh) ;
exec_progress_callback(11, 12, 0, 1) ;
MRIor(mri_int_lh, mri_int_rh, mri_interior, 0) ;
MRIfree(&mri_int_lh) ;
MRIfree(&mri_int_rh) ;
MRIbinarize(mri_interior, mri_interior, 1, 0, 1) ;
if (Gdiag & DIAG_WRITE)
{
MRIwrite(mri_interior, "int.mgz") ;
}
MRIdistanceTransform(mri_interior,
mri_dist,
1,
2*MAX_DIST,
DTRANS_MODE_SIGNED,
NULL);
if (Gdiag & DIAG_WRITE)
{
MRIwrite(mri_dist, "dist.mgz") ;
}
mri_pvals = build_distance_by_intensity_histo(fcd->mri_norm,
mri_dist,
fcd->mri_aseg,
DIST_SPACING,
MAX_DIST) ;
exec_progress_callback(12, 12, 0, 1) ;
augment_thicknesses(fcd, mri_pvals, 1.5, 5, 1) ;
MRISrestoreVertexPositions(fcd->mris_lh, WHITE_VERTICES) ;
MRISrestoreVertexPositions(fcd->mris_rh, WHITE_VERTICES) ;
MRIfree(&mri_dist) ;
MRIfree(&mri_interior) ;
MRIfree(&mri_pvals) ;
return(fcd) ;
}
