static LTA * ltaFSLread(const char *fname) { LTA *lta ; LINEAR_TRANSFORM *lt ; char *cp, line[1000] ; FILE *fp ; int row ; MATRIX *m_L ; fp = fopen(fname, "r") ; if (!fp) ErrorReturn(NULL, (ERROR_NOFILE, "ltFSLread: could not open file %s",fname)); lta = LTAalloc(1, NULL) ; lt = <a->xforms[0] ; lt->sigma = 1.0f ; lt->x0 = lt->y0 = lt->z0 = 0 ; m_L = lt->m_L ; for (row = 1 ; row <= 3 ; row++) { cp = fgetl(line, 900, fp) ; if (!cp) { LTAfree(<a) ; ErrorReturn(NULL, (ERROR_BADFILE, "ltFSLread: could not read row %d from %s", row, fname)) ; } sscanf(cp, "%f %f %f %f", MATRIX_RELT(m_L,row,1), MATRIX_RELT(m_L,row,2), MATRIX_RELT(m_L,row,3), MATRIX_RELT(m_L,row,4)) ; } fclose(fp) ; lta->type = LINEAR_VOX_TO_VOX; return(lta) ; }
int main(int argc, char *argv[]) { char **av, *in_surf_fname, *out_fname, fname[STRLEN], *cp ; int ac, nargs, msec, err ; MRI_SURFACE *mris ; struct timeb then ; float max_dim ; char cmdline[CMD_LINE_LEN] ; make_cmd_version_string (argc, argv, "$Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $", "$Name: stable5 $", cmdline); /* rkt: check for and handle version tag */ nargs = handle_version_option (argc, argv, "$Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $", "$Name: stable5 $"); if (nargs && argc - nargs == 1) { exit (0); } argc -= nargs; #ifdef FS_CUDA /* print GPU device info */ MRISCdeviceInfo(); #endif // FS_CUDA TimerStart(&then) ; Progname = argv[0] ; ErrorInit(NULL, NULL, NULL) ; DiagInit(NULL, NULL, NULL) ; memset(&parms, 0, sizeof(parms)) ; parms.dt = .05 ; parms.projection = PROJECT_ELLIPSOID ; parms.tol = .5 /*1e-1*/ ; parms.n_averages = 1024 ; parms.min_averages = 0 ; parms.l_angle = 0.0 /* L_ANGLE */ ; parms.l_area = 0.0 /* L_AREA */ ; parms.l_neg = 0.0 ; parms.l_dist = 1.0 ; parms.l_spring = 0.0 ; parms.l_area = 1.0 ; parms.l_boundary = 0.0 ; parms.l_curv = 0.0 ; parms.niterations = 25 ; parms.write_iterations = 1000 ; parms.a = parms.b = parms.c = 0.0f ; /* ellipsoid parameters */ parms.dt_increase = 1.01 /* DT_INCREASE */; parms.dt_decrease = 0.99 /* 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.Hdesired = 0.0 ; /* a flat surface */ parms.nbhd_size = 7 ; parms.max_nbrs = 8 ; ac = argc ; av = argv ; for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) { nargs = get_option(argc, argv) ; argc -= nargs ; argv += nargs ; } parms.scale = scale ; if (argc != 3) // catches args beyond the expected two { usage_exit() ; } parms.base_dt = base_dt_scale * parms.dt ; in_surf_fname = argv[1] ; out_fname = argv[2] ; printf("%s\n",vcid); printf(" %s\n",MRISurfSrcVersion()); fflush(stdout); if (parms.base_name[0] == 0) { FileNameOnly(out_fname, fname) ; cp = strchr(fname, '.') ; if (cp) { strcpy(parms.base_name, cp+1) ; } else { strcpy(parms.base_name, "sphere") ; } } mris = MRISread(in_surf_fname) ; if (!mris) ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s", Progname, in_surf_fname) ; MRISaddCommandLine(mris, cmdline) ; fprintf(stderr, "reading original vertex positions...\n") ; if (!FZERO(disturb)) { mrisDisturbVertices(mris, disturb) ; } if (quick == 0) { // don't need original properties unless preserving metric err = MRISreadOriginalProperties(mris, orig_name) ; if(err) { exit(1); } } if (smooth_avgs > 0) { MRISsaveVertexPositions(mris, TMP_VERTICES) ; MRISrestoreVertexPositions(mris, ORIGINAL_VERTICES) ; MRISaverageVertexPositions(mris, smooth_avgs) ; MRISsaveVertexPositions(mris, ORIGINAL_VERTICES) ; MRISrestoreVertexPositions(mris, TMP_VERTICES) ; } if (!FZERO(ralpha) || !FZERO(rbeta) || !FZERO(rgamma)) { MRISrotate(mris,mris,RADIANS(ralpha),RADIANS(rbeta),RADIANS(rgamma)) ; // if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON) MRISwrite(mris, "rot") ; } fprintf(stderr, "unfolding cortex into spherical form...\n"); if (talairach) { MRIStalairachTransform(mris, mris) ; MRISwrite(mris, "tal") ; } if (xform_fname) { LTA *lta ; MRI *mri ; TRANSFORM transform ; lta = LTAread(xform_fname) ; if (lta == NULL) { ErrorExit(ERROR_NOFILE, "%s: could not load %s", xform_fname) ; } mri = MRIread(vol_fname) ; if (mri == NULL) { ErrorExit(ERROR_NOFILE, "%s: could not load %s", vol_fname) ; } transform.type = lta->type ; transform.xform = (void *)lta ; MRIStransform(mris, mri, &transform, mri) ; MRIfree(&mri) ; LTAfree(<a) ; MRISwrite(mris, "xfm") ; } #if 0 max_dim = MAX(abs(mris->xlo), abs(mris->xhi)) ; max_dim = MAX(abs(max_dim), abs(mris->ylo)) ; max_dim = MAX(abs(max_dim), abs(mris->yhi)) ; max_dim = MAX(abs(max_dim), abs(mris->zlo)) ; max_dim = MAX(abs(max_dim), abs(mris->zhi)) ; #else max_dim = MAX(abs(mris->xhi-mris->xlo), abs(mris->yhi-mris->ylo)) ; max_dim = MAX(max_dim,abs(mris->zhi-mris->zlo)) ; #endif if (max_dim > .75*DEFAULT_RADIUS) { float ratio = .75*DEFAULT_RADIUS / (max_dim) ; printf("scaling brain by %2.3f...\n", ratio) ; MRISscaleBrain(mris, mris, ratio) ; } if (target_radius < 0) { target_radius = sqrt(mris->total_area / (4*M_PI)) ; printf("setting target radius to be %2.3f to match surface areas\n", target_radius) ; } // MRISsampleAtEachDistance(mris, parms.nbhd_size, parms.max_nbrs) ; if (!load && inflate) { INTEGRATION_PARMS inflation_parms ; MRIScenter(mris, mris) ; memset(&inflation_parms, 0, sizeof(INTEGRATION_PARMS)) ; strcpy(inflation_parms.base_name, parms.base_name) ; inflation_parms.write_iterations = parms.write_iterations ; inflation_parms.niterations = inflate_iterations ; inflation_parms.l_spring_norm = l_spring_norm ; inflation_parms.l_spring = inflate_spring ; inflation_parms.l_nlarea = inflate_nlarea ; inflation_parms.l_area = inflate_area ; inflation_parms.n_averages = inflate_avgs ; inflation_parms.l_expand = l_expand ; inflation_parms.l_tspring = inflate_tspring ; inflation_parms.l_sphere = l_sphere ; inflation_parms.l_convex = l_convex ; #define SCALE_UP 2 inflation_parms.a = SCALE_UP*DEFAULT_RADIUS ; inflation_parms.tol = inflate_tol ; inflation_parms.integration_type = INTEGRATE_MOMENTUM ; inflation_parms.momentum = 0.9 ; inflation_parms.dt = inflate_dt ; /* store the inflated positions in the v->c? field so that they can be used in the repulsive term. */ /* inflation_parms.l_repulse_ratio = .1 ;*/ MRISsaveVertexPositions(mris, CANONICAL_VERTICES) ; if (l_expand > 0) { MRISexpandSurface(mris, target_radius/2, &inflation_parms, 0, 1) ; l_expand = parms.l_expand = 0 ; } MRIScenter(mris, mris) ; mris->x0 = mris->xctr ; mris->y0 = mris->yctr ; mris->z0 = mris->zctr ; MRISinflateToSphere(mris, &inflation_parms) ; if (inflation_parms.l_expand > 0) { inflation_parms.l_expand = 0 ; inflation_parms.niterations += (inflate_iterations*.1) ; MRISinflateToSphere(mris, &inflation_parms) ; } MRISscaleBrain(mris, mris, target_radius/(DEFAULT_RADIUS*SCALE_UP)) ; parms.start_t = inflation_parms.start_t ; MRISresetNeighborhoodSize(mris, nbrs) ; } if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON) { MRISwrite(mris, "before") ; } MRISprojectOntoSphere(mris, mris, target_radius) ; if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON) { MRISwrite(mris, "after") ; } fprintf(stderr,"surface projected - minimizing metric distortion...\n"); MRISsetNeighborhoodSize(mris, nbrs) ; if (quick) { if (!load) { #if 0 parms.n_averages = 32 ; parms.tol = .1 ; parms.l_parea = parms.l_dist = 0.0 ; parms.l_nlarea = 1 ; #endif MRISprintTessellationStats(mris, stderr) ; MRISquickSphere(mris, &parms, max_passes) ; } } else { MRISunfold(mris, &parms, max_passes) ; } if (remove_negative) { parms.niterations = 1000 ; MRISremoveOverlapWithSmoothing(mris,&parms) ; } if (!load) { fprintf(stderr, "writing spherical brain to %s\n", out_fname) ; MRISwrite(mris, out_fname) ; } msec = TimerStop(&then) ; fprintf(stderr, "spherical transformation took %2.2f hours\n", (float)msec/(1000.0f*60.0f*60.0f)); exit(0) ; return(0) ; /* for ansi */ }
int main(int argc, char *argv[]) { char **av, *avg_surf_name, *canon_surf_name, fname[STRLEN], *mdir, ico_fname[STRLEN], *hemi, *out_sname ; int ac, nargs, i, vno, n ; VERTEX *v ; MRI_SURFACE *mris_ico ; MRI_SP *mrisp_total ; LTA *lta ; VOL_GEOM vg; float average_surface_area = 0.0 ; MATRIX *XFM=NULL; GCA_MORPH *gcam=NULL; memset((void *) &vg, 0, sizeof (VOL_GEOM)); /* rkt: check for and handle version tag */ nargs = handle_version_option (argc, argv, "$Id: mris_make_average_surface.c,v 1.29 2011/03/02 00:04:33 nicks Exp $", "$Name: stable5 $"); if (nargs && argc - nargs == 1) exit (0); argc -= nargs; Progname = argv[0] ; ErrorInit(NULL, NULL, NULL) ; DiagInit(NULL, NULL, NULL) ; mdir = getenv("FREESURFER_HOME") ; if (!mdir) ErrorExit(ERROR_BADPARM, "%s: no FREESURFER_HOME in environment.\n",Progname); ac = argc ; av = argv ; for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) { nargs = get_option(argc, argv) ; argc -= nargs ; argv += nargs ; } if (sdir == NULL) { sdir = getenv("SUBJECTS_DIR"); if (!sdir) ErrorExit(ERROR_BADPARM, "%s: no SUBJECTS_DIR in environment.\n",Progname); } if (sdirout == NULL) sdirout = sdir; if (argc < 6) usage_exit() ; hemi = argv[1] ; avg_surf_name = argv[2] ; canon_surf_name = argv[3] ; out_sname = argv[4] ; printf("---------------------------------------------------\n"); printf("hemi = %s\n",hemi); printf("avg_surf_name = %s\n",avg_surf_name); printf("canon_surf_name = %s\n",canon_surf_name); printf("out_sname = %s\n",out_sname); printf("xform = %s\n",xform_name); printf("---------------------------------------------------\n"); printf("\n\n"); fflush(stdout); #define SCALE 1 mrisp_total = MRISPalloc(SCALE, 3) ; for (n = 0, i = 5 ; i < argc ; i++) { MRI *mri; MRI_SURFACE *mris; MRI_SP *mrisp; printf("\n---------------------------------------------------\n"); printf("#@# processing subject %d/%d %s...\n", i-4,argc-5,argv[i]) ; fflush(stdout); // read sphere.reg sprintf(fname, "%s/%s/surf/%s.%s", sdir, argv[i], hemi, canon_surf_name) ; printf(" Reading %s\n",fname); fflush(stdout); mris = MRISread(fname) ; if (!mris) { ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s", Progname, fname) ; exit(1); } // get "pial" surface vertex into ->origx, origy, origz if (MRISreadOriginalProperties(mris, orig_name) != NO_ERROR) ErrorExit(ERROR_BADFILE,"%s: could not read orig file for %s.\n", Progname, argv[1]); // read transform if (0) { sprintf(fname, "%s/%s/mri/transforms/%s", sdir, argv[i], xform_name) ; lta = LTAreadEx(fname) ; if (!lta) ErrorExit(ERROR_BADPARM, "%s: could not read transform from %s", Progname, fname) ; } // read T1 volume sprintf(fname, "%s/%s/mri/T1.mgz", sdir, argv[i]) ; if (fio_FileExistsReadable(fname)) mri = MRIreadHeader(fname,MRI_MGH_FILE); else { sprintf(fname, "%s/%s/mri/T1", sdir, argv[i]) ; mri = MRIreadHeader(fname, MRI_UCHAR); // MRI_CORONAL_SLICE_DIRECTORY) ; } printf(" Read %s\n",fname); fflush(stdout); if (!mri) ErrorExit(ERROR_BADPARM, "%s: could not read reference MRI volume from %s", Progname, fname) ; // save current vertex position into ->cx MRISsaveVertexPositions(mris, CANONICAL_VERTICES) ; // get the vertex position from ->origx, ... // (get the "pial" vertex position) MRISrestoreVertexPositions(mris, ORIGINAL_VERTICES) ; MRIScomputeMetricProperties(mris) ; printf(" Surface area: %2.1f cm^2\n", mris->total_area/100) ; fflush(stdout); average_surface_area += mris->total_area ; // this means that we transform "pial" surface if (xform_name) { if (!strcmp(xform_name,"talairach.xfm")) { printf(" Applying linear transform\n"); fflush(stdout); XFM = DevolveXFMWithSubjectsDir(argv[i], NULL, "talairach.xfm", sdir); if (XFM == NULL) exit(1); MRISmatrixMultiply(mris, XFM); MatrixFree(&XFM); } else if (!strcmp(xform_name,"talairach.m3z")) { printf(" Applying GCA Morph\n"); fflush(stdout); sprintf(fname, "%s/%s/mri/transforms/talairach.m3z", sdir, argv[i]) ; gcam = GCAMreadAndInvert(fname); if (gcam == NULL) exit(1); GCAMmorphSurf(mris, gcam); GCAMfree(&gcam); } else { printf("ERROR: don't know what to do with %s\n",xform_name); exit(1); } } // save transformed position in ->orig // (store "pial" vertices position in orig) MRIScomputeMetricProperties(mris) ; MRISsaveVertexPositions(mris, ORIGINAL_VERTICES) ; // get the vertex position from ->cx // (note that this is not transformed) sphere.reg vertices MRISrestoreVertexPositions(mris, CANONICAL_VERTICES) ; // mris contains sphere.reg in vertex and pial vertices in orig // map to a theta-phi space and accumulate values mrisp = MRIScoordsToParameterization(mris, NULL, SCALE, ORIGINAL_VERTICES) ; MRISPaccumulate(mrisp, mrisp_total, 0) ; MRISPaccumulate(mrisp, mrisp_total, 1) ; MRISPaccumulate(mrisp, mrisp_total, 2) ; MRISPfree(&mrisp) ; MRISfree(&mris) ; MRIfree(&mri) ; //LTAfree(<a) ; fflush(stdout); n++ ; } printf("Finished loading all data\n"); average_surface_area /= (float)n ; printf("Avg surf area = %g cm\n",average_surface_area/100.0); fflush(stdout); // mrisp_total lost info on the modified surface sprintf(ico_fname, "%s/lib/bem/ic%d.tri", mdir, ico_no) ; printf("Reading icosahedron from %s...\n", ico_fname) ; mris_ico = ICOread(ico_fname) ; if (!mris_ico) ErrorExit(ERROR_NOFILE, "%s: could not read icosahedron file %s\n", Progname,ico_fname) ; MRISscaleBrain(mris_ico, mris_ico, DEFAULT_RADIUS/MRISaverageRadius(mris_ico)) ; // save current ico position to ->cx, cy, cz MRISsaveVertexPositions(mris_ico, CANONICAL_VERTICES) ; // using mrisp_total to calculate position into ->origx, origy, origz // (orig is the "pial" vertices) MRIScoordsFromParameterization(mrisp_total, mris_ico, ORIGINAL_VERTICES) ; // copy geometry info memcpy((void *) &mris_ico->vg, (void *) &vg, sizeof (VOL_GEOM)); if (Gdiag_no >= 0 && Gdiag_no < mris_ico->nvertices) { int n ; VERTEX *vn ; v = &mris_ico->vertices[Gdiag_no] ; printf( "v %d: x = (%2.2f, %2.2f, %2.2f)\n", Gdiag_no, v->origx, v->origy, v->origz) ; for (n = 0 ; n < v->vnum ; n++) { vn = &mris_ico->vertices[v->v[n]] ; printf( "v %d: x = (%2.2f, %2.2f, %2.2f)\n", v->v[n], vn->origx, vn->origy, vn->origz) ; } } // write *h.sphere.reg sprintf(fname, "%s/%s/surf/%s.%s", sdirout, out_sname, hemi, canon_surf_name) ; if (Gdiag & DIAG_SHOW) printf("writing average canonical surface to %s\n", fname); MRISwrite(mris_ico, fname) ; // get "pial vertices" from orig MRISrestoreVertexPositions(mris_ico, ORIG_VERTICES); for (vno = 0 ; vno < mris_ico->nvertices ; vno++) { v = &mris_ico->vertices[vno] ; // n = number of subjects v->x /= (float)n ; v->y /= (float)n ; v->z /= (float)n ; } if (normalize_area) { MRIScomputeMetricProperties(mris_ico) ; printf("setting group surface area to be %2.1f cm^2 (scale=%2.2f)\n", average_surface_area/100.0, sqrt(average_surface_area/mris_ico->total_area)) ; #if 0 MRISscaleBrain(mris_ico, mris_ico, sqrt(average_surface_area/mris_ico->total_area)) ; #else mris_ico->group_avg_surface_area = average_surface_area ; #endif MRIScomputeMetricProperties(mris_ico) ; } sprintf(fname, "%s/%s/surf/%s.%s", sdirout,out_sname, hemi, avg_surf_name) ; printf("writing average %s surface to %s\n", avg_surf_name, fname); MRISwrite(mris_ico, fname) ; if (0) { char path[STRLEN] ; LTA *lta ; FileNamePath(fname, path) ; lta = LTAalloc(1, NULL) ; // write to a different location sprintf(fname, "%s/../mri/transforms/%s", path,xform_name) ; LTAwriteEx(lta, fname) ; LTAfree(<a) ; } MRISfree(&mris_ico) ; MRISPfree(&mrisp_total) ; printf("mris_make_average_surface done\n"); exit(0) ; return(0) ; /* for ansi */ }
int main(int argc, char *argv[]) { char **av, *ltafn1, *ltafn2, *ltafn_total; LTA *lta1, *lta2, *lta_total; FILE *fo; MATRIX *r_to_i_1, *i_to_r_1, *i_to_r_2, *r_to_i_2; MATRIX *RAS_1_to_1, *RAS_2_to_2, *m_tmp; int nargs, ac; int type = 0; Progname = argv[0]; nargs = handle_version_option (argc, argv, "$Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 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 != 4) { usage(1); } ltafn1 = argv[1]; ltafn2 = argv[2]; ltafn_total = argv[3]; printf("Read individual LTAs\n"); //lta1 = ltaReadFileEx(ltafn1); TRANSFORM * trans = TransformRead(ltafn1); lta1 = (LTA *)trans->xform ; if (!lta1) { ErrorExit(ERROR_BADFILE, "%s: can't read file %s",Progname, ltafn1); } if (invert1) { VOL_GEOM vgtmp; LT *lt; MATRIX *m_tmp = lta1->xforms[0].m_L ; lta1->xforms[0].m_L = MatrixInverse(lta1->xforms[0].m_L, NULL) ; MatrixFree(&m_tmp) ; lt = <a1->xforms[0]; if (lt->dst.valid == 0 || lt->src.valid == 0) { fprintf (stderr, "WARNING:********************************************************\n"); fprintf (stderr, "WARNING:dst or src volume is invalid. Inverse likely wrong.\n"); fprintf (stderr, "WARNING:********************************************************\n"); } copyVolGeom(<->dst, &vgtmp); copyVolGeom(<->src, <->dst); copyVolGeom(&vgtmp, <->src); } if (strcmp(ltafn2,"identity.nofile") == 0) { type = TransformFileNameType(ltafn_total); if (type == MNI_TRANSFORM_TYPE) { ltaMNIwrite(lta1, ltafn_total); } else { //change type to VOXEL_VOXEL if (lta1->type != out_type) { LTAchangeType(lta1, out_type); } printf("Writing LTA to file %s...\n", ltafn_total); fo = fopen(ltafn_total,"w"); if (fo==NULL) ErrorExit(ERROR_BADFILE, "%s: can't create file %s",Progname, ltafn_total); LTAprint(fo, lta1); fclose(fo); } LTAfree(<a1); printf("%s successful.\n", Progname); return 0; } type = TransformFileNameType(ltafn2); if (type == MNI_TRANSFORM_TYPE) { if (invert2 != 0) ErrorExit (ERROR_BADFILE, "%s: LTA2 is talairach.xfm, and shouldn't be inverted ", Progname); lta2 = ltaMNIreadEx(ltafn2) ; //the talairach xform is supposed to be linear_RAS_TO_RAS, right? Yes lta2->type = LINEAR_RAS_TO_RAS; if (tal_src_file == 0 && lta2->xforms[0].src.valid == 0) ErrorExit (ERROR_BADFILE, "%s: pls use -tal option to give talairach src and " "template filenames",Progname); if (tal_dst_file == 0 && lta2->xforms[0].dst.valid == 0) ErrorExit (ERROR_BADFILE, "%s: pls use -tal option to give talairach src and " "template filenames",Progname); if (tal_src_file != 0) { LTAmodifySrcDstGeom(lta2, tal_src, NULL); // add src and dst information } if (tal_dst_file != 0) { LTAmodifySrcDstGeom(lta2, NULL, tal_dst); // add src and dst information } } else { TRANSFORM * trans = TransformRead(ltafn2); lta2 = (LTA *)trans->xform ; //lta2 = ltaReadFileEx(ltafn2); } if (!lta2) { ErrorExit(ERROR_BADFILE, "%s: can't read file %s",Progname, ltafn2); } if (invert2) { VOL_GEOM vgtmp; LT *lt; MATRIX *m_tmp = lta2->xforms[0].m_L ; lta2->xforms[0].m_L = MatrixInverse(lta2->xforms[0].m_L, NULL) ; MatrixFree(&m_tmp) ; lt = <a2->xforms[0]; if (lt->dst.valid == 0 || lt->src.valid == 0) { fprintf (stderr, "WARNING:********************************************************\n"); fprintf (stderr, "WARNING:dst or src volume is invalid. Inverse likely wrong.\n"); fprintf (stderr, "WARNING:********************************************************\n"); } copyVolGeom(<->dst, &vgtmp); copyVolGeom(<->src, <->dst); copyVolGeom(&vgtmp, <->src); } if (vg_isEqual(<a1->xforms[0].dst, <a2->xforms[0].src) == 0) { /* ErrorExit(ERROR_BADFILE, "%s: dst volume of lta1 doesn't match src volume of lta2",Progname);*/ printf("Warning: dst volume of lta1 doesn't match src volume of lta2\n"); printf("Volume geometry for lta1-dst: \n"); vg_print(<a1->xforms[0].dst); printf("Volume geometry for lta2-src:\n"); vg_print(<a2->xforms[0].src); } printf("Combining the two LTAs to get a RAS-to-RAS from src " "of LTA1 to dst of LTA2...\n"); if (lta1->type == LINEAR_RAS_TO_RAS) { RAS_1_to_1 = MatrixCopy(lta1->xforms[0].m_L, NULL); } else if (lta1->type == LINEAR_VOX_TO_VOX) { r_to_i_1 = vg_r_to_i(<a1->xforms[0].src); i_to_r_1 = vg_i_to_r(<a1->xforms[0].dst); if (!r_to_i_1 || !i_to_r_1) ErrorExit(ERROR_BADFILE, "%s: failed to convert LTA1 to RAS_to_RAS",Progname); m_tmp = MatrixMultiply(lta1->xforms[0].m_L, r_to_i_1, NULL); RAS_1_to_1 = MatrixMultiply(i_to_r_1, m_tmp, NULL); MatrixFree(&m_tmp); } else { ErrorExit(ERROR_BADFILE, "%s: unknown transform type for LTA1",Progname); } if (lta2->type == LINEAR_RAS_TO_RAS) { RAS_2_to_2 = MatrixCopy(lta2->xforms[0].m_L, NULL); } else if (lta2->type == LINEAR_VOX_TO_VOX) { r_to_i_2 = vg_r_to_i(<a2->xforms[0].src); i_to_r_2 = vg_i_to_r(<a2->xforms[0].dst); if (!r_to_i_2 || !i_to_r_2) ErrorExit(ERROR_BADFILE, "%s: failed to convert LTA1 to RAS_to_RAS",Progname); m_tmp = MatrixMultiply(lta2->xforms[0].m_L, r_to_i_2, NULL); RAS_2_to_2 = MatrixMultiply(i_to_r_2, m_tmp, NULL); MatrixFree(&m_tmp); } else { ErrorExit(ERROR_BADFILE, "%s: unknown transform type for LTA1",Progname); } lta_total = LTAalloc(1, NULL); lta_total->type = LINEAR_RAS_TO_RAS; MatrixMultiply(RAS_2_to_2, RAS_1_to_1, lta_total->xforms[0].m_L); lta_total->xforms[0].src = lta1->xforms[0].src; lta_total->xforms[0].dst = lta2->xforms[0].dst; lta_total->xforms[0].x0 = 0; lta_total->xforms[0].y0 = 0; lta_total->xforms[0].z0 = 0; lta_total->xforms[0].sigma = 1.0f; type = TransformFileNameType(ltafn_total); if (type == MNI_TRANSFORM_TYPE) { ltaMNIwrite(lta_total, ltafn_total); } else { //change type to VOXEL_VOXEL if (lta_total->type != out_type) { LTAchangeType(lta_total, out_type); } printf("Writing combined LTA to file %s...\n", ltafn_total); fo = fopen(ltafn_total,"w"); if (fo==NULL) ErrorExit(ERROR_BADFILE, "%s: can't create file %s",Progname, ltafn_total); LTAprint(fo, lta_total); fclose(fo); } LTAfree(<a1); LTAfree(<a2); LTAfree(<a_total); MatrixFree(&RAS_1_to_1); MatrixFree(&RAS_2_to_2); if (tal_src) { MRIfree(&tal_src); } if (tal_dst) { MRIfree(&tal_dst); } printf("%s successful.\n", Progname); return(0); } /* end main() */
static LTA *ltaMNIreadEx(const char *fname) { LTA *lta = 0; LINEAR_TRANSFORM *lt ; char *cp, line[1000], infoline[1024], infoline2[1024]; FILE *fp ; int row ; MATRIX *m_L ; int no_volinfo = 0; fp = fopen(fname, "r") ; if (!fp) ErrorReturn(NULL, (ERROR_NOFILE, "ltMNIreadEx: could not open file %s",fname)); lta = LTAalloc(1, NULL) ; lt = <a->xforms[0] ; lt->sigma = 1.0f ; lt->x0 = lt->y0 = lt->z0 = 0 ; fgetl(line, 900, fp) ; /* MNI Transform File */ if (strncmp("MNI Transform File", line, 18)) ErrorReturn(NULL, (ERROR_NOFILE, "ltMNIreadEx:%s does not start as 'MNI Transform File'", fname)); fgetl(line, 900, fp) ; /* fileinfo line */ if (line[0] == '%') { strcpy(infoline, line); } else { no_volinfo = 1; if (!strncmp("Transform_Type", line, 14)) { fgetl(line,900,fp); goto get_transform; } } // second line in % fgetl(line, 900, fp); if (line[0] == '%') { strcpy(infoline2, line); while (line[0] == '%') { fgetl(line, 900, fp) ; /* variable # of comments */ } fgetl(line, 900, fp) ; if (!strncmp("Transform_Type", line, 14)) { fgetl(line,900,fp); goto get_transform; } } else { if (!strncmp("Transform_Type", line, 14)) { fgetl(line, 900, fp); goto get_transform; } while (line[0] == '%') { fgetl(line, 900, fp) ; /* variable # of comments */ } } get_transform: m_L = lt->m_L ; for (row = 1 ; row <= 3 ; row++) { cp = fgetl(line, 900, fp) ; if (!cp) { LTAfree(<a) ; ErrorReturn (NULL, (ERROR_BADFILE, "ltMNIreadEx: could not read row %d from %s (%s)", row, fname, line)) ; } sscanf(cp, "%f %f %f %f", MATRIX_RELT(m_L,row,1), MATRIX_RELT(m_L,row,2), MATRIX_RELT(m_L,row,3), MATRIX_RELT(m_L,row,4)) ; } if (!lta) { fclose(fp); return NULL; } fclose(fp); // add original src and dst information if (no_volinfo == 0) mincGetVolInfo(infoline, infoline2, <a->xforms[0].src, <a->xforms[0].dst); lta->type = LINEAR_RAS_TO_RAS; return lta; }
/* ---------------------------------------------------------- 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; 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; char *fslfn, *ltafn; MRI *mri_src, *mri_tgt; int ac, nargs; LTA *mylta = 0; FILE *fo; VOL_GEOM srcG, dstG; MATRIX *invTgt, *Dsrc, *V_to_V; Progname = argv[0]; nargs = handle_version_option (argc, argv, "$Id: mri_fslmat_to_lta.c,v 1.3 2011/03/02 00:04:15 nicks Exp $", "$Name: $"); 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 != 5) usage(1); printf("Read source volume file %s\n", argv[1]); mri_src = MRIread(argv[1]) ; if (!mri_src) ErrorExit(ERROR_BADPARM, "%s: could not read source volume %s", Progname, argv[1]) ; printf("Read destination volume file %s\n", argv[2]); mri_tgt = MRIread(argv[2]) ; if (!mri_tgt) ErrorExit(ERROR_BADPARM, "%s: could not read label volume %s", Progname, argv[2]) ; fslfn = argv[3]; ltafn = argv[4]; printf("Read fsl transformation from file %s\n", fslfn); mylta = ltaFSLread(fslfn); getVolGeom(mri_src, &srcG); getVolGeom(mri_tgt, &dstG); if (invert_flag) { mylta->xforms[0].src = dstG; mylta->xforms[0].dst = srcG; } else { mylta->xforms[0].src = srcG; mylta->xforms[0].dst = dstG; } invTgt = MatrixAlloc(4,4,MATRIX_REAL); invTgt->rptr[1][1] = 1.0/dstG.xsize; invTgt->rptr[2][2] = 1.0/dstG.ysize; invTgt->rptr[3][3] = 1.0/dstG.zsize; invTgt->rptr[4][4] = 1.0; Dsrc = MatrixAlloc(4,4,MATRIX_REAL); Dsrc->rptr[1][1] = srcG.xsize; Dsrc->rptr[2][2] = srcG.ysize; Dsrc->rptr[3][3] = srcG.zsize; Dsrc->rptr[4][4] = 1.0; V_to_V = MatrixMultiply(invTgt, mylta->xforms[0].m_L, NULL); V_to_V = MatrixMultiply(V_to_V, Dsrc, V_to_V); if (invert_flag) { mylta->xforms[0].m_L = MatrixInverse(V_to_V, mylta->xforms[0].m_L); } else { mylta->xforms[0].m_L = MatrixCopy(V_to_V, mylta->xforms[0].m_L); } if (!mylta) { MRIfree(&mri_src); MRIfree(&mri_tgt); ErrorExit(ERROR_BADFILE, "%s: can't read in transformation",Progname); } printf("Write transformation to lta file %s\n", ltafn); fo = fopen(ltafn,"w"); if (fo==NULL) ErrorExit(ERROR_BADFILE, "%s: can't create file %s",Progname, ltafn); LTAprint(fo, mylta); fclose(fo); MRIfree(&mri_src); MRIfree(&mri_tgt); LTAfree(&mylta); MatrixFree(&invTgt); MatrixFree(&Dsrc); MatrixFree(&V_to_V); return(0); } /* end main() */
int main(int argc, char *argv[]) { char **av, *cp ; int ac, nargs, i, dof, no_transform, which, sno = 0, nsubjects = 0 ; MRI *mri=0, *mri_mean = NULL, *mri_std=0, *mri_T1=0,*mri_binary=0,*mri_dof=NULL, *mri_priors = NULL ; char *subject_name, *out_fname, fname[STRLEN] ; /* LTA *lta;*/ MRI *mri_tmp=0 ; /* rkt: check for and handle version tag */ nargs = handle_version_option (argc, argv, "$Id: mri_make_template.c,v 1.26 2011/03/02 00:04:22 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 (!strlen(subjects_dir)) { cp = getenv("SUBJECTS_DIR") ; if (!cp) ErrorExit(ERROR_BADPARM,"%s: SUBJECTS_DIR not defined in environment.\n", Progname) ; strcpy(subjects_dir, cp) ; } if (argc < 3) usage_exit(1) ; out_fname = argv[argc-1] ; no_transform = first_transform ; if (binary_name) /* generate binarized volume with priors and */ { /* separate means and variances */ for (which = BUILD_PRIORS ; which <= OFF_STATS ; which++) { /* for each subject specified on cmd line */ for (dof = 0, i = 1 ; i < argc-1 ; i++) { if (*argv[i] == '-') /* don't do transform for next subject */ { no_transform = 1 ; continue ; } dof++ ; subject_name = argv[i] ; if (which != BUILD_PRIORS) { sprintf(fname, "%s/%s/mri/%s", subjects_dir, subject_name, T1_name); fprintf(stderr, "%d of %d: reading %s...\n", i, argc-2, fname) ; mri_T1 = MRIread(fname) ; if (!mri_T1) ErrorExit(ERROR_NOFILE,"%s: could not open volume %s", Progname,fname); } sprintf(fname, "%s/%s/mri/%s",subjects_dir,subject_name,binary_name); fprintf(stderr, "%d of %d: reading %s...\n", i, argc-2, fname) ; mri_binary = MRIread(fname) ; if (!mri_binary) ErrorExit(ERROR_NOFILE,"%s: could not open volume %s", Progname,fname); /* only count voxels which are mostly labeled */ MRIbinarize(mri_binary, mri_binary, WM_MIN_VAL, 0, 100) ; if (transform_fname && no_transform-- <= 0) { sprintf(fname, "%s/%s/mri/transforms/%s", subjects_dir, subject_name, transform_fname) ; fprintf(stderr, "reading transform %s...\n", fname) ; //////////////////////////////////////////////////////// #if 1 { TRANSFORM *transform ; transform = TransformRead(fname) ; if (transform == NULL) ErrorExit(ERROR_NOFILE, "%s: could not open transform file %s\n",Progname, fname) ; mri_tmp = TransformApply(transform, mri_T1, NULL) ; TransformFree(&transform) ; } #else lta = LTAreadEx(fname); if (lta == NULL) ErrorExit(ERROR_NOFILE, "%s: could not open transform file %s\n", Progname, fname) ; /* LTAtransform() runs either MRIapplyRASlinearTransform() for RAS2RAS or MRIlinearTransform() for Vox2Vox. */ /* MRIlinearTransform() calls MRIlinearTransformInterp() */ mri_tmp = LTAtransform(mri_T1, NULL, lta); MRIfree(&mri_T1) ; mri_T1 = mri_tmp ; LTAfree(<a); lta = NULL; #endif if (DIAG_VERBOSE_ON) fprintf(stderr, "transform application complete.\n") ; } if (which == BUILD_PRIORS) { mri_priors = MRIupdatePriors(mri_binary, mri_priors) ; } else { if (!mri_mean) { mri_dof = MRIalloc(mri_T1->width, mri_T1->height, mri_T1->depth, MRI_UCHAR) ; mri_mean = MRIalloc(mri_T1->width, mri_T1->height,mri_T1->depth,MRI_FLOAT); mri_std = MRIalloc(mri_T1->width,mri_T1->height,mri_T1->depth,MRI_FLOAT); if (!mri_mean || !mri_std) ErrorExit(ERROR_NOMEMORY, "%s: could not allocate templates.\n", Progname) ; } if (DIAG_VERBOSE_ON) fprintf(stderr, "updating mean and variance estimates...\n") ; if (which == ON_STATS) { MRIaccumulateMaskedMeansAndVariances(mri_T1, mri_binary, mri_dof, 90, 100, mri_mean, mri_std) ; fprintf(stderr, "T1 = %d, binary = %d, mean = %2.1f\n", (int)MRIgetVoxVal(mri_T1, 141,100,127,0), MRIvox(mri_binary, 141,100,127), MRIFvox(mri_mean, 141,100,127)) ; } else /* computing means and vars for off */ MRIaccumulateMaskedMeansAndVariances(mri_T1, mri_binary, mri_dof, 0, WM_MIN_VAL-1, mri_mean, mri_std) ; MRIfree(&mri_T1) ; } MRIfree(&mri_binary) ; } if (which == BUILD_PRIORS) { mri = MRIcomputePriors(mri_priors, dof, NULL) ; MRIfree(&mri_priors) ; fprintf(stderr, "writing priors to %s...\n", out_fname) ; } else { MRIcomputeMaskedMeansAndStds(mri_mean, mri_std, mri_dof) ; mri_mean->dof = dof ; fprintf(stderr, "writing T1 means with %d dof to %s...\n", mri_mean->dof, out_fname) ; if (!which) MRIwrite(mri_mean, out_fname) ; else MRIappend(mri_mean, out_fname) ; MRIfree(&mri_mean) ; fprintf(stderr, "writing T1 variances to %s...\n", out_fname); if (dof <= 1) MRIreplaceValues(mri_std, mri_std, 0, 1) ; mri = mri_std ; } if (!which) MRIwrite(mri, out_fname) ; else MRIappend(mri, out_fname) ; MRIfree(&mri) ; } } else { /* for each subject specified on cmd line */ if (xform_mean_fname) { m_xform_mean = MatrixAlloc(4,4,MATRIX_REAL) ; /* m_xform_covariance = MatrixAlloc(12,12,MATRIX_REAL) ;*/ } dof = 0; for (i = 1 ; i < argc-1 ; i++) { if (*argv[i] == '-') { /* don't do transform for next subject */ no_transform = 1 ; continue ; } dof++ ; subject_name = argv[i] ; sprintf(fname, "%s/%s/mri/%s", subjects_dir, subject_name, T1_name); fprintf(stderr, "%d of %d: reading %s...\n", i, argc-2, fname) ; mri_T1 = MRIread(fname) ; if (!mri_T1) ErrorExit(ERROR_NOFILE,"%s: could not open volume %s",Progname,fname); check_mri(mri_T1) ; if (binarize) MRIbinarize(mri_T1, mri_T1, binarize, 0, 1) ; if (erode) { int i ; printf("eroding input %d times\n", erode) ; for (i = 0 ; i < erode ; i++) MRIerode(mri_T1, mri_T1) ; } if (open) { int i ; printf("opening input %d times\n", open) ; for (i = 0 ; i < open ; i++) MRIerode(mri_T1, mri_T1) ; for (i = 0 ; i < open ; i++) MRIdilate(mri_T1, mri_T1) ; } check_mri(mri_T1) ; if (transform_fname) { sprintf(fname, "%s/%s/mri/transforms/%s", subjects_dir, subject_name, transform_fname) ; fprintf(stderr, "reading transform %s...\n", fname) ; //////////////////////////////////////////////////////// #if 1 { TRANSFORM *transform ; transform = TransformRead(fname) ; if (transform == NULL) ErrorExit(ERROR_NOFILE, "%s: could not open transform file %s\n",Progname, fname) ; mri_tmp = TransformApply(transform, mri_T1, NULL) ; if (DIAG_VERBOSE_ON) MRIwrite(mri_tmp, "t1.mgz") ; TransformFree(&transform) ; } #else lta = LTAreadEx(fname); if (lta == NULL) ErrorExit(ERROR_NOFILE, "%s: could not open transform file %s\n", Progname, fname) ; printf("transform matrix -----------------------\n"); MatrixPrint(stdout,lta->xforms[0].m_L); /* LTAtransform() runs either MRIapplyRASlinearTransform() for RAS2RAS or MRIlinearTransform() for Vox2Vox. */ /* MRIlinearTransform() calls MRIlinearTransformInterp() */ mri_tmp = LTAtransform(mri_T1, NULL, lta); printf("----- -----------------------\n"); LTAfree(<a); #endif MRIfree(&mri_T1); mri_T1 = mri_tmp ; // reassign pointers if (DIAG_VERBOSE_ON) fprintf(stderr, "transform application complete.\n") ; } if (!mri_mean) { mri_mean = MRIalloc(mri_T1->width, mri_T1->height, mri_T1->depth, MRI_FLOAT) ; mri_std = MRIalloc(mri_T1->width, mri_T1->height, mri_T1->depth, MRI_FLOAT) ; if (!mri_mean || !mri_std) ErrorExit(ERROR_NOMEMORY, "%s: could not allocate templates.\n", Progname) ; // if(transform_fname == NULL){ if (DIAG_VERBOSE_ON) printf("Copying geometry\n"); MRIcopyHeader(mri_T1,mri_mean); MRIcopyHeader(mri_T1,mri_std); // } } check_mri(mri_mean) ; if (!stats_only) { if (DIAG_VERBOSE_ON) fprintf(stderr, "updating mean and variance estimates...\n") ; MRIaccumulateMeansAndVariances(mri_T1, mri_mean, mri_std) ; } check_mri(mri_mean) ; if (DIAG_VERBOSE_ON) MRIwrite(mri_mean, "t2.mgz") ; MRIfree(&mri_T1) ; no_transform = 0; } /* end loop over subjects */ if (xform_mean_fname) { FILE *fp ; VECTOR *v = NULL, *vT = NULL ; MATRIX *m_vvT = NULL ; int rows, cols ; nsubjects = sno ; fp = fopen(xform_covariance_fname, "w") ; if (!fp) ErrorExit(ERROR_NOFILE, "%s: could not open covariance file %s", Progname, xform_covariance_fname) ; fprintf(fp, "nsubjects=%d\n", nsubjects) ; MatrixScalarMul(m_xform_mean, 1.0/(double)nsubjects, m_xform_mean) ; printf("means:\n") ; MatrixPrint(stdout, m_xform_mean) ; MatrixAsciiWrite(xform_mean_fname, m_xform_mean) ; /* subtract the mean from each transform */ rows = m_xform_mean->rows ; cols = m_xform_mean->cols ; for (sno = 0 ; sno < nsubjects ; sno++) { MatrixSubtract(m_xforms[sno], m_xform_mean, m_xforms[sno]) ; v = MatrixReshape(m_xforms[sno], v, rows*cols, 1) ; vT = MatrixTranspose(v, vT) ; m_vvT = MatrixMultiply(v, vT, m_vvT) ; if (!m_xform_covariance) m_xform_covariance = MatrixAlloc(m_vvT->rows, m_vvT->cols,MATRIX_REAL) ; MatrixAdd(m_vvT, m_xform_covariance, m_xform_covariance) ; MatrixAsciiWriteInto(fp, m_xforms[sno]) ; } MatrixScalarMul(m_xform_covariance, 1.0/(double)nsubjects, m_xform_covariance) ; printf("covariance:\n") ; MatrixPrint(stdout, m_xform_covariance) ; MatrixAsciiWriteInto(fp, m_xform_covariance) ; fclose(fp) ; if (stats_only) exit(0) ; } MRIcomputeMeansAndStds(mri_mean, mri_std, dof) ; check_mri(mri_mean) ; check_mri(mri_std) ; mri_mean->dof = dof ; if (smooth) { MRI *mri_kernel, *mri_smooth ; printf("applying smoothing kernel\n") ; mri_kernel = MRIgaussian1d(smooth, 100) ; mri_smooth = MRIconvolveGaussian(mri_mean, NULL, mri_kernel) ; MRIfree(&mri_kernel) ; MRIfree(&mri_mean) ; mri_mean = mri_smooth ; } fprintf(stderr, "\nwriting T1 means with %d dof to %s...\n", mri_mean->dof, out_fname) ; MRIwrite(mri_mean, out_fname) ; MRIfree(&mri_mean) ; if (dof <= 1) /* can't calculate variances - set them to reasonable val */ { // src dst MRIreplaceValues(mri_std, mri_std, 0, 1) ; } if (!novar) { // mri_std contains the variance here (does it?? I don't think so -- BRF) if (!var_fname) { fprintf(stderr, "\nwriting T1 standard deviations to %s...\n", out_fname); MRIappend(mri_std, out_fname) ; } else { fprintf(stderr, "\nwriting T1 standard deviations to %s...\n", var_fname); MRIwrite(mri_std, var_fname) ; } } MRIfree(&mri_std) ; if (mri) MRIfree(&mri); } /* end if binarize */ return(0) ; }
int main(int argc, char *argv[]) { char **av; MRI *mri_src, *mri_mask, *mri_dst ; int nargs, ac, nmask; int x, y, z; float value; MRI_REGION *region; LTA *lta = 0; int transform_type; MRI *mri_tmp; nargs = handle_version_option ( argc, argv, "$Id: mri_mask.c,v 1.18 2012/12/07 22:45:50 greve 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) { printf("Incorrect number of arguments, argc = %d\n", argc); usage(1); } mri_src = MRIread(argv[1]) ; if (!mri_src) ErrorExit(ERROR_BADPARM, "%s: could not read source volume %s", Progname, argv[1]) ; mri_mask = MRIread(argv[2]) ; if (!mri_mask) ErrorExit(ERROR_BADPARM, "%s: could not read mask volume %s", Progname, argv[2]) ; if(mri_src->width != mri_mask->width) { printf("ERROR: dimension mismatch between source and mask\n"); exit(1); } printf("DoAbs = %d\n",DoAbs); /* Read LTA transform and apply it to mri_mask */ if (xform_fname != NULL) { printf("Apply the given LTA xfrom to the mask volume\n"); // 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); } 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) { VOL_GEOM vgtmp; LT *lt; MATRIX *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 information is invalid. " "Most likely produced wrong inverse.\n"); fprintf(stderr, "WARNING:**************************************" "*************************\n"); } copyVolGeom(<->dst, &vgtmp); copyVolGeom(<->src, <->dst); copyVolGeom(&vgtmp, <->src); } // LTAchangeType(lta, LINEAR_VOX_TO_VOX); mri_tmp = MRIalloc(mri_src->width, mri_src->height, mri_src->depth, mri_mask->type) ; MRIcopyHeader(mri_src, mri_tmp) ; mri_tmp = LTAtransformInterp(mri_mask, mri_tmp, lta, InterpMethod); // mri_tmp = //MRIlinearTransformInterp // ( // mri_mask, mri_tmp, lta->xforms[0].m_L, InterpMethod // ); MRIfree(&mri_mask); mri_mask = mri_tmp; if (lta_src) { MRIfree(<a_src); } if (lta_dst) { MRIfree(<a_dst); } if (lta) { LTAfree(<a); } } /* if (xform_fname != NULL) */ // Threshold mask nmask = 0; for (z = 0 ; z <mri_mask->depth ; z++) { for (y = 0 ; y < mri_mask->height ; y++) { for (x = 0 ; x < mri_mask->width ; x++) { value = MRIgetVoxVal(mri_mask, x, y, z, 0); if(DoAbs) { value = fabs(value); } if(value <= threshold) { MRIsetVoxVal(mri_mask,x,y,z,0,0); } else { nmask ++; } } } } printf("Found %d voxels in mask (pct=%6.2f)\n",nmask, 100.0*nmask/(mri_mask->width*mri_mask->height*mri_mask->depth)); if(DoBB){ printf("Computing bounding box, npad = %d\n",nPadBB); region = REGIONgetBoundingBox(mri_mask,nPadBB); REGIONprint(stdout, region); mri_tmp = MRIextractRegion(mri_mask, NULL, region); if(mri_tmp == NULL) exit(1); MRIfree(&mri_mask); mri_mask = mri_tmp; mri_tmp = MRIextractRegion(mri_src, NULL, region); if(mri_tmp == NULL) exit(1); MRIfree(&mri_src); mri_src = mri_tmp; } int mask=0; float out_val=0; if (do_transfer) { mask = (int)transfer_val; out_val = transfer_val; } mri_dst = MRImask(mri_src, mri_mask, NULL, mask, out_val) ; if (!mri_dst) { ErrorExit(Gerror, "%s: stripping failed", Progname) ; } if (keep_mask_deletion_edits) { mri_dst = MRImask(mri_dst, mri_mask, NULL, 1, 1) ; // keep voxels = 1 if (!mri_dst) ErrorExit(Gerror, "%s: stripping failed on keep_mask_deletion_edits", Progname) ; } printf("Writing masked volume to %s...", argv[3]) ; MRIwrite(mri_dst, argv[3]); printf("done.\n") ; MRIfree(&mri_src); MRIfree(&mri_mask); MRIfree(&mri_dst); exit(0); } /* end main() */