/*---------------------------------------------------------------*/ MRI *fMRIhsynth(MRI *res, MRI *mask, int DoTNorm) { int c,r,s,f,nvox; double val; MRI *hsynth, *tvar=NULL; double *svar, svarsum, tstdvox; // Compute temporal variance at each voxel if(DoTNorm) tvar = fMRIcovariance(res, 0, -1, mask, NULL); // Compute spatial variance at each frame svar = (double *) calloc(res->nframes,sizeof(double)); svarsum = 0; for (f=0; f < res->nframes; f++) { svar[f] = 0; nvox = 0; for (c=0; c < res->width; c++) { for (r=0; r < res->height; r++) { for (s=0; s < res->depth; s++) { if(mask && MRIgetVoxVal(mask,c,r,s,0) == 0) continue; val = MRIgetVoxVal(res,c,r,s,f); if(DoTNorm){ tstdvox = sqrt(MRIgetVoxVal(tvar,c,r,s,0)); val /= tstdvox; } svar[f] += (val*val); nvox ++; } } } svar[f] /= nvox; svarsum += svar[f]; } for (f=0; f < res->nframes; f++) svar[f] /= (svarsum/res->nframes); for (f=0; f < res->nframes; f++) printf("%2d %g\n",f,svar[f]); // Synth noise that is both spatially and temporally white and gaussian hsynth = MRIrandn(res->width, res->height, res->depth, res->nframes, 0, 1, NULL); MRIcopyHeader(res,hsynth); // Scale by frame. Noise is still independent across // space and time, but it is no longer homogeneous. for (f=0; f < res->nframes; f++) { for (c=0; c < res->width; c++) { for (r=0; r < res->height; r++) { for (s=0; s < res->depth; s++) { if(mask && MRIgetVoxVal(mask,c,r,s,0) == 0) { MRIsetVoxVal(hsynth,c,r,s,f,0); continue; } val = MRIgetVoxVal(hsynth,c,r,s,f); val *= sqrt(svar[f]); MRIsetVoxVal(hsynth,c,r,s,f,val); } } } } free(svar); if(DoTNorm) MRIfree(&tvar); return(hsynth); }
/*--------------------------------------------------*/ 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); }