/* --------------------------------------------- */
static void dump_options(FILE *fp) {
fprintf(fp,"\n");
fprintf(fp,"%s\n",vcid);
fprintf(fp,"%s\n",Progname);
fprintf(fp,"FREESURFER_HOME %s\n",getenv("FREESURFER_HOME"));
fprintf(fp,"SUBJECTS_DIR %s\n",getenv("SUBJECTS_DIR"));
if (SUBJECTS_DIR1) fprintf(fp,"SUBJECTS_DIR1 %s\n",SUBJECTS_DIR1);
if (SUBJECTS_DIR2) fprintf(fp,"SUBJECTS_DIR2 %s\n",SUBJECTS_DIR2);
fprintf(fp, "cwd %s\n",cwd);
fprintf(fp, "cmdline %s\n",cmdline);
fprintf(fp, "timestamp %s\n",VERcurTimeStamp());
fprintf(fp, "sysname %s\n",uts.sysname);
fprintf(fp, "hostname %s\n",uts.nodename);
fprintf(fp, "machine %s\n",uts.machine);
fprintf(fp, "user %s\n",VERuser());
fprintf(fp, "surf1path %s\n",surf1path);
fprintf(fp, "surf2path %s\n",surf2path);
if (subject1) fprintf(fp,"subject1 %s\n",subject1);
if (subject2) fprintf(fp,"subject2 %s\n",subject2);
if (hemi) fprintf(fp,"hemi %s\n",hemi);
if (surfname) fprintf(fp,"surfname %s\n",surfname);
if (curvname) fprintf(fp,"curvname %s\n",curvname);
if (aparcname)fprintf(fp,"aparcname %s\n",aparcname);
if (aparc2name)fprintf(fp,"aparc2name %s\n",aparc2name);
fprintf(fp,"\n");
fprintf(fp,"\n");
return;
}
/* ------ Doxygen markup ends on the line above (this line not needed for Doxygen) -- */
static void dump_options(FILE *fp) {
fprintf(fp,"\n");
fprintf(fp,"%s\n",vcid);
fprintf(fp,"cwd %s\n",cwd);
fprintf(fp,"cmdline %s\n",cmdline);
fprintf(fp,"sysname %s\n",uts.sysname);
fprintf(fp,"hostname %s\n",uts.nodename);
fprintf(fp,"machine %s\n",uts.machine);
fprintf(fp,"user %s\n",VERuser());
return;
}
/*--------------------------------------------------------------*/
static void dump_options(FILE *fp) {
fprintf(fp,"\n");
fprintf(fp,"%s\n",vcid);
fprintf(fp,"cwd %s\n",cwd);
fprintf(fp,"cmdline %s\n",cmdline);
fprintf(fp,"sysname %s\n",uts.sysname);
fprintf(fp,"hostname %s\n",uts.nodename);
fprintf(fp,"machine %s\n",uts.machine);
fprintf(fp,"user %s\n",VERuser());
fprintf(fp,"srcvalfile %s\n",SrcValFile);
fprintf(fp,"trgvalfile %s\n",TrgValFile);
fprintf(fp,"nsurfs %d\n",nsurfs);
fprintf(fp,"jac %d\n",DoJac);
fprintf(fp,"revmap %d\n",ReverseMapFlag);
return;
}
/* --------------------------------------------- */
static void dump_options(FILE *fp) {
fprintf(fp,"\n");
fprintf(fp,"%s\n",vcid);
fprintf(fp,"%s\n",Progname);
fprintf(fp,"FREESURFER_HOME %s\n",getenv("FREESURFER_HOME"));
fprintf(fp,"cwd %s\n",cwd);
fprintf(fp,"cmdline %s\n",cmdline);
fprintf(fp,"timestamp %s\n",VERcurTimeStamp());
fprintf(fp,"sysname %s\n",uts.sysname);
fprintf(fp,"hostname %s\n",uts.nodename);
fprintf(fp,"machine %s\n",uts.machine);
fprintf(fp,"user %s\n",VERuser());
fprintf(fp,"input %s\n",inpath);
fprintf(fp,"synth %d\n",synth);
if (Xfile) fprintf(fp,"xfile %s\n",Xfile);
if (DetrendOrder >= 0) fprintf(fp,"detrend %d\n",DetrendOrder);
fprintf(fp,"infwhm %lf\n",infwhm);
fprintf(fp,"ingstd %lf\n",ingstd);
fprintf(fp,"tofwhm %lf\n",tofwhm);
if (tofwhm > 0) {
fprintf(fp,"byfwhm-tofwhm %lf\n",byfwhm);
fprintf(fp,"tofwhm-tol %lf\n",tofwhmtol);
fprintf(fp,"tofwhm-niters %d\n",tofwhmniters);
fprintf(fp,"tofwhm-niters-max %d\n",tofwhmnitersmax);
}
if (maskpath) fprintf(fp,"mask %s\n",maskpath);
if (automask) fprintf(fp,"automaskthresh %g\n",automaskthresh);
if (mask) {
fprintf(fp,"maskthresh %g\n",maskthresh);
fprintf(fp,"maskinv %d\n",maskinv);
fprintf(fp,"nerode %d\n",nerode);
}
if (outmaskpath) {
fprintf(fp,"outmask %s\n",outmaskpath);
fprintf(fp,"SaveDetrended %d\n",SaveDetrended);
fprintf(fp,"SaveUnmasked %d\n",SaveUnmasked);
}
if (synth) {
fprintf(fp,"synth-frames %d\n",nframes);
fprintf(fp,"seed %d\n",SynthSeed);
}
if (outpath) fprintf(fp,"out %s\n",outpath);
return;
}
/* --------------------------------------------- */
static void dump_options(FILE *fp) {
fprintf(fp,"\n");
fprintf(fp,"%s\n",vcid);
fprintf(fp,"cwd %s\n",cwd);
fprintf(fp,"cmdline %s\n",cmdline);
fprintf(fp,"sysname %s\n",uts.sysname);
fprintf(fp,"hostname %s\n",uts.nodename);
fprintf(fp,"machine %s\n",uts.machine);
fprintf(fp,"user %s\n",VERuser());
fprintf(fp,"OutTop %s\n",OutTop);
fprintf(fp,"CSDBase %s\n",csdbase);
fprintf(fp,"nreps %d\n",nRepetitions);
fprintf(fp,"subject %s\n",subject);
fprintf(fp,"hemi %s\n",hemi);
if(MaskFile) fprintf(fp,"mask %s\n",MaskFile);
fprintf(fp,"UseAvgVtxArea %d\n",UseAvgVtxArea);
fprintf(fp,"SaveFile %s\n",SaveFile);
fprintf(fp,"StopFile %s\n",StopFile);
fflush(fp);
return;
}
/* --------------------------------------------- */
static void dump_options(FILE *fp) {
fprintf(fp,"\n");
fprintf(fp,"%s\n",vcid);
fprintf(fp,"cwd %s\n",cwd);
fprintf(fp,"cmdline %s\n",cmdline);
fprintf(fp,"sysname %s\n",uts.sysname);
fprintf(fp,"hostname %s\n",uts.nodename);
fprintf(fp,"machine %s\n",uts.machine);
fprintf(fp,"user %s\n",VERuser());
fprintf(fp,"\n");
fprintf(fp,"subject %s\n",subject);
fprintf(fp,"hemi %s\n",hemi);
fprintf(fp,"SUBJECTS_DIR %s\n",SUBJECTS_DIR);
fprintf(fp,"ColorTable %s\n",CTabFile);
if(AnnotName) fprintf(fp,"AnnotName %s\n",AnnotName);
if(AnnotPath) fprintf(fp,"AnnotPath %s\n",AnnotPath);
if (NHitsFile) fprintf(fp,"NHitsFile %s\n",NHitsFile);
fprintf(fp,"nlables %d\n",nlabels);
fprintf(fp,"LabelThresh %d %lf\n",DoLabelThresh,LabelThresh);
return;
}
/*---------------------------------------------------------------*/
int main(int argc, char **argv) {
SDCMFILEINFO **sdfi_list;
SDCMFILEINFO *sdfi=NULL;
int nlist;
int NRuns;
int nthfile;
char *fname, *psname, *protoname;
int PrevRunNo;
Progname = argv[0] ;
argc --;
argv++;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
if (argc == 0) usage_exit();
cmdline = argv2cmdline(argc,argv);
parse_commandline(argc, argv);
check_options();
uname(&uts);
getcwd(cwd,2000);
fprintf(stdout,"%s\n",vcid);
fprintf(stdout,"cwd %s\n",cwd);
fprintf(stdout,"cmdline %s\n",cmdline);
fprintf(stdout,"sysname %s\n",uts.sysname);
fprintf(stdout,"hostname %s\n",uts.nodename);
fprintf(stdout,"machine %s\n",uts.machine);
fprintf(stdout,"user %s\n",VERuser());
strip_leading_slashes(sdicomdir);
/* open the output file, or set output stream to stdout */
if (outfile != NULL) {
outstream = fopen(outfile,"w");
if (outstream == NULL) {
fprintf(stderr,"ERROR: could not open %s for writing\n",outfile);
exit(1);
}
} else outstream = stdout;
/* Get all the Siemens DICOM files from this directory */
fprintf(stderr,"INFO: scanning path to Siemens DICOM DIR:\n %s\n",
sdicomdir);
sdfi_list = ScanSiemensDCMDir(sdicomdir, &nlist);
if (sdfi_list == NULL) {
fprintf(stderr,"ERROR: scanning directory %s\n",sdicomdir);
exit(1);
}
printf("INFO: found %d Siemens files\n",nlist);
printf("%s\n",sdfi_list[0]->NumarisVer);
tmpstring = sdcmExtractNumarisVer(sdfi_list[0]->NumarisVer, &Maj, &Min, &MinMin);
if (tmpstring == NULL) free(tmpstring);
else {
if ((Min == 1 && MinMin <= 6) && Maj < 4) {
// This should only be run for pretty old data. I've lost
// track as to which versions should do this. With Maj<4,
// I'm pretty sure that this section of code will never
// be run. It might need to be run with version 4VA16
// and earlier. Note: this same code is in DICOMRead.c
printf("Computing TR with number of slices\n");
TRSlice = 1;
}
}
/* Sort the files by Series, Slice Position, and Image Number */
printf("Sorting\n");
fflush(stdout);
fflush(stderr);
SortSDCMFileInfo(sdfi_list,nlist);
/* Assign run numbers to each file (count number of runs)*/
if (sortbyrun) {
fprintf(stderr,"Assigning Run Numbers\n");
fflush(stderr);
NRuns = sdfiAssignRunNo2(sdfi_list, nlist);
if (NRuns == 0) {
fprintf(stderr,"ERROR: sorting runs\n");
fflush(stderr);
exit(1);
}
}
PrevRunNo = -1;
for (nthfile = 0; nthfile < nlist; nthfile++) {
sdfi = sdfi_list[nthfile];
if (summarize && PrevRunNo == sdfi->RunNo) continue;
PrevRunNo = sdfi->RunNo;
sdfi->RepetitionTime /= 1000.0;
// Old version of Siemens software had reptime as time between
// slices. New has reptime as time between volumes.
// Code (above) looks at version and does the right thing.
if (sdfi->IsMosaic && TRSlice) sdfi->RepetitionTime *= sdfi->VolDim[2];
fname = fio_basename(sdfi->FileName,NULL);
psname = strip_white_space(sdfi->PulseSequence);
protoname = strip_white_space(sdfi->ProtocolName);
fprintf(outstream,
"%4d %s %3d %d %4d %d %3d %3d %3d %3d %8.4f %8.4f %s\n",
nthfile+1, fname,
sdfi->SeriesNo, sdfi->ErrorFlag,
sdfi->ImageNo, sdfi->IsMosaic,
sdfi->VolDim[0], sdfi->VolDim[1], sdfi->VolDim[2], sdfi->NFrames,
sdfi->RepetitionTime, sdfi->EchoTime,
protoname);
fflush(outstream);
free(fname);
free(psname);
free(protoname);
}
while (nlist--) {
// free strings
free(sdfi_list[nlist]->FileName);
free(sdfi_list[nlist]->StudyDate);
free(sdfi_list[nlist]->StudyTime);
free(sdfi_list[nlist]->PatientName);
free(sdfi_list[nlist]->SeriesTime);
free(sdfi_list[nlist]->AcquisitionTime);
free(sdfi_list[nlist]->ScannerModel);
free(sdfi_list[nlist]->NumarisVer);
free(sdfi_list[nlist]->PulseSequence);
free(sdfi_list[nlist]->ProtocolName);
free(sdfi_list[nlist]->PhEncDir);
//
free(sdfi_list[nlist]);
}
free(sdfi_list);
if (outfile != NULL) fclose(outstream);
fflush(stdout);
fflush(stderr);
exit(0);
return(0);
}