/* --------------------------------------------- */
static int parse_commandline(int argc, char **argv) {
int nargc , nargsused;
char **pargv, *option ;
if (argc < 1) usage_exit();
nargc = argc;
pargv = argv;
while (nargc > 0) {
option = pargv[0];
if (debug) printf("%d %s\n",nargc,option);
nargc -= 1;
pargv += 1;
nargsused = 0;
if (!strcasecmp(option, "--help")) print_help() ;
else if (!strcasecmp(option, "--version")) print_version() ;
else if (!strcasecmp(option, "--debug")) debug = 1;
else if (!strcasecmp(option, "--checkopts")) checkoptsonly = 1;
else if (!strcasecmp(option, "--nocheckopts")) checkoptsonly = 0;
else if (!strcasecmp(option, "--allow-res")) AllowResolution = 1;
else if (!strcasecmp(option, "--allow-prec")) AllowPrecision = 1;
else if (!strcasecmp(option, "--allow-vox2ras")) AllowVox2RAS = 1;
else if (!strcmp(option, "--v1")) {
if (nargc < 1) CMDargNErr(option,1);
vol1File = fio_fullpath(pargv[0]);
nargsused = 1;
} else if (!strcmp(option, "--v2")) {
if (nargc < 1) CMDargNErr(option,1);
vol2File = fio_fullpath(pargv[0]);
nargsused = 1;
} else if (!strcmp(option, "--pix")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%lf",&pixdiff_thresh);
nargsused = 1;
} else if (!strcmp(option, "--vox2ras")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%lf",&vox2ras_thresh);
nargsused = 1;
} else {
fprintf(stderr,"ERROR: Option %s unknown\n",option);
if (CMDsingleDash(option))
fprintf(stderr," Did you really mean -%s ?\n",option);
exit(1);
}
nargc -= nargsused;
pargv += nargsused;
}
return(0);
}
/* ------ Doxygen markup ends on the line above ---- */
static int parse_commandline(int argc, char **argv) {
int nargc , nargsused;
char **pargv, *option ;
return(NO_ERROR) ;
if (argc < 1) usage_exit();
nargc = argc;
pargv = argv;
while (nargc > 0) {
option = pargv[0];
if (debug) printf("%d %s\n",nargc,option);
nargc -= 1;
pargv += 1;
nargsused = 0;
if (!strcasecmp(option, "--help")) print_help() ;
else if (!strcasecmp(option, "--version")) print_version() ;
else if (!strcasecmp(option, "--debug")) debug = 1;
else if (!strcasecmp(option, "--checkopts")) checkoptsonly = 1;
else if (!strcasecmp(option, "--nocheckopts")) checkoptsonly = 0;
else if (!strcasecmp(option, "--temp-vol")) {
if (nargc < 1) CMDargNErr(option,1);
TempVolFile = pargv[0];
nargsused = 1;
} else {
fprintf(stderr,"ERROR: Option %s unknown\n",option);
if (CMDsingleDash(option))
fprintf(stderr," Did you really mean -%s ?\n",option);
exit(-1);
}
nargc -= nargsused;
pargv += nargsused;
}
return(0);
}
/* --------------------------------------------- */
static int parse_commandline(int argc, char **argv) {
int nargc , nargsused;
char **pargv, *option ;
double fwhm;
if (argc < 1) usage_exit();
nargc = argc;
pargv = argv;
while (nargc > 0) {
option = pargv[0];
if (debug) printf("%d %s\n",nargc,option);
nargc -= 1;
pargv += 1;
nargsused = 0;
if (!strcasecmp(option, "--help")) print_help() ;
else if (!strcasecmp(option, "--version")) print_version() ;
else if (!strcasecmp(option, "--debug")) debug = 1;
else if (!strcasecmp(option, "--checkopts")) checkoptsonly = 1;
else if (!strcasecmp(option, "--nocheckopts")) checkoptsonly = 0;
else if (!strcasecmp(option, "--test")){
double fwhm;
nFWHMList = 0;
for(fwhm = 3; fwhm <= 6; fwhm++){
FWHMList[nFWHMList] = fwhm;
nFWHMList++;
}
nThreshList = 2;
ThreshList[0] = 2.0;
ThreshList[1] = 3.0;
nSignList = 2;
subject = "fsaverage5";
hemi = "lh";
nRepetitions = 2;
csdbase = "junk";
SynthSeed = 53;
}
else if (!strcasecmp(option, "--o")) {
if(nargc < 1) CMDargNErr(option,1);
OutTop = pargv[0];
nargsused = 1;
}
else if (!strcasecmp(option, "--done")) {
if(nargc < 1) CMDargNErr(option,1);
DoneFile = pargv[0];
nargsused = 1;
}
else if (!strcasecmp(option, "--log")) {
if(nargc < 1) CMDargNErr(option,1);
LogFile = pargv[0];
nargsused = 1;
}
else if (!strcasecmp(option, "--stop")) {
if(nargc < 1) CMDargNErr(option,1);
StopFile = pargv[0];
nargsused = 1;
}
else if (!strcasecmp(option, "--save")) {
if(nargc < 1) CMDargNErr(option,1);
SaveFile = pargv[0];
nargsused = 1;
}
else if (!strcasecmp(option, "--save-iter")) {
SaveEachIter = 1;
}
else if (!strcasecmp(option, "--no-save-iter")) {
SaveEachIter = 0;
}
else if (!strcasecmp(option, "--base")) {
if(nargc < 1) CMDargNErr(option,1);
csdbase = pargv[0];
nargsused = 1;
}
else if (!strcasecmp(option, "--surf") ||
!strcasecmp(option, "--surface")) {
if(nargc < 2) CMDargNErr(option,1);
subject = pargv[0];
hemi = pargv[1];
nargsused = 2;
}
else if (!strcasecmp(option, "--surfname")) {
if(nargc < 1) CMDargNErr(option,1);
surfname = pargv[0];
nargsused = 1;
}
else if (!strcasecmp(option, "--avgvtxarea")) UseAvgVtxArea = 1;
else if (!strcasecmp(option, "--no-avgvtxarea")) UseAvgVtxArea = 0;
else if (!strcasecmp(option, "--seed")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%d",&SynthSeed);
nargsused = 1;
}
else if (!strcasecmp(option, "--mask")) {
if(nargc < 1) CMDargNErr(option,1);
MaskFile = pargv[0];
LabelFile = NULL;
nargsused = 2;
}
else if (!strcasecmp(option, "--label")) {
if(nargc < 1) CMDargNErr(option,1);
LabelFile = pargv[0];
MaskFile = NULL;
nargsused = 1;
}
else if (!strcasecmp(option, "--no-label")) {
LabelFile = NULL;
}
else if (!strcasecmp(option, "--no-save-mask")) SaveMask = 0;
else if (!strcasecmp(option, "--nreps")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%d",&nRepetitions);
nargsused = 1;
}
else if (!strcasecmp(option, "--fwhm")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%lf",&fwhm);
FWHMList[nFWHMList] = fwhm;
nFWHMList++;
nargsused = 1;
}
else {
fprintf(stderr,"ERROR: Option %s unknown\n",option);
if (CMDsingleDash(option))
fprintf(stderr," Did you really mean -%s ?\n",option);
exit(-1);
}
nargc -= nargsused;
pargv += nargsused;
}
return(0);
}
/* --------------------------------------------- */
static int parse_commandline(int argc, char **argv) {
int nargc , nargsused;
char **pargv, *option ;
if (argc < 1) usage_exit();
nargc = argc;
pargv = argv;
while (nargc > 0) {
option = pargv[0];
if (debug) printf("%d %s\n",nargc,option);
nargc -= 1;
pargv += 1;
nargsused = 0;
if (!strcasecmp(option, "--help")) print_help() ;
else if (!strcasecmp(option, "--version")) print_version() ;
else if (!strcasecmp(option, "--debug")) debug = 1;
else if (!strcasecmp(option, "--checkopts")) checkoptsonly = 1;
else if (!strcasecmp(option, "--nocheckopts")) checkoptsonly = 0;
else if (!strcasecmp(option, "--synth")) synth = 1;
else if (!strcasecmp(option, "--nosynth")) synth = 0;
else if (!strcasecmp(option, "--mask-inv")) maskinv = 1;
else if (!strcasecmp(option, "--save-detrended")) SaveDetrended = 1;
else if (!strcasecmp(option, "--save-unmasked")) SaveUnmasked = 1;
else if (!strcasecmp(option, "--smooth-only")) SmoothOnly = 1;
else if (!strcasecmp(option, "--so")) SmoothOnly = 1;
else if (!strcasecmp(option, "--sqr")) DoSqr = 1;
else if (!strcasecmp(option, "--ispm")) InValsType = MRI_ANALYZE_FILE;
else if (!strcasecmp(option, "--ar2")) DoAR2 = 1;
else if (!strcasecmp(option, "--gdiag")) Gdiag_no = 1;
else if (!strcasecmp(option, "--i")) {
if (nargc < 1) CMDargNErr(option,1);
inpath = pargv[0];
nargsused = 1;
} else if (!strcasecmp(option, "--mask")) {
if (nargc < 1) CMDargNErr(option,1);
maskpath = pargv[0];
nargsused = 1;
} else if (!strcasecmp(option, "--mask-thresh")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%lf",&maskthresh);
nargsused = 1;
} else if (!strcasecmp(option, "--auto-mask")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%lf",&automaskthresh);
automask = 1;
nargsused = 1;
} else if (!strcasecmp(option, "--out-mask")) {
if (nargc < 1) CMDargNErr(option,1);
outmaskpath = pargv[0];
nargsused = 1;
} else if (!strcasecmp(option, "--sum")) {
if (nargc < 1) CMDargNErr(option,1);
sumfile = pargv[0];
nargsused = 1;
} else if (!strcasecmp(option, "--dat")) {
if (nargc < 1) CMDargNErr(option,1);
datfile = pargv[0];
nargsused = 1;
} else if (!strcasecmp(option, "--fwhm")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%lf",&infwhm);
ingstd = infwhm/sqrt(log(256.0));
nargsused = 1;
} else if (!strcasecmp(option, "--fwhmc")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%lf",&infwhmc);
ingstdc = infwhmc/sqrt(log(256.0));
nargsused = 1;
} else if (!strcasecmp(option, "--fwhmr")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%lf",&infwhmr);
ingstdr = infwhmr/sqrt(log(256.0));
nargsused = 1;
} else if (!strcasecmp(option, "--fwhms")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%lf",&infwhms);
ingstds = infwhms/sqrt(log(256.0));
nargsused = 1;
} else if (!strcasecmp(option, "--gstd")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%lf",&ingstd);
infwhm = ingstd*sqrt(log(256.0));
nargsused = 1;
} else if (!strcasecmp(option, "--to-fwhm")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%lf",&tofwhm);
nargsused = 1;
} else if (!strcasecmp(option, "--to-gstd")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%lf",&togstd);
tofwhm = togstd*sqrt(log(256.0));
nargsused = 1;
} else if (!strcasecmp(option, "--to-fwhm-tol")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%lf",&tofwhmtol);
nargsused = 1;
} else if (!strcasecmp(option, "--to-fwhm-nmax")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%d",&tofwhmnitersmax);
nargsused = 1;
} else if (!strcasecmp(option, "--to-fwhm-file")) {
if (nargc < 1) CMDargNErr(option,1);
tofwhmfile = pargv[0];
nargsused = 1;
} else if (!strcasecmp(option, "--nerode")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%d",&nerode);
nargsused = 1;
} else if (!strcasecmp(option, "--nframesmin")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%d",&nframesmin);
nargsused = 1;
} else if (!strcasecmp(option, "--synth-frames")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%d",&nframes);
synth = 1;
nargsused = 1;
} else if (!strcasecmp(option, "--seed")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%d",&SynthSeed);
synth = 1;
nargsused = 1;
} else if (!strcasecmp(option, "--tr")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%lf",&TR);
SetTR = 1;
nargsused = 1;
} else if (!strcasecmp(option, "--o")) {
if (nargc < 1) CMDargNErr(option,1);
outpath = pargv[0];
nargsused = 1;
} else if (!strcasecmp(option, "--ar1")) {
if (nargc < 1) CMDargNErr(option,1);
ar1path = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--sum2")) {
if (nargc < 1) CMDargNErr(option,1);
sum2file = pargv[0];
nargsused = 1;
} else if (!strcasecmp(option, "--X")) {
if (nargc < 1) CMDargNErr(option,1);
Xfile = pargv[0];
//X = MatrixReadTxt(Xfile, NULL);
X = MatlabRead(Xfile);
if (X == NULL) {
printf("ERROR: reading %s\n",Xfile);
exit(1);
}
nargsused = 1;
} else if (!strcasecmp(option, "--detrend")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%d",&DetrendOrder);
if (DetrendOrder > 2) {
printf("ERROR: cannot have detrending order > 2\n");
exit(1);
}
nargsused = 1;
} else if (!strcasecmp(option, "--in_nspmzeropad")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%d",&N_Zero_Pad_Input);
InValsType = MRI_ANALYZE_FILE;
nargsused = 1;
} else {
fprintf(stderr,"ERROR: Option %s unknown\n",option);
if (CMDsingleDash(option))
fprintf(stderr," Did you really mean -%s ?\n",option);
exit(-1);
}
nargc -= nargsused;
pargv += nargsused;
}
return(0);
}
/*------------------------------------------------------------*/
static int parse_commandline(int argc, char **argv) {
int nargc , nargsused;
char **pargv, *option ;
if (argc < 1) usage_exit();
nargc = argc;
pargv = argv;
while (nargc > 0) {
option = pargv[0];
if (debug) printf("%d %s\n",nargc,option);
nargc -= 1;
pargv += 1;
nargsused = 0;
if (!strcasecmp(option, "--help")) print_help() ;
else if (!strcasecmp(option, "--version")) print_version() ;
else if (!strcasecmp(option, "--debug")) debug = 1;
else if (!strcasecmp(option, "--checkopts")) checkoptsonly = 1;
else if (!strcasecmp(option, "--nocheckopts")) checkoptsonly = 0;
else if (!strcasecmp(option, "--norev")) ReverseMapFlag = 0;
else if (!strcasecmp(option, "--no-rev")) ReverseMapFlag = 0;
else if (!strcasecmp(option, "--nnf")) ReverseMapFlag = 0;
else if (!strcasecmp(option, "--nnfr")) ReverseMapFlag = 1;
else if (!strcasecmp(option, "--no-hash")) UseHash = 0;
else if (!strcasecmp(option, "--jac")) DoJac = 1;
else if (!strcasecmp(option, "--no-jac")) DoJac = 0;
else if (!strcasecmp(option, "--randn")) DoSynthRand = 1;
else if (!strcasecmp(option, "--ones")) DoSynthOnes = 1;
else if (!strcasecmp(option, "--src") || !strcasecmp(option, "--sval")) {
if (nargc < 1) CMDargNErr(option,1);
SrcValFile = pargv[0];
if(!fio_FileExistsReadable(SrcValFile)) {
printf("ERROR: %s does not exist or is not readable by you\n",SrcValFile);
exit(1);
}
nargsused = 1;
}
else if (!strcasecmp(option, "--trg") || !strcasecmp(option, "--tval")
|| !strcasecmp(option, "--o")) {
if (nargc < 1) CMDargNErr(option,1);
TrgValFile = pargv[0];
nargsused = 1;
}
else if (!strcasecmp(option, "--streg")) {
if (nargc < 2) CMDargNErr(option,2);
SurfRegFile[nsurfs] = pargv[0];
nsurfs++;
SurfRegFile[nsurfs] = pargv[1];
nsurfs++;
nargsused = 2;
}
else {
fprintf(stderr,"ERROR: Option %s unknown\n",option);
if (CMDsingleDash(option))
fprintf(stderr," Did you really mean -%s ?\n",option);
exit(-1);
}
nargc -= nargsused;
pargv += nargsused;
}
return(0);
}
/* --------------------------------------------- */
static int parse_commandline(int argc, char **argv) {
int nargc , nargsused;
char **pargv, *option ;
if (argc < 1) usage_exit();
nargc = argc;
pargv = argv;
while (nargc > 0) {
option = pargv[0];
if (debug) printf("%d %s\n",nargc,option);
nargc -= 1;
pargv += 1;
nargsused = 0;
if (!strcasecmp(option, "--help")) print_help() ;
else if (!strcasecmp(option, "--version")) print_version() ;
else if (!strcasecmp(option, "--debug")) debug = 1;
else if (!strcasecmp(option, "--checkopts")) checkoptsonly = 1;
else if (!strcasecmp(option, "--nocheckopts")) checkoptsonly = 0;
else if (!strcasecmp(option, "--no-check-xyz")) CheckXYZ = 0;
else if (!strcasecmp(option, "--no-check-nxyz")) CheckNXYZ = 0;
else if (!strcasecmp(option, "--ndist")) {
ComputeNormalDist = 1;
out_fname = pargv[0];
nargsused = 1;
} else if (!strcasecmp(option, "--s1")) {
if (nargc < 1) CMDargNErr(option,1);
subject1 = pargv[0];
nargsused = 1;
} else if (!strcasecmp(option, "--s2")) {
if (nargc < 1) CMDargNErr(option,1);
subject2 = pargv[0];
nargsused = 1;
} else if (!strcasecmp(option, "--sd1")) {
if (nargc < 1) CMDargNErr(option,1);
SUBJECTS_DIR1 = pargv[0];
nargsused = 1;
} else if (!strcasecmp(option, "--sd2")) {
if (nargc < 1) CMDargNErr(option,1);
SUBJECTS_DIR2 = pargv[0];
nargsused = 1;
} else if (!strcasecmp(option, "--hemi")) {
if (nargc < 1) CMDargNErr(option,1);
hemi = pargv[0];
nargsused = 1;
} else if (!strcasecmp(option, "--surf")) {
if (nargc < 1) CMDargNErr(option,1);
surfname = pargv[0];
CheckSurf=1;
nargsused = 1;
} else if (!strcasecmp(option, "--curv")) {
if (nargc < 1) CMDargNErr(option,1);
curvname = pargv[0];
CheckCurv=1;
nargsused = 1;
} else if (!strcasecmp(option, "--aparc")) {
if (nargc < 1) CMDargNErr(option,1);
aparcname = pargv[0];
CheckAParc=1;
nargsused = 1;
} else if (!strcasecmp(option, "--aparc2")) {
if (nargc < 1) CMDargNErr(option,1);
aparc2name = pargv[0];
CheckAParc=1;
nargsused = 1;
} else if (!strcasecmp(option, "--thresh")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%lf",&thresh);
nargsused = 1;
} else if (!strcasecmp(option, "--maxerrs")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%d",&MAX_NUM_ERRORS);
nargsused = 1;
} else {
if (surf1path == NULL) {
surf1path = option;
CheckSurf=1;
} else if (surf2path == NULL) surf2path = option;
else {
fprintf(stderr,"ERROR: Option %s unknown\n",option);
if (CMDsingleDash(option))
fprintf(stderr," Did you really mean -%s ?\n",option);
exit(-1);
}
}
nargc -= nargsused;
pargv += nargsused;
}
return(0);
}
/* --------------------------------------------- */
static int parse_commandline(int argc, char **argv) {
int nargc , nargsused;
char **pargv, *option ;
if (argc < 1) usage_exit();
nargc = argc;
pargv = argv;
while (nargc > 0) {
option = pargv[0];
if (debug) printf("%d %s\n",nargc,option);
nargc -= 1;
pargv += 1;
nargsused = 0;
if (!strcmp(option, "--help")) print_help() ;
else if (!strcmp(option, "--version")) print_version() ;
else if (!strcmp(option, "--debug")) debug = 1;
else if (!strcmp(option, "--checkopts")) checkoptsonly = 1;
else if (!strcmp(option, "--nocheckopts")) checkoptsonly = 0;
else if (!strcmp(option, "--no-unknown")) MapUnhitToUnknown = 0;
else if (!strcmp(option, "--ldir-default")) labeldirdefault = 1;
else if (!strcmp(option, "--noverbose")) verbose = 0;
else if (!strcmp(option, "--maxstatwinner")) maxstatwinner = 1;
else if (!strcmp(option, "--dilate-into-unknown"))
{
dilate_label_name = pargv[0] ;
printf("dilating label %s into bordering unknown vertices\n",
dilate_label_name) ;
nargsused = 1;
}
else if (!strcmp(option, "--s") || !strcmp(option, "--subject")) {
if (nargc < 1) CMDargNErr(option,1);
subject = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--h") || !strcmp(option, "--hemi")) {
if (nargc < 1) CMDargNErr(option,1);
hemi = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--ctab")) {
if (nargc < 1) CMDargNErr(option,1);
if (!fio_FileExistsReadable(pargv[0])) {
printf("ERROR: cannot find or read %s\n",pargv[0]);
exit(1);
}
CTabFile = pargv[0];
nargsused = 1;
}
else if (!strcmp(option, "--l")) {
if (nargc < 1) CMDargNErr(option,1);
if (!fio_FileExistsReadable(pargv[0])) {
printf("ERROR: cannot find or read %s\n",pargv[0]);
exit(1);
}
LabelFiles[nlabels] = pargv[0];
nlabels++;
nargsused = 1;
}
else if (!strcmp(option, "--thresh")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%lf",&LabelThresh);
DoLabelThresh = 1;
nargsused = 1;
}
else if (!strcmp(option, "--ldir")) {
if (nargc < 1) CMDargNErr(option,1);
labeldir = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--a") || !strcmp(option, "--annot")) {
if (nargc < 1) CMDargNErr(option,1);
AnnotName = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--annot-path")) {
if (nargc < 1) CMDargNErr(option,1);
AnnotPath = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--nhits")) {
if (nargc < 1) CMDargNErr(option,1);
NHitsFile = pargv[0];
nargsused = 1;
} else {
fprintf(stderr,"ERROR: Option %s unknown\n",option);
if (CMDsingleDash(option))
fprintf(stderr," Did you really mean -%s ?\n",option);
exit(-1);
}
nargc -= nargsused;
pargv += nargsused;
}
return(0);
}
/* --------------------------------------------- */
static int parse_commandline(int argc, char **argv) {
int nargc , nargsused;
char **pargv, *option ;
if (argc < 1) usage_exit();
nargc = argc;
pargv = argv;
while (nargc > 0) {
option = pargv[0];
if (debug) printf("%d %s\n",nargc,option);
nargc -= 1;
pargv += 1;
nargsused = 0;
if (!strcasecmp(option, "--help")) print_help() ;
else if (!strcasecmp(option, "--version")) print_version() ;
else if (!strcasecmp(option, "--debug")) debug = 1;
else if (!strcasecmp(option, "--checkopts")) checkoptsonly = 1;
else if (!strcasecmp(option, "--nocheckopts")) checkoptsonly = 0;
else if (!strcasecmp(option, "--no-log10")) log10flag = 0;
else if (!strcasecmp(option, "--no-strip4")) DoStrip4 = 0;
else if (!strcasecmp(option, "--stat")) {
if (nargc < 1) CMDargNErr(option,1);
statfile = pargv[0];
DoDavid = 1;
nargsused = 1;
} else if (!strcasecmp(option, "--sue")) {
if (nargc < 2) CMDargNErr(option,2);
statfile = pargv[0];
sscanf(pargv[1],"%d",&datcol1);
log10flag = 1;
DoSue = 1;
nargsused = 2;
} else if (!strcasecmp(option, "--seg")) {
if (nargc < 1) CMDargNErr(option,1);
segfile = pargv[0];
nargsused = 1;
} else if (!strcasecmp(option, "--annot")) {
if (nargc < 3) CMDargNErr(option,3);
annot = pargv[0];
subject = pargv[1];
hemi = pargv[2];
nargsused = 3;
} else if (!strcasecmp(option, "--o")) {
if (nargc < 1) CMDargNErr(option,1);
outfile = pargv[0];
nargsused = 1;
} else {
fprintf(stderr,"ERROR: Option %s unknown\n",option);
if (CMDsingleDash(option))
fprintf(stderr," Did you really mean -%s ?\n",option);
exit(-1);
}
nargc -= nargsused;
pargv += nargsused;
}
return(0);
}
/*-----------------------------------------------------------*/
static int parse_commandline(int argc, char **argv) {
int nargc , nargsused;
char **pargv, *option ;
if (argc < 1) usage_exit();
nargc = argc;
pargv = argv;
while (nargc > 0) {
option = pargv[0];
if (debug) printf("%d %s\n",nargc,option);
nargc -= 1;
pargv += 1;
nargsused = 0;
if (!strcasecmp(option, "--help")) print_help() ;
else if (!strcasecmp(option, "--version")) print_version() ;
else if (!strcasecmp(option, "--debug")) debug = 1;
else if (!strcasecmp(option, "--checkopts")) checkoptsonly = 1;
else if (!strcasecmp(option, "--nocheckopts")) checkoptsonly = 0;
else if (!strcasecmp(option, "--single")) single_path = 1;
else if (!strcasecmp(option, "--label2path")) label_to_path = 1;
else if (!strcasecmp(option, "--path2label")) path_to_label = 1;
else if (!strcasecmp(option, "--connect")){
if(nargc < 2) CMDargNErr(option,2);
connect = 1;
subject = pargv[0];
hemi = pargv[1];
nargsused = 2;
}
else if (!strcasecmp(option, "--fill")){
if(nargc < 3) CMDargNErr(option,3);
fill = 1;
subject = pargv[0];
hemi = pargv[1];
sscanf(pargv[2],"%d",&fillseed);
nargsused = 3;
}
else if (!strcasecmp(option, "--confillx")){
if(nargc < 2) CMDargNErr(option,3);
con_and_fillx = 1;
surfacefname = pargv[0];
sscanf(pargv[1],"%d",&fillseed);
nargsused = 2;
}
else if (!strcasecmp(option, "--confillxfn")){
if(nargc < 2) CMDargNErr(option,3);
con_and_fillx = 1;
surfacefname = pargv[0];
con_and_fillx_fname = pargv[1];
path_to_label = 1;
nargsused = 2;
}
else if (!strcasecmp(option, "--confill")){
if(nargc < 3) CMDargNErr(option,3);
con_and_fill = 1;
subject = pargv[0];
hemi = pargv[1];
sscanf(pargv[2],"%d",&fillseed);
nargsused = 3;
}
else if (!strcasecmp(option, "--i")){
if(nargc < 1) CMDargNErr(option,1);
source_file = pargv[0];
nargsused = 1;
}
else if (!strcasecmp(option, "--o")){
if(nargc < 1) CMDargNErr(option,1);
dest_file = pargv[0];
nargsused = 1;
}
else {
if(source_file == NULL) source_file = option;
else if(dest_file == NULL) dest_file = option;
else {
fprintf(stderr,"ERROR: Option %s unknown\n",option);
if(CMDsingleDash(option))
fprintf(stderr," Did you really mean -%s ?\n",option);
exit(-1);
}
}
nargc -= nargsused;
pargv += nargsused;
}
return(0);
}
