/* --------------------------------------------- */
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 (!strcmp(option, "--s")) {
if (nargc < 1) argnerr(option,1);
subject = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--wmseg")) {
if (nargc < 1) argnerr(option,1);
WMSegFile = pargv[0];
nargsused = 1;
} else {
fprintf(stderr,"ERROR: Option %s unknown\n",option);
if (singledash(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")||
!strcasecmp(option, "-h")||
!strcasecmp(option, "--usage")||
!strcasecmp(option, "-u"))
{
print_help() ;
}
else if (!strcasecmp(option, "--version"))
{
print_version() ;
}
else if (!strcasecmp(option, "--debug"))
{
debug = 1;
}
// This was --ribbon, but changed to --old-ribbon 4/17/08 DNG
else if (!strcasecmp(option, "--old-ribbon"))
{
UseRibbon = 1;
UseNewRibbon = 0;
}
else if (!strcasecmp(option, "--volmask") ||
!strcasecmp(option, "--new-ribbon"))
{
UseNewRibbon = 1;
}
else if (!strcasecmp(option, "--noribbon"))
{
UseRibbon = 0;
UseNewRibbon = 0;
}
else if (!strcasecmp(option, "--labelwm"))
{
LabelWM = 1;
}
else if (!strcasecmp(option, "--fix-parahipwm"))
{
FixParaHipWM = 1;
}
else if (!strcasecmp(option, "--no-fix-parahipwm"))
{
FixParaHipWM = 0;
}
else if (!strcasecmp(option, "--hypo-as-wm"))
{
LabelHypoAsWM = 1;
}
else if (!strcasecmp(option, "--rip-unknown"))
{
RipUnknown = 1;
}
else if (!strcasecmp(option, "--no-hash"))
{
UseHash = 0;
}
else if (!strcmp(option, "--sd"))
{
if (nargc < 1)
{
argnerr(option,1);
}
SUBJECTS_DIR = pargv[0];
setenv("SUBJECTS_DIR",SUBJECTS_DIR,1);
nargsused = 1;
}
else if (!strcmp(option, "--s"))
{
if (nargc < 1)
{
argnerr(option,1);
}
subject = pargv[0];
nargsused = 1;
}
else if (!strcmp(option, "--oaseg") || !strcmp(option, "--o"))
{
if (nargc < 1)
{
argnerr(option,1);
}
OutASegFile = pargv[0];
nargsused = 1;
}
else if (!strcmp(option, "--a2005s"))
{
annotname = "aparc.a2005s";
baseoffset = 100;
}
else if (!strcmp(option, "--a2009s"))
{
annotname = "aparc.a2009s";
baseoffset = 10100;
}
else if (!strcmp(option, "--annot"))
{
if (nargc < 1)
{
argnerr(option,1);
}
annotname = pargv[0];
nargsused = 1;
}
else if (!strcmp(option, "--annot-table"))
{
if (nargc < 1)
{
argnerr(option,1);
}
// annotation_table_file is declared in annotation.h
// default is $FREESURFER_HOME/Simple_surface_labels2009.txt
annotation_table_file = pargv[0];
nargsused = 1;
}
else if (!strcmp(option, "--oaparc"))
{
if (nargc < 1)
{
argnerr(option,1);
}
OutAParcFile = pargv[0];
nargsused = 1;
}
else if (!strcmp(option, "--ctxseg"))
{
if (nargc < 1)
{
argnerr(option,1);
}
CtxSegFile = pargv[0];
nargsused = 1;
}
else if (!strcmp(option, "--dist"))
{
if (nargc < 1)
{
argnerr(option,1);
}
OutDistFile = pargv[0];
nargsused = 1;
}
else if (!strcmp(option, "--hashres"))
{
if (nargc < 1)
{
argnerr(option,1);
}
sscanf(pargv[0],"%f",&hashres);
nargsused = 1;
}
else if (!strcmp(option, "--wmparc-dmax"))
{
if (nargc < 1)
{
argnerr(option,1);
}
sscanf(pargv[0],"%f",&dmaxctx);
nargsused = 1;
}
else if (!strcmp(option, "--crs-test"))
{
if (nargc < 3)
{
argnerr(option,3);
}
sscanf(pargv[0],"%d",&ctest);
sscanf(pargv[1],"%d",&rtest);
sscanf(pargv[2],"%d",&stest);
crsTest = 1;
nargsused = 3;
}
else
{
fprintf(stderr,"ERROR: Option %s unknown\n",option);
if (singledash(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 ;
DVT *dvttmp;
float ftmp[2000];
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, "--keepid")) KeepSubjId = 1;
else if (!strcmp(option, "--gdf")) {
if (nargc < 1) argnerr(option,1);
GDFile = pargv[0];
fsgd0 = gdfRead(GDFile,0);
if (fsgd0 == NULL) exit(1);
nargsused = 1;
} else if (!strcmp(option, "--dvt")) {
if (nargc < 1) argnerr(option,1);
DVTFile = pargv[0];
dvttmp = DVTread(DVTFile);
dvt0 = DVTtranspose(dvttmp);
DVTfree(&dvttmp);
nargsused = 1;
} else if (!strcmp(option, "--classes")) {
if (nargc < 1) argnerr(option,1);
while (nth_is_arg(nargc, pargv, nargsused)) {
ClassList[nClassList] = pargv[nargsused];
nClassList++;
nargsused++;
}
} else if (!strcmp(option, "--covar")) {
if (nargc < 1) argnerr(option,1);
while (nth_is_arg(nargc, pargv, nargsused)) {
CovarList[nCovarList] = pargv[nargsused];
nCovarList++;
nargsused++;
}
} else if (!strcmp(option, "--covarprune")) {
if (nargc < 3) argnerr(option,3);
CovarPrune[nCovarPrune].Covar = pargv[0];
sscanf(pargv[1],"%f",&CovarPrune[nCovarPrune].Min);
sscanf(pargv[2],"%f",&CovarPrune[nCovarPrune].Max);
if (CovarPrune[nCovarPrune].Min > CovarPrune[nCovarPrune].Max) {
printf("ERROR: covarprune min > max\n");
exit(1);
}
nCovarPrune++;
nargsused = 3;
} else if (!strcmp(option, "--depvar")) {
if (nargc < 1) argnerr(option,1);
while (nth_is_arg(nargc, pargv, nargsused)) {
DepVarList[nDepVarList] = pargv[nargsused];
nDepVarList++;
nargsused++;
}
} else if (!strcmp(option, "--wdepvar")) {
if (nargc < 1) argnerr(option,1);
while (nth_is_arg(nargc, pargv, nargsused)) {
sscanf(pargv[nargsused],"%f",&ftmp[nwDepVar]);
nwDepVar++;
nargsused++;
}
wDepVar = (float *)calloc(sizeof(float),nwDepVar);
memmove(wDepVar,ftmp,sizeof(float)*nwDepVar);
} else if (!strcmp(option, "--wlms")) {
if (nargc < 1) argnerr(option,1);
WLMSDepVar = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--wclass")) {
if (nargc < 1) argnerr(option,1);
while (nth_is_arg(nargc, pargv, nargsused)) {
sscanf(pargv[nargsused],"%f",&ftmp[nwClass]);
nwClass++;
nargsused++;
}
wClass = (float *)calloc(sizeof(float),nwClass);
memmove(wClass,ftmp,sizeof(float)*nwClass);
} else if (!strcmp(option, "--wcovar")) {
if (nargc < 1) argnerr(option,1);
while (nth_is_arg(nargc, pargv, nargsused)) {
sscanf(pargv[nargsused],"%f",&ftmp[nwCovar]);
nwCovar++;
nargsused++;
}
wCovar = (float *)calloc(sizeof(float),nwCovar+1);
memmove(&wCovar[1],ftmp,sizeof(float)*nwCovar);
wCovar[0] = 0.0;
//Note: the first weight is for offset
} else if (!strcmp(option, "--testoffset")) TestOffset = 1;
else if (!strcmp(option, "--o")) {
if (nargc < 1) argnerr(option,1);
OutBase = pargv[0];
nargsused = 1;
} else {
fprintf(stderr,"ERROR: Option %s unknown\n",option);
if (singledash(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 i, nargc , nargsused;
char **pargv, *option ;
char tmpstr[1000];
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, "--abs")) DoAbs = 1;
else if (!strcasecmp(option, "--nogmnnorm")) gmnnorm = 0;
else if (!strcasecmp(option, "--rescale")) rescale=1;
else if (!strcasecmp(option, "--norescale")) rescale=0;
else if (!strcasecmp(option, "--no-output")) NoOutput = 1;
else if (!strcasecmp(option, "--fft")) UseFFT = 1;
else if (!strcasecmp(option, "--offset")) AddOffset=1;
else if (!strcasecmp(option, "--offset-mid")){
AddOffset = 1;
OffsetFrame = -1;
}
else if (!strcmp(option, "--hsc")) {
if (nargc < 2) argnerr(option,2);
sscanf(pargv[0],"%lf",&HSCMin);
sscanf(pargv[1],"%lf",&HSCMax);
DoHSC = 1;
nargsused = 2;
}
else if (!strcmp(option, "--sum2")) {
if (nargc < 1) argnerr(option,1);
sum2file = pargv[0];
pdfname = "delta";
//NoOutput = 1;
nframes = 1;
nargsused = 1;
}
else if (!strcmp(option, "--hsynth")) {
// eres mask DoTnorm out
if (nargc < 3) argnerr(option,3);
mri = MRIread(pargv[0]);
mask = MRIread(pargv[1]);
sscanf(pargv[2],"%d",&DoTNorm);
mri2 = fMRIhsynth(mri, mask, DoTNorm);
MRIwrite(mri2,pargv[3]);
exit(0);
nargsused = 2;
}
else if (!strcmp(option, "--vol") || !strcmp(option, "--o")) {
if (nargc < 1) argnerr(option,1);
volid = pargv[0];
nargsused = 1;
if (nth_is_arg(nargc, pargv, 1)) {
volfmt = pargv[1];
nargsused ++;
volfmtid = checkfmt(volfmt);
}
}
else if (!strcmp(option, "--temp") || !strcmp(option, "--template")) {
if(DoCurv){
printf("ERROR: cannot use --temp and --curv\n");
exit(1);
}
if(nargc < 1) argnerr(option,1);
tempid = pargv[0];
nargsused = 1;
if (nth_is_arg(nargc, pargv, 1)) {
tempfmt = pargv[1];
nargsused ++;
tempfmtid = checkfmt(tempfmt);
} else tempfmtid = getfmtid(tempid);
} else if (!strcmp(option, "--curv")) {
if(tempid != NULL){
printf("ERROR: cannot use --temp and --curv\n");
exit(1);
}
if(nargc < 2) argnerr(option,2);
subject = pargv[0];
hemi = pargv[1];
DoCurv = 1;
nargsused = 2;
sprintf(tmpstr,"%s/%s/surf/%s.thickness",getenv("SUBJECTS_DIR"),subject,hemi);
tempid = strcpyalloc(tmpstr);
} else if ( !strcmp(option, "--dim") ) {
if (nargc < 4) argnerr(option,4);
for (i=0;i<4;i++) sscanf(pargv[i],"%d",&dim[i]);
nargsused = 4;
dimSpeced = 1;
}
else if ( !strcmp(option, "--nframes") ) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%d",&nframes);
nargsused = 1;
}
else if ( !strcmp(option, "--TR") || !strcmp(option, "--tr") ) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%lf",&TR);
nargsused = 1;
}
else if ( !strcmp(option, "--res") ) {
if (nargc < 4) argnerr(option,4);
for (i=0;i<4;i++) sscanf(pargv[i],"%f",&res[i]);
nargsused = 4;
resSpeced = 1;
}
else if ( !strcmp(option, "--vox-size") ) {
if (nargc < 3) argnerr(option,3);
for (i=0;i<3;i++) sscanf(pargv[i],"%f",&res[i]);
nargsused = 4;
resSpeced = 1;
NewVoxSizeSpeced = 1;
}
else if ( !strcmp(option, "--c_ras") ) {
if (nargc < 3) argnerr(option,3);
for (i=0;i<3;i++) sscanf(pargv[i],"%f",&cras[i]);
nargsused = 3;
}
else if ( !strcmp(option, "--p0") ) {
if (nargc < 3) argnerr(option,3);
for (i=0;i<3;i++) sscanf(pargv[i],"%f",&p0[i]);
usep0 = 1;
nargsused = 3;
}
else if ( !strcmp(option, "--cdircos") ) {
if (nargc < 3) argnerr(option,3);
for (i=0;i<3;i++) sscanf(pargv[i],"%f",&cdircos[i]);
nargsused = 3;
} else if ( !strcmp(option, "--rdircos") ) {
if (nargc < 3) argnerr(option,3);
for (i=0;i<3;i++) sscanf(pargv[i],"%f",&rdircos[i]);
nargsused = 3;
} else if ( !strcmp(option, "--sdircos") ) {
if (nargc < 3) argnerr(option,3);
for (i=0;i<3;i++) sscanf(pargv[i],"%f",&sdircos[i]);
nargsused = 3;
} else if ( !strcmp(option, "--fwhm") ) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%f",&fwhm);
gstd = fwhm/sqrt(log(256.0));
nargsused = 1;
} else if (!strcmp(option, "--precision")) {
if (nargc < 1) argnerr(option,1);
precision = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--seed")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%ld",&seed);
nargsused = 1;
} else if (!strcmp(option, "--seedfile")) {
if (nargc < 1) argnerr(option,1);
seedfile = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--pdf")) {
if (nargc < 1) argnerr(option,1);
pdfname = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--bb")) {
if (nargc < 6) argnerr(option,6);
sscanf(pargv[0],"%d",&boundingbox.x);
sscanf(pargv[1],"%d",&boundingbox.y);
sscanf(pargv[2],"%d",&boundingbox.z);
sscanf(pargv[3],"%d",&boundingbox.dx);
sscanf(pargv[4],"%d",&boundingbox.dy);
sscanf(pargv[5],"%d",&boundingbox.dz);
pdfname = "boundingbox";
nargsused = 6;
}
else if (!strcasecmp(option, "--checker"))
pdfname = "checker";
else if (!strcmp(option, "--dof-num")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%d",&numdof);
nargsused = 1;
} else if (!strcmp(option, "--val-a")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%lf",&ValueA);
nargsused = 1;
} else if (!strcmp(option, "--val-b")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%lf",&ValueB);
nargsused = 1;
} else if (!strcmp(option, "--radius")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%lf",&voxradius);
nargsused = 1;
} else if (!strcmp(option, "--dof-den") || !strcmp(option, "--dof")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%d",&dendof);
nargsused = 1;
} else if (!strcmp(option, "--gmean")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%lf",&gausmean);
nargsused = 1;
} else if (!strcmp(option, "--gstd")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%lf",&gausstd);
nargsused = 1;
} else if (!strcmp(option, "--delta-crsf")) {
if (nargc < 4) argnerr(option,4);
sscanf(pargv[0],"%d",&delta_crsf[0]);
sscanf(pargv[1],"%d",&delta_crsf[1]);
sscanf(pargv[2],"%d",&delta_crsf[2]);
sscanf(pargv[3],"%d",&delta_crsf[3]);
delta_crsf_speced = 1;
nargsused = 4;
} else if (!strcmp(option, "--delta-val")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%lf",&delta_value);
nargsused = 1;
} else if (!strcmp(option, "--delta-val-off")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%lf",&delta_off_value);
nargsused = 1;
} else if (!strcmp(option, "--spike")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%d",&SpikeTP);
nargsused = 1;
} else {
fprintf(stderr,"ERROR: Option %s unknown\n",option);
if (singledash(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, "--oldtxtstyle")) oldtxtstyle = 1;
else if (!strcasecmp(option, "--plaintxtstyle")) plaintxtstyle = 1;
else if (!strcasecmp(option, "--mskinvert")) mskinvert = 1;
else if (!strcmp(option, "--fixxfm")) fixxfm = 1;
else if (!strcmp(option, "--nofixxfm")) fixxfm = 0;
/* -------- ROI output file ------ */
else if (!strcmp(option, "--roiavgtxt")) {
if (nargc < 1) argnerr(option,1);
roitxtfile = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--roiavg")) {
if (nargc < 1) argnerr(option,1);
roifile = pargv[0];
nargsused = 1;
}
/* -------- source volume inputs ------ */
else if (!strcmp(option, "--srcvol")) {
if (nargc < 1) argnerr(option,1);
srcvolid = IDnameFromStem(pargv[0]);
if(srcvolid == NULL) srcvolid = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--srcfmt")) {
if (nargc < 1) argnerr(option,1);
srcfmt = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--srcreg")) {
if (nargc < 1) argnerr(option,1);
srcregfile = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--srcoldreg")) {
srcoldreg = 1;
} else if (!strcmp(option, "--srcwarp")) {
if (nargc < 1) argnerr(option,1);
srcwarp = pargv[0];
nargsused = 1;
}
/* -------- label inputs ------ */
else if (!strcmp(option, "--labelfile") ||
!strcmp(option, "--label")) {
if (nargc < 1) argnerr(option,1);
labelfile = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--labelreg")) {
if (nargc < 1) argnerr(option,1);
src2lblregfile = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--labeltal")) {
labeltal = 1;
fixxfm = 1;
nargsused = 0;
} else if (!strcmp(option, "--talxfm")) {
if (nargc < 1) argnerr(option,1);
talxfm = pargv[0];
labeltal = 1;
fixxfm = 1;
nargsused = 1;
} else if (!strcmp(option, "--labelfillthresh")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%f",&labelfillthresh);
nargsused = 1;
}
/* -------- mask volume inputs ------ */
else if (!strcmp(option, "--mskvol")) {
if (nargc < 1) argnerr(option,1);
mskvolid = IDnameFromStem(pargv[0]);
if(mskvolid == NULL) mskvolid = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--mskfmt")) {
if (nargc < 1) argnerr(option,1);
mskfmt = pargv[0];
nargsused = 1;
}
else if (!strcmp(option, "--msktail")) {
if (nargc < 1) argnerr(option,1);
msktail = pargv[0];
nargsused = 1;
if (strncasecmp(msktail,"abs",3) &&
strncasecmp(msktail,"pos",3) &&
strncasecmp(msktail,"neg",3)) {
fprintf(stderr,"ERROR: msk tail = %s, must be abs, pos, or neg\n",
msktail);
exit(1);
}
} else if (!strcmp(option, "--mskthresh")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%f",&mskthresh);
nargsused = 1;
} else if (!strcmp(option, "--mskframe")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%d",&mskframe);
nargsused = 1;
} else if (!strcmp(option, "--finalmskvol")) {
if (nargc < 1) argnerr(option,1);
finalmskvolid = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--srcmskvol")) {
if (nargc < 1) argnerr(option,1);
srcmskvolid = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--finalmskcrs")) {
if (nargc < 1) argnerr(option,1);
finalmskcrs = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--list")) {
if (nargc < 1) argnerr(option,1);
ListFile = pargv[0];
nargsused = 1;
} else {
fprintf(stderr,"ERROR: Option %s unknown\n",option);
if (singledash(option))
fprintf(stderr," Did you really mean -%s ?\n",option);
//printf("Match %d\n",strcmp(option, "--roiavgtxt"));
exit(-1);
}
nargc -= nargsused;
pargv += nargsused;
}
return(0);
}
/* --------------------------------------------- */
static int parse_commandline(int argc, char **argv)
{
int nargc , nargsused, rt;
char **pargv, *option, listfile[2000] ;
FILE *fp0;
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, "--check"))
{
DoCheck = 1;
}
else if (!strcasecmp(option, "--no-check"))
{
DoCheck = 0;
}
else if (!strcasecmp(option, "--mean"))
{
DoMean = 1;
}
else if (!strcasecmp(option, "--median"))
{
DoMedian = 1;
}
else if (!strcasecmp(option, "--mean-div-n"))
{
DoMeanDivN = 1;
}
else if (!strcasecmp(option, "--mean2"))
{
DoMeanDivN = 1;
}
else if (!strcasecmp(option, "--sum"))
{
DoSum = 1;
}
else if (!strcasecmp(option, "--std"))
{
DoStd = 1;
}
else if (!strcasecmp(option, "--var"))
{
DoVar = 1;
}
else if (!strcasecmp(option, "--abs"))
{
DoAbs = 1;
}
else if (!strcasecmp(option, "--pos"))
{
DoPos = 1;
}
else if (!strcasecmp(option, "--neg"))
{
DoNeg = 1;
}
else if (!strcasecmp(option, "--max"))
{
DoMax = 1;
}
else if (!strcasecmp(option, "--max-index"))
{
DoMaxIndex = 1;
}
else if (!strcasecmp(option, "--min"))
{
DoMin = 1;
}
else if (!strcasecmp(option, "--conjunct"))
{
DoConjunction = 1;
}
else if (!strcasecmp(option, "--vote"))
{
DoVote = 1;
}
else if (!strcasecmp(option, "--sort"))
{
DoSort = 1;
}
else if (!strcasecmp(option, "--norm-mean"))
{
DoNormMean = 1;
}
else if (!strcasecmp(option, "--norm1"))
{
DoNorm1 = 1;
}
else if (!strcasecmp(option, "--prune"))
{
DoPrune = 1;
}
else if (!strcasecmp(option, "--max-bonfcor"))
{
DoMax = 1;
DoBonfCor = 1;
}
else if (!strcasecmp(option, "--asl"))
{
DoASL = 1;
}
else if (!strcasecmp(option, "--paired-avg"))
{
DoPaired = 1;
DoPairedAvg = 1;
}
else if (!strcasecmp(option, "--paired-sum"))
{
DoPaired = 1;
DoPairedSum = 1;
}
else if (!strcasecmp(option, "--paired-diff"))
{
DoPaired = 1;
DoPairedDiff = 1;
}
else if (!strcasecmp(option, "--paired-diff-norm"))
{
DoPairedDiff = 1;
DoPairedDiffNorm = 1;
DoPaired = 1;
}
else if (!strcasecmp(option, "--paired-diff-norm1"))
{
DoPairedDiff = 1;
DoPairedDiffNorm1 = 1;
DoPaired = 1;
}
else if (!strcasecmp(option, "--paired-diff-norm2"))
{
DoPairedDiff = 1;
DoPairedDiffNorm2 = 1;
DoPaired = 1;
}
else if (!strcasecmp(option, "--combine"))
{
DoCombine = 1;
}
else if (!strcasecmp(option, "--rms"))
{
DoRMS = 1;
}
else if (!strcasecmp(option, "--keep-datatype"))
{
DoKeepDatatype = 1;
}
else if (!strcasecmp(option, "--pca"))
{
DoPCA = 1;
}
else if (!strcasecmp(option, "--chunk"))
{
setenv("FS_USE_MRI_CHUNK","1",1);
}
else if (!strcasecmp(option, "--scm"))
{
DoSCM = 1;
}
else if ( !strcmp(option, "--pca-mask") )
{
if(nargc < 1)
{
argnerr(option,1);
}
PCAMaskFile = pargv[0];
nargsused = 1;
}
else if ( !strcmp(option, "--i") )
{
if (nargc < 1)
{
argnerr(option,1);
}
inlist[ninputs] = pargv[0];
ninputs ++;
nargsused = 1;
}
else if ( !strcmp(option, "--mtx") )
{
if (nargc < 1)
{
argnerr(option,1);
}
matfile = pargv[0];
M = MatrixReadTxt(matfile, NULL);
if(M==NULL)
{
printf("ERROR: reading %s\n",matfile);
exit(1);
}
nargsused = 1;
}
else if ( !strcmp(option, "--gmean") )
{
if (nargc < 1)
{
argnerr(option,1);
}
sscanf(pargv[0],"%d",&ngroups);
nargsused = 1;
}
else if ( !strcmp(option, "--rep") )
{
if (nargc < 1)
{
argnerr(option,1);
}
sscanf(pargv[0],"%d",&NReplications);
nargsused = 1;
}
else if ( !strcmp(option, "--o") )
{
if (nargc < 1)
{
argnerr(option,1);
}
out = pargv[0];
nargsused = 1;
}
else if ( !strcmp(option, "--mask") )
{
if (nargc < 1)
{
argnerr(option,1);
}
maskfile = pargv[0];
nargsused = 1;
}
else if ( !strcmp(option, "--mul") )
{
if (nargc < 1)
{
argnerr(option,1);
}
if(! isdigit(pargv[0][0]))
{
printf("ERROR: value passed to the --mul flag must be a number\n");
printf(" If you want to multiply two images, use fscalc\n");
exit(1);
}
sscanf(pargv[0],"%lf",&MultiplyVal);
DoMultiply = 1;
nargsused = 1;
}
else if ( !strcmp(option, "--add") )
{
if (nargc < 1)
{
argnerr(option,1);
}
if(! isdigit(pargv[0][0]))
{
printf("ERROR: value passed to the --add flag must be a number\n");
printf(" If you want to add two images, use --sum or fscalc\n");
exit(1);
}
sscanf(pargv[0],"%lf",&AddVal);
DoAdd = 1;
nargsused = 1;
}
else if (!strcasecmp(option, "--tar1"))
{
if(nargc < 1)
{
argnerr(option,1);
}
sscanf(pargv[0],"%d",&TAR1DOFAdjust);
DoTAR1 = 1;
nargsused = 1;
}
else if (!strcasecmp(option, "--f"))
{
if(nargc < 1)
{
argnerr(option,1);
}
sscanf(pargv[0],"%s",listfile);
fp0 = fopen(listfile,"r");
if(fp0==NULL)
{
printf("ERROR: opening %s\n",listfile);
exit(1);
}
while(1)
{
rt = fscanf(fp0,"%s",flist[nthf]);
if(rt == EOF)
{
fclose(fp0);
break;
}
inlist[ninputs] = flist[nthf];
nthf++;
ninputs ++;
}
nargsused = 1;
}
else
{
inlist[ninputs] = option;
ninputs ++;
if(ninputs > NInMAX)
{
printf("ERROR: ninputs > %d\n",NInMAX);
exit(1);
}
//fprintf(stderr,"ERROR: Option %s unknown\n",option);
//if(singledash(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, "--verbose")) verbose = 1;
else if (!strcasecmp(option, "--fileinfo")) dumpfileinfo = 1;
/* -------- source volume inputs ------ */
else if (!strcmp(option, "--i")) {
if (nargc < 1) argnerr(option,1);
imafile = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--attr")) {
if (nargc < 1) argnerr(option,1);
attrname = pargv[0];
getattr = 1;
nargsused = 1;
} else if (!strcmp(option, "--ob")) {
if (nargc < 1) argnerr(option,1);
bstem = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--dictionary")) {
DumpImaDictionary(stdout);
exit(0);
nargsused = 1;
} else if (!strcmp(option, "--key")) {
if (nargc < 1) argnerr(option,1);
key = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--keyno")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%d",&keyno);
nargsused = 1;
} else if (!strcmp(option, "--o")) {
if (nargc < 2) argnerr(option,2);
sscanf(pargv[0],"%d",&offset);
typestring = pargv[1];
nargsused = 2;
if (strcmp(typestring,"string") == 0) {
if (nargc < 3) {
printf("ERROR: type string needs length argument\n");
exit(1);
}
sscanf(pargv[2],"%d",&stringlen);
if (stringlen < 1) {
printf("ERROR: string length = %d, must be >= 1\n",
stringlen);
exit(1);
}
nargsused = 3;
}
} else {
fprintf(stderr,"ERROR: Option %s unknown\n",option);
if (singledash(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 ;
FILE *fptmp;
int nargs;
/* rkt: check for and handle version tag */
nargs = handle_version_option (argc, argv, "$Id: mri_parse_sdcmdir.c,v 1.21 2011/03/02 00:04:23 nicks Exp $", "$Name: $");
if (nargs && argc - nargs == 1)
exit (0);
argc -= nargs;
if (argc < 1) usage_exit();
nargc = argc;
pargv = argv;
while (nargc > 0) {
option = pargv[0];
if (debug) printf("%d %s\n",nargc,option);
nargc -= 1;
pargv += 1;
nargsused = 0;
if (!strcasecmp(option, "--help")) print_help() ;
else if (!strcasecmp(option, "--version")) print_version() ;
else if (!strcasecmp(option, "--debug")) debug = 1;
else if (!strcasecmp(option, "--verbose")) verbose = 1;
else if (!strcmp(option, "--d")) {
if (nargc < 1) argnerr(option,1);
sdicomdir = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--o")) {
if (nargc < 1) argnerr(option,1);
outfile = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--summarize") || !strcmp(option, "--sum")) {
summarize = 1;
} else if (!strcmp(option, "--status")) {
if (nargc < 1) argnerr(option,1);
SDCMStatusFile = (char *) calloc(strlen(pargv[0])+1,sizeof(char));
memmove(SDCMStatusFile,pargv[0],strlen(pargv[0]));
fptmp = fopen(SDCMStatusFile,"w");
if (fptmp == NULL) {
fprintf(stderr,"ERROR: could not open %s for writing\n",
SDCMStatusFile);
exit(1);
}
fprintf(fptmp,"0\n");
fclose(fptmp);
nargsused = 1;
} else if (!strcmp(option, "--sortbyrun")) {
sortbyrun = 1;
} else {
fprintf(stderr,"ERROR: Option %s unknown\n",option);
if (singledash(option))
fprintf(stderr," Did you really mean -%s ?\n",option);
exit(-1);
}
nargc -= nargsused;
pargv += nargsused;
}
return(0);
}
/* ------------------------------------------------------------------ */
static int parse_commandline(int argc, char **argv) {
int nargc , nargsused;
char **pargv, *option ;
int nargs;
if (argc < 1) usage_exit();
/* rkt: check for and handle version tag */
nargs = handle_version_option (argc, argv, "$Id: mkxsubjreg.c,v 1.5 2011/03/02 00:04:13 nicks Exp $", "$Name: stable5 $");
if (nargs && argc - nargs == 1)
exit (0);
argc -= nargs;
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 (!strcmp(option, "--srcreg")) {
if (nargc < 1) argnerr(option,1);
srcregpath = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--targreg")) {
if (nargc < 1) argnerr(option,1);
targregpath = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--targsubj")) {
if (nargc < 1) argnerr(option,1);
targsubj = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--xfm")) {
if (nargc < 1) argnerr(option,1);
xfmrname = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--fvol")) {
if (nargc < 1) argnerr(option,1);
fvolid = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--sd")) {
if (nargc < 1) argnerr(option,1);
subjects_dir = pargv[0];
nargsused = 1;
} else {
fprintf(stderr,"ERROR: Option %s unknown\n",option);
if (singledash(option))
fprintf(stderr," Did you really mean -%s ?\n",option);
exit(-1);
}
nargc -= nargsused;
pargv += nargsused;
}
return(0);
}
