void VParseFilterCmd (int noptions, VOptionDescRec opts[],
int argc, char **argv, FILE **inp, FILE **outp)
{
static VStringConst in_file, out_file;
static VBoolean in_found, out_found;
static VOptionDescRec io_opts[] = {
{ "in", VStringRepn, 1, & in_file, & in_found, NULL, "Input file" },
{ "out", VStringRepn, 1, & out_file, & out_found, NULL, "Output file" }
};
int i, n;
VOptionDescRec options[100];
/* Check that number of options will not overflow the options array. */
if (noptions >= 98) {
VWarning("VParseFilterCmd: Too many options allowed");
noptions = 98;
}
/* Copy options into a new list and add the "in" and "out" options. */
n = 0;
if (inp)
options[n++] = io_opts[0];
if (outp)
options[n++] = io_opts[1];
for (i = 0; i < noptions; i++, n++)
options[n] = opts[i];
/* Parse command line arguments and identify the input and output files: */
if (! VParseCommand (n, options, & argc, argv) ||
(inp && ! VIdentifyFiles (n, options, "in", & argc, argv, 0)) ||
(outp && ! VIdentifyFiles (n, options, "out", & argc, argv, 1)))
goto Usage;
/* Any remaining unparsed arguments are erroneous: */
if (argc > 1) {
VReportBadArgs (argc, argv);
Usage: VReportUsage (argv[0], n, options,
inp ? (outp ? "[infile] [outfile]" : "[infile]") :
(outp ? "[outfile]" : NULL));
exit (EXIT_FAILURE);
}
/* Open the input and output files: */
if (inp)
*inp = VOpenInputFile (in_file, TRUE);
if (outp)
*outp = VOpenOutputFile (out_file, TRUE);
}
int
main(int argc, char *argv[]) {
static VArgVector in_files;
static VString out_filename;
static VBoolean in_found, out_found;
static VOptionDescRec options[] = {
{"in", VStringRepn, 0, & in_files, & in_found, NULL, "Input files" },
{"out", VStringRepn, 1, & out_filename, & out_found, NULL, "Output file" }
};
FILE *fp = NULL;
VStringConst in_filename;
VAttrList list = NULL, out_list = NULL;
VImage *design = NULL, tmp = NULL, dest = NULL;
VAttrListPosn posn;
int i, nimages;
char prg_name[100];
char ver[100];
getLipsiaVersion(ver, sizeof(ver));
sprintf(prg_name, "vcatdesign V%s", ver);
fprintf(stderr, "%s\n", prg_name);
/* Parse command line arguments: */
if(! VParseCommand(VNumber(options), options, & argc, argv) ||
! VIdentifyFiles(VNumber(options), options, "in", & argc, argv, 0) ||
! VIdentifyFiles(VNumber(options), options, "out", & argc, argv, -1))
goto Usage;
if(argc > 1) {
VReportBadArgs(argc, argv);
Usage:
VReportUsage(argv[0], VNumber(options), options, NULL);
exit(EXIT_FAILURE);
}
/* Read each input file */
nimages = in_files.number;
design = (VImage *) VMalloc(sizeof(VImage) * nimages);
for(i = 0; i < nimages; i++) {
in_filename = ((VStringConst *) in_files.vector)[i];
fprintf(stderr, " reading: %s\n", in_filename);
fp = VOpenInputFile(in_filename, TRUE);
list = VReadFile(fp, NULL);
if(! list)
VError("Error reading file %s", in_filename);
fclose(fp);
for(VFirstAttr(list, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
if(VGetAttrRepn(& posn) != VImageRepn)
continue;
VGetAttrValue(& posn, NULL, VImageRepn, & tmp);
if(VPixelRepn(tmp) == VFloatRepn || VPixelRepn(tmp) == VDoubleRepn) {
design[i] = tmp;
break;
}
}
}
/* process */
dest = ConcatDesigns(design, nimages);
out_list = VCreateAttrList();
VAppendAttr(out_list, "image", NULL, VImageRepn, dest);
/* Output: */
VHistory(VNumber(options), options, prg_name, &list, &out_list);
fp = VOpenOutputFile(out_filename, TRUE);
if(!fp)
VError(" error opening outout file %s", out_filename);
if(! VWriteFile(fp, out_list))
exit(1);
fprintf(stderr, "%s: done.\n", argv[0]);
return 0;
}
int main (int argc, char* argv[])
{
VString inname; /* name of input images */
VString outname; /* name of output images */
VString fieldname; /* name of deformation field */
VBoolean verbose = TRUE; /* verbose flag */
VOptionDescRec options[] = /* options of program */
{
{"in", VStringRepn, 1, &inname, VRequiredOpt, NULL, "Input image"},
{"out", VStringRepn, 1, &outname, VRequiredOpt, NULL, "Deformed output image"},
{"field", VStringRepn, 1, &fieldname, VRequiredOpt, NULL, "3D deformation field"},
{"verbose", VBooleanRepn, 1, &verbose, VOptionalOpt, NULL, "Show status messages. Optional"}
};
VAttrList in_history=NULL; /* history of input images */
VAttrList field_history=NULL; /* history of deformation field */
VAttrList In; /* input images */
VImage Dx, Dy, Dz; /* field images */
VAttrListPosn pos; /* position in list */
VImage in; /* image in list */
float fx, fy, fz; /* scaling factors */
VImage dx, dy, dz; /* scaled deformation field */
VAttrListPosn rider; /* functional data rider */
int bands, rows, columns, steps; /* size of functional data */
VImage data; /* functional data */
VShort *src, *dest; /* functional data pointer */
VBoolean success; /* success flag */
int n, t, z; /* indices */
/* print information */
char prg_name[100];
char ver[100];
getLipsiaVersion(ver, sizeof(ver));
sprintf(prg_name, "vdeform V%s", ver);
fprintf (stderr, "%s\n", prg_name); fflush (stderr);
/* parse command line */
if (!VParseCommand (VNumber (options), options, &argc, argv))
{
if (argc > 1) VReportBadArgs (argc, argv);
VReportUsage (argv[0], VNumber (options), options, NULL);
exit (1);
}
/* read input images */
if (verbose) {fprintf (stderr, "Reading input image '%s' ...\n", inname); fflush (stderr);}
ReadImages (inname, In, in_history);
if (!In) exit (2);
/* read deformation field */
if (verbose) {fprintf (stderr, "Reading 3D deformation field '%s' ...\n", fieldname); fflush (stderr);}
ReadField (fieldname, Dx, Dy, Dz, field_history);
if (!Dx || !Dy || !Dz) exit (3);
/* deform anatomical images */
for (VFirstAttr (In, &pos); VAttrExists (&pos); VNextAttr (&pos))
{
/* get image */
VGetAttrValue (&pos, NULL, VImageRepn, &in);
if (VPixelRepn (in) != VUByteRepn) break;
/* compare image and field */
if (verbose) {fprintf (stderr, "Comparing anatomical image and deformation field ...\n"); fflush (stderr);}
if (!Compatible (in, Dx)) exit (4);
if (!Compatible (in, Dy)) exit (4);
if (!Compatible (in, Dz)) exit (4);
/* deform image */
if (verbose) {fprintf (stderr, "Deforming anatomical image ...\n"); fflush (stderr);}
RTTI (in, TrilinearInverseDeform, (in, Dx, Dy, Dz));
VSetAttrValue (&pos, NULL, VImageRepn, in);
}
/* deform map images */
for (; VAttrExists (&pos); VNextAttr (&pos))
{
/* get image */
VGetAttrValue (&pos, NULL, VImageRepn, &in);
if (VPixelRepn (in) != VFloatRepn) break;
/* scale field */
if (verbose) {fprintf (stderr, "Scaling deformation field ...\n"); fflush (stderr);}
fx = (float) VImageNColumns (in) / (float) VImageNColumns (Dx);
fy = (float) VImageNRows (in) / (float) VImageNRows (Dy);
fz = (float) VImageNBands (in) / (float) VImageNBands (Dz);
TrilinearScale<VFloat> (Dx, fx, fy, fz, dx); Multiply<VFloat> (dx, fx);
TrilinearScale<VFloat> (Dy, fx, fy, fz, dy); Multiply<VFloat> (dy, fy);
TrilinearScale<VFloat> (Dz, fx, fy, fz, dz); Multiply<VFloat> (dz, fz);
/* compare image and field */
if (verbose) {fprintf (stderr, "Comparing map image and deformation field ...\n"); fflush (stderr);}
if (!Compatible (in, dx)) exit (5);
if (!Compatible (in, dy)) exit (5);
if (!Compatible (in, dz)) exit (5);
/* deform image */
if (verbose) {fprintf (stderr, "Deforming map image ...\n"); fflush (stderr);}
RTTI (in, TrilinearInverseDeform, (in, dx, dy, dz));
VSetAttrValue (&pos, NULL, VImageRepn, in);
/* clean-up */
VDestroyImage (dx);
VDestroyImage (dy);
VDestroyImage (dz);
}
/* deform functional images */
if (VAttrExists (&pos))
{
/* get data size */
bands = rows = columns = steps = 0;
for (rider = pos; VAttrExists (&rider); VNextAttr (&rider))
{
/* get image */
VGetAttrValue (&rider, NULL, VImageRepn, &data);
if (VPixelRepn (data) != VShortRepn) break;
/* store image size */
if (VImageNBands (data) > steps) steps = VImageNBands (data);
if (VImageNRows (data) > rows) rows = VImageNRows (data);
if (VImageNColumns (data) > columns) columns = VImageNColumns (data);
bands++;
}
in = VCreateImage (bands, rows, columns, VShortRepn);
/* scale field */
if (verbose) {fprintf (stderr, "Scaling deformation field ...\n"); fflush (stderr);}
fx = (float) VImageNColumns (in) / (float) VImageNColumns (Dx);
fy = (float) VImageNRows (in) / (float) VImageNRows (Dy);
fz = (float) VImageNBands (in) / (float) VImageNBands (Dz);
TrilinearScale<VFloat> (Dx, fx, fy, fz, dx); Multiply<VFloat> (dx, fx);
TrilinearScale<VFloat> (Dy, fx, fy, fz, dy); Multiply<VFloat> (dy, fy);
TrilinearScale<VFloat> (Dz, fx, fy, fz, dz); Multiply<VFloat> (dz, fz);
/* compare image and field */
if (verbose) {fprintf (stderr, "Comparing functional images and deformation field ...\n"); fflush (stderr);}
if (!Compatible (in, dx)) exit (6);
if (!Compatible (in, dy)) exit (6);
if (!Compatible (in, dz)) exit (6);
/* expand zero images */
for (rider = pos, z = 0; z < bands; z++, VNextAttr (&rider))
{
VGetAttrValue (&rider, NULL, VImageRepn, &data);
if (FunctionalZero (data))
{
FunctionalResize (data, steps, rows, columns);
VSetAttrValue (&rider, NULL, VImageRepn, data);
}
}
/* deform images */
if (verbose) {fprintf (stderr, "Deforming functional images ...\n"); fflush (stderr);}
for (t = 0; t < steps; t++)
{
/* collect data */
dest = (VShort*) VPixelPtr (in, 0, 0, 0);
for (rider = pos, z = 0; z < bands; z++, VNextAttr (&rider))
{
VGetAttrValue (&rider, NULL, VImageRepn, &data);
src = (VShort*) VPixelPtr (data, t, 0, 0);
for (n = 0; n < rows * columns; ++n)
*(dest++) = *(src++);
}
/* deform image */
if (verbose) {fprintf (stderr, "Timestep %d of %d ...\r", t + 1, steps); fflush (stderr);}
RTTI (in, TrilinearInverseDeform, (in, dx, dy, dz));
/* spread data */
src = (VShort*) VPixelPtr (in, 0, 0, 0);
for (rider = pos, z = 0; z < bands; z++, VNextAttr (&rider))
{
VGetAttrValue (&rider, NULL, VImageRepn, &data);
dest = (VShort*) VPixelPtr (data, t, 0, 0);
for (n = 0; n < rows * columns; ++n)
*(dest++) = *(src++);
}
}
/* collapse zero images */
for (rider = pos, z = 0; z < bands; z++, VNextAttr (&rider))
{
VGetAttrValue (&rider, NULL, VImageRepn, &data);
if (FunctionalZero (data))
{
FunctionalResize (data, 1, 1, 1);
VSetAttrValue (&rider, NULL, VImageRepn, data);
}
}
/* clean-up */
VDestroyImage (in);
VDestroyImage (dx);
VDestroyImage (dy);
VDestroyImage (dz);
/* proceed */
pos = rider;
}
/* check list */
if (VAttrExists (&pos))
{
VError ("Remaining image does not contain valid data");
exit (7);
}
/* Prepend History */
VPrependHistory(VNumber(options),options,prg_name,&in_history);
/* write output images */
if (verbose) {fprintf (stderr, "Writing output image '%s' ...\n", outname); fflush (stderr);}
success = WriteImages (outname, In, in_history);
if (!success) exit (8);
/* clean-up
VDestroyAttrList (inhistory);
VDestroyAttrList (fieldhistory);
VDestroyAttrList (In);
VDestroyImage (Dx);
VDestroyImage (Dy);
VDestroyImage (Dz); */
/* exit */
if (verbose) {fprintf (stderr, "Finished.\n"); fflush (stderr);}
return 0;
} /* main */
int main(int argc, char *argv[]) {
static VArgVector in_files1;
static VArgVector in_files2;
static VString out_filename;
static VShort type = 1;
static VBoolean gauss = FALSE;
static VOptionDescRec options[] = {
{"in1", VStringRepn, 0, & in_files1, VRequiredOpt, NULL, "Input files 1" },
{"in2", VStringRepn, 0, & in_files2, VRequiredOpt, NULL, "Input files 2" },
{"type", VShortRepn, 1, (VPointer) &type, VOptionalOpt, TypeDict, "output type"},
{"gaussianize", VBooleanRepn, 1, (VPointer) &gauss, VOptionalOpt, NULL, "Whether to Gaussianize"},
{"out", VStringRepn, 1, & out_filename, VRequiredOpt, NULL, "Output file" }
};
FILE *fp = NULL;
VStringConst in_filename, buf1, buf2;
VAttrList list1, list2, out_list;
VAttrListPosn posn;
VString str;
VImage src, *src1, *src2, dest = NULL;
int i, nimages, npix = 0;
char prg_name[100];
char ver[100];
getLipsiaVersion(ver, sizeof(ver));
sprintf(prg_name, "vpaired_ttest V%s", ver);
fprintf(stderr, "%s\n", prg_name);
/*
** parse command line
*/
if(! VParseCommand(VNumber(options), options, & argc, argv)) {
VReportUsage(argv[0], VNumber(options), options, NULL);
exit(EXIT_FAILURE);
}
if(argc > 1) {
VReportBadArgs(argc, argv);
exit(EXIT_FAILURE);
}
if(type < 0 || type > 1)
VError(" illegal type");
/* ini */
nimages = in_files1.number;
if(in_files2.number != nimages)
VError(" inconsistent number of files %d %d", nimages, in_files2.number);
for(i = 0; i < nimages; i++) {
buf1 = ((VStringConst *) in_files1.vector)[i];
buf2 = ((VStringConst *) in_files2.vector)[i];
fprintf(stderr, "%3d: %s %s\n", i, buf1, buf2);
}
fprintf(stderr, "\n");
/* images 1 */
src1 = (VImage *) VCalloc(nimages, sizeof(VImage));
for(i = 0; i < nimages; i++) {
src1[i] = NULL;
in_filename = ((VStringConst *) in_files1.vector)[i];
fp = VOpenInputFile(in_filename, TRUE);
list1 = VReadFile(fp, NULL);
if(! list1)
VError("Error reading image");
fclose(fp);
for(VFirstAttr(list1, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
if(VGetAttrRepn(& posn) != VImageRepn)
continue;
VGetAttrValue(& posn, NULL, VImageRepn, & src);
if(VPixelRepn(src) != VFloatRepn)
continue;
if(VGetAttr(VImageAttrList(src), "modality", NULL, VStringRepn, &str) == VAttrFound) {
if(strcmp(str, "conimg") != 0)
continue;
}
if(i == 0)
npix = VImageNPixels(src);
else if(npix != VImageNPixels(src))
VError(" inconsistent image dimensions");
src1[i] = src;
break;
}
if(src1[i] == NULL)
VError(" no contrast image found in %s", in_filename);
}
/* images 2 */
src2 = (VImage *) VCalloc(nimages, sizeof(VImage));
for(i = 0; i < nimages; i++) {
src2[i] = NULL;
in_filename = ((VStringConst *) in_files2.vector)[i];
fp = VOpenInputFile(in_filename, TRUE);
list2 = VReadFile(fp, NULL);
if(! list2)
VError("Error reading image");
fclose(fp);
for(VFirstAttr(list2, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
if(VGetAttrRepn(& posn) != VImageRepn)
continue;
VGetAttrValue(& posn, NULL, VImageRepn, & src);
if(VPixelRepn(src) != VFloatRepn)
continue;
if(VGetAttr(VImageAttrList(src), "modality", NULL, VStringRepn, &str) == VAttrFound) {
if(strcmp(str, "conimg") != 0)
continue;
}
if(npix != VImageNPixels(src))
VError(" inconsistent image dimensions");
src2[i] = src;
break;
}
if(src2[i] == NULL)
VError(" no contrast image found in %s", in_filename);
}
/* make normally distributed */
if(gauss) {
VGaussianize(src1, nimages);
VGaussianize(src2, nimages);
}
/* paired t-test */
dest = PairedTest(src1, src2, dest, nimages, type);
/*
** output
*/
out_list = VCreateAttrList();
VHistory(VNumber(options), options, prg_name, &list1, &out_list);
VAppendAttr(out_list, "image", NULL, VImageRepn, dest);
fp = VOpenOutputFile(out_filename, TRUE);
if(! VWriteFile(fp, out_list))
exit(1);
fclose(fp);
fprintf(stderr, "%s: done.\n", argv[0]);
exit(0);
}
int
main(int argc, char *argv[]) {
static VArgVector in_files;
static VString out_filename;
static VString filename;
static VShort minval = 0;
static VFloat fwhm = 4.0;
static VOptionDescRec options[] = {
{"in", VStringRepn, 0, & in_files, VRequiredOpt, NULL, "Input files" },
{"out", VStringRepn, 1, & out_filename, VRequiredOpt, NULL, "Output file" },
{"design", VStringRepn, 1, (VPointer) &filename, VRequiredOpt, NULL, "Design file"},
{
"fwhm", VFloatRepn, 1, (VPointer) &fwhm, VOptionalOpt, NULL,
"FWHM of temporal Gaussian filter in seconds"
},
{"minval", VShortRepn, 1, (VPointer) &minval, VOptionalOpt, NULL, "Signal threshold"}
};
FILE *fp = NULL, *f = NULL;
VStringConst in_filename;
VString ifilename;
VAttrList list = NULL, list1 = NULL;
VAttrList out_list = NULL, history_list = NULL;
VAttrListPosn posn;
VImage design = NULL;
ListInfo *linfo;
VLong itr = 0;
VFloat sigma = 0, tr = 0;
int i, n, nimages;
char prg_name[100];
char ver[100];
getLipsiaVersion(ver, sizeof(ver));
sprintf(prg_name, "vcolorglm V%s", ver);
fprintf(stderr, "%s\n", prg_name);
/*
** parse command line
*/
if(! VParseCommand(VNumber(options), options, & argc, argv)) {
VReportUsage(argv[0], VNumber(options), options, NULL);
exit(EXIT_FAILURE);
}
if(argc > 1) {
VReportBadArgs(argc, argv);
exit(EXIT_FAILURE);
}
/*
** read design matrix
*/
fp = VOpenInputFile(filename, TRUE);
list1 = VReadFile(fp, NULL);
if(! list1)
VError("Error reading design file");
fclose(fp);
n = 0;
for(VFirstAttr(list1, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
if(VGetAttrRepn(& posn) != VImageRepn)
continue;
VGetAttrValue(& posn, NULL, VImageRepn, & design);
if(VPixelRepn(design) != VFloatRepn /* && VPixelRepn(design) != VDoubleRepn */)
continue;
n++;
break;
}
if(n == 0)
VError(" design matrix not found ");
/*
** get pre-coloring info
*/
if(VGetAttr(VImageAttrList(design), "repetition_time", NULL, VLongRepn, &itr) != VAttrFound)
VError(" TR info missing in header");
tr = (float) itr / 1000.0;
sigma = 0;
if(tr > 0.001 && fwhm > 0.001) {
fprintf(stderr, " TR: %.3f seconds\n", tr);
sigma = fwhm / 2.35482;
sigma /= tr;
if(sigma < 0.1) {
VWarning(" 'fwhm/sigma' too small (%.3f / %.3f), will be set to zero", fwhm, sigma);
sigma = 0;
}
}
/*
** Read each input file
*/
nimages = in_files.number;
linfo = (ListInfo *) VMalloc(sizeof(ListInfo) * nimages);
for(i = 0; i < nimages; i++) {
in_filename = ((VStringConst *) in_files.vector)[i];
ifilename = VNewString(in_filename);
fprintf(stderr, " file: %s\n", ifilename);
list = GetListInfo(ifilename, &linfo[i]);
/* Create history */
if(i == 0) {
history_list = VReadHistory(&list);
if(history_list == NULL)
history_list = VCreateAttrList();
VPrependHistory(VNumber(options), options, prg_name, &history_list);
}
}
/*
** GLM
*/
out_list = VRegression(linfo, nimages, minval, design, sigma, itr);
/*
** Output:
*/
VPrependAttr(out_list, "history", NULL, VAttrListRepn, history_list);
f = VOpenOutputFile(out_filename, TRUE);
if(!f)
VError(" error opening outout file %s", out_filename);
if(! VWriteFile(f, out_list))
exit(1);
fprintf(stderr, "%s: done.\n", argv[0]);
return 0;
}
/* the main routine */
int main (int argc,char *argv[]) {
QApplication::setColorSpec( QApplication::ManyColor );
/* initialize preferences variables */
pr = prefsini();
/* write out the revision string */
char prg_name[100];
char ver[100];
getLipsiaVersion(ver, sizeof(ver));
sprintf(prg_name, "vlview V%s", ver);
fprintf (stderr, "%s\n", prg_name);
/* Parse command line arguments and identify files: */
if (! VParseCommand (VNumber (options), options, & argc, argv) ||
! VIdentifyFiles (VNumber (options), options, "in", & argc, argv, 0))
goto Usage;
if (argc > 1) {
VReportBadArgs (argc, argv);
Usage: VReportUsage (argv[0], VNumber (options), options, NULL);
exit (EXIT_FAILURE);
}
/* A. Hagert: exceptions */
if (mincol == 123456 && maxcol == 123456) { pr->col_min = 0; pr->col_max = 0; }
else if (mincol != 123456 && maxcol == 123456)
{ printf("ERROR: maximum not given -> ignoring given minimum.\n"); pr->col_min = 0; pr->col_max = 0; }
else if (mincol == 123456 && maxcol != 123456)
{ printf("ERROR: minimum not given -> ignoring given maximum.\n"); pr->col_min = 0; pr->col_max = 0; }
else if (mincol<=maxcol) { pr->col_min=mincol; pr->col_max=maxcol; }
else { printf("ERROR: given minimum is higher than maximum -> ignoring both.\n");
pr->col_min = 0; pr->col_max = 0;
}
/* set verbose option to prefs */
pr->prg_name=prg_name;
pr->verbose=verbose;
pr->raw=rawfile;
pr->des=desfile;
pr->beta=betafile;
pr->colortable=colortable_filename;
pr->graph[0]=graphfile;
pr->files=0;
pr->infilenum=in_files.number;
pr->zmapfilenum=zmap_files.number;
pr->thresh=th11;
pr->background0=background[0];
pr->background1=background[1];
if (pr->infilenum > pr->zmapfilenum)
pr->files=pr->infilenum;
else
pr->files=pr->zmapfilenum;
if (pr->infilenum==0)
VError("No infile specified");
if (pr->files>1)
VError("Use 'vlv' for visualization of data sets > 1");
/* get the number of graphs (pr->g_number) */
myload_.testFiles();
/* initialize open the main window */
QApplication a( argc, argv );
lView ww;
a.setMainWidget( &ww );
ww.show();
return a.exec();
/* end of the program */
}
int main(int argc, char *argv[]) {
static VArgVector in_files1;
static VArgVector in_files2;
static VString out_filename;
static VOptionDescRec options[] = {
{ "in1", VStringRepn, 0, & in_files1, VRequiredOpt, NULL, "Input files 1" },
{ "in2", VStringRepn, 0, & in_files2, VRequiredOpt, NULL, "Input files 2" },
{ "out", VStringRepn, 1, & out_filename, VRequiredOpt, NULL, "Output file" }
};
FILE *fp = NULL;
VStringConst in_filename, buf1, buf2;
VAttrList list1, list2, out_list;
VAttrListPosn posn;
VImage src, *src1, *src2, dest = NULL;
int i, nimages, npix = 0;
char prg_name[100];
char ver[100];
getLipsiaVersion(ver, sizeof(ver));
sprintf(prg_name, "vpaired_wilcoxtest V%s", ver);
fprintf(stderr, "%s\n", prg_name);
/*
** parse command line
*/
if(! VParseCommand(VNumber(options), options, & argc, argv)) {
VReportUsage(argv[0], VNumber(options), options, NULL);
exit(EXIT_FAILURE);
}
if(argc > 1) {
VReportBadArgs(argc, argv);
exit(EXIT_FAILURE);
}
/* number of images */
nimages = in_files1.number;
if(in_files2.number != nimages)
VError(" inconsistent number of files ");
for(i = 0; i < nimages; i++) {
buf1 = ((VStringConst *) in_files1.vector)[i];
buf2 = ((VStringConst *) in_files2.vector)[i];
fprintf(stderr, "%3d: %s %s\n", i, buf1, buf2);
}
fprintf(stderr, "\n");
/*
** read images 1
*/
src1 = (VImage *) VCalloc(nimages, sizeof(VImage));
for(i = 0; i < nimages; i++) {
src1[i] = NULL;
in_filename = ((VStringConst *) in_files1.vector)[i];
fp = VOpenInputFile(in_filename, TRUE);
list1 = VReadFile(fp, NULL);
if(! list1)
VError("Error reading image");
fclose(fp);
for(VFirstAttr(list1, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
if(VGetAttrRepn(& posn) != VImageRepn)
continue;
VGetAttrValue(& posn, NULL, VImageRepn, & src);
if(VPixelRepn(src) != VFloatRepn)
continue;
src1[i] = src;
break;
}
if(i == 0)
npix = VImageNPixels(src1[i]);
else if(npix != VImageNPixels(src1[i]))
VError(" inconsistent image dimensions");
if(src1[i] == NULL)
VError(" no image found in %s", in_filename);
}
/*
** read images 2
*/
src2 = (VImage *) VCalloc(nimages, sizeof(VImage));
for(i = 0; i < nimages; i++) {
src2[i] = NULL;
in_filename = ((VStringConst *) in_files2.vector)[i];
fp = VOpenInputFile(in_filename, TRUE);
list2 = VReadFile(fp, NULL);
if(! list2)
VError("Error reading image");
fclose(fp);
for(VFirstAttr(list2, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
if(VGetAttrRepn(& posn) != VImageRepn)
continue;
VGetAttrValue(& posn, NULL, VImageRepn, & src);
if(VPixelRepn(src) != VFloatRepn)
continue;
src2[i] = src;
break;
}
if(npix != VImageNPixels(src2[i]))
VError(" inconsistent image dimensions");
if(src2[i] == NULL)
VError(" no image found in %s", in_filename);
}
/*
** paired wilcoxon test
*/
dest = PairedWilcoxTest(src1, src2, dest, nimages);
/*
** output
*/
out_list = VCreateAttrList();
VHistory(VNumber(options), options, prg_name, &list1, &out_list);
VAppendAttr(out_list, "image", NULL, VImageRepn, dest);
fp = VOpenOutputFile(out_filename, TRUE);
if(! VWriteFile(fp, out_list))
exit(1);
fclose(fp);
fprintf(stderr, "%s: done.\n", argv[0]);
exit(0);
}
int main(int argc, char *argv[]) {
VAttrList list, out_list;
VImage src;
VImage dest = NULL;
VAttrListPosn posn;
VString str;
int nimages;
char historystr[] = "history";
char prg_name[100];
char ver[100];
getLipsiaVersion(ver, sizeof(ver));
sprintf(prg_name, "vdelcereb V%s", ver);
fprintf(stderr, "%s\n", prg_name);
/* Parse command line arguments: */
if(!VParseCommand(VNumber(options), options, &argc, argv) ||
! VIdentifyFiles(VNumber(options), options, "in", & argc, argv, 0) ||
! VIdentifyFiles(VNumber(options), options, "out", & argc, argv, -1))
goto Usage;
if(argc > 1) {
VReportBadArgs(argc, argv);
Usage:
VReportUsage(argv[0], VNumber(options), options, NULL);
exit(EXIT_FAILURE);
}
/* Read source image(s): */
if(strcmp(in_filename, "-") == 0)
in_file = stdin;
else {
in_file = fopen(in_filename, "r");
if(! in_file)
VError("Failed to open input file %s", in_filename);
}
if(!(list = VReadFile(in_file, NULL)))
exit(EXIT_FAILURE);
fclose(in_file);
/* Process image */
nimages = 0;
for(VFirstAttr(list, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
if(VGetAttrRepn(& posn) != VImageRepn)
continue;
VGetAttrValue(& posn, NULL, VImageRepn, & src);
dest = VCerebellum(src);
VSetAttrValue(& posn, NULL, VImageRepn, dest);
VDestroyImage(src);
nimages++;
break;
}
/* Create outlist */
out_list = VCreateAttrList();
/* Make History */
VHistory(VNumber(options), options, prg_name, &list, &out_list);
/* Alle Attribute (ausser history:) in die neue Liste schreiben: */
for(VFirstAttr(list, &posn); VAttrExists(&posn); VNextAttr(&posn)) {
if(strncmp(VGetAttrName(&posn), historystr, strlen(historystr)) == 0)
continue;
switch(VGetAttrRepn(&posn)) {
case VImageRepn:
VGetAttrValue(&posn, NULL, VImageRepn, &src);
VAppendAttr(out_list, VGetAttrName(&posn), NULL, VImageRepn, src);
break;
case VStringRepn:
VGetAttrValue(&posn, NULL, VStringRepn, &str);
VAppendAttr(out_list, VGetAttrName(&posn), NULL, VImageRepn, str);
break;
default:
break;
}
}
/* Write the results to the output file: */
if(strcmp(out_filename, "-") == 0)
out_file = stdout;
else {
out_file = fopen(out_filename, "w");
if(! out_file)
VError("Failed to open output file %s", out_filename);
}
if(VWriteFile(out_file, out_list)) {
if(verbose >= 1)
fprintf(stderr, "%s: processed %d image%s.\n",
argv[0], nimages, nimages == 1 ? "" : "s");
fprintf(stderr, "%s: done.\n", argv[0]);
}
return 0;
}
int main(int argc, char *argv[]) {
static VArgVector in_files;
static VString out_filename;
static VBoolean level = FALSE;
static VBoolean zscore = FALSE;
static VBoolean in_found, out_found;
static VOptionDescRec options[] = {
{
"in", VStringRepn, 0, & in_files, & in_found, NULL,
"Contrast images"
},
{
"out", VStringRepn, 1, & out_filename, & out_found, NULL,
"Output file"
},
{
"level", VBooleanRepn, 1, & level, VOptionalOpt, NULL,
"Whether to produce output to be used for 3rd level analysis"
}
/* { "zscore", VBooleanRepn, 1, & zscore, VOptionalOpt, NULL,
"Whether to produce z-scores as output"} */
};
FILE *f;
VStringConst in_filename;
VAttrList list, out_list;
VAttrListPosn posn;
VImage src = NULL;
VImage cbeta_images[N], sd_images[N];
int i, nimages = 0;
VString str = NULL;
char prg_name[100];
char ver[100];
getLipsiaVersion(ver, sizeof(ver));
sprintf(prg_name, "vbayes V%s", ver);
fprintf(stderr, "%s\n", prg_name);
/* Parse command line arguments: */
if(! VParseCommand(VNumber(options), options, & argc, argv) ||
! VIdentifyFiles(VNumber(options), options, "in", & argc, argv, 0) ||
! VIdentifyFiles(VNumber(options), options, "out", & argc, argv, -1))
goto Usage;
if(argc > 1) {
VReportBadArgs(argc, argv);
Usage:
VReportUsage(argv[0], VNumber(options), options, NULL);
exit(EXIT_FAILURE);
}
nimages = in_files.number;
fprintf(stderr, "Processing %d input files\n\n", nimages);
if(nimages >= N)
VError("Too many input images, max: %d", N);
if(nimages == 0)
VError("Input images missing");
/* loop through all input files */
for(i = 0; i < nimages; i++) {
in_filename = ((VStringConst *) in_files.vector)[i];
fprintf(stderr, "%s\n", in_filename);
f = fopen((char *)in_filename, "r");
if(! f)
VError("Failed to open input file %s", in_filename);
if(!(list = VReadFile(f, NULL)))
exit(EXIT_FAILURE);
fclose(f);
for(VFirstAttr(list, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
if(VGetAttrRepn(& posn) != VImageRepn)
continue;
VGetAttrValue(& posn, NULL, VImageRepn, & src);
if(VPixelRepn(src) != VFloatRepn)
continue;
VGetAttr(VImageAttrList(src), "modality", NULL, VStringRepn, &str);
if(strcmp(str, "conimg") == 0) {
cbeta_images[i] = VCopyImage(src, NULL, VAllBands);
} else if(strcmp(str, "std_dev") == 0 || strcmp(str, "sd") == 0) {
sd_images[i] = VCopyImage(src, NULL, VAllBands);
} else
VError(" Illegal input file! Make sure to use con-images as input");
}
}
/* calculate probabilities */
out_list = VBayes(cbeta_images, sd_images, nimages, level, zscore);
if(out_list == NULL)
VError(" no result");
/*
** output
*/
VHistory(VNumber(options), options, prg_name, &list, &out_list);
if(strcmp(out_filename, "-") == 0)
VError("Output file required");
f = fopen(out_filename, "w");
if(! f)
VError("Failed to open output file %s", out_filename);
if(! VWriteFile(f, out_list))
exit(EXIT_FAILURE);
fprintf(stderr, "\n%s: done \n", argv[0]);
return EXIT_SUCCESS;
}
int main(int argc, char *argv[]) {
/* command line arguments */
static VString out_filename;
static VArgVector in_files;
static VString trans_filename = "";
static VBoolean in_found, out_found;
static VShort minval = 0;
static VBoolean compress = TRUE;
static VFloat resolution = 3;
static VOptionDescRec options[] = {
{ "in", VStringRepn, 0, & in_files, & in_found, NULL, "Input file" },
{ "out", VStringRepn, 1, & out_filename, & out_found, NULL, "Output file" },
{
"trans", VStringRepn, 1, &trans_filename, VRequiredOpt, NULL,
"File containing transformation matrix"
},
{
"resolution", VFloatRepn, 1, &resolution, VOptionalOpt, NULL,
"Output voxel resolution in mm"
},
{
"minval", VShortRepn, 1, &minval, VOptionalOpt, NULL,
"Signal threshold"
},
{
"compress", VBooleanRepn, 1, &compress, VOptionalOpt, NULL,
"Whether to compress empty slices"
}
};
VStringConst in_filename;
FILE *in_file, *out_file, *fp;
VAttrList list, list1, out_list;
VAttrListPosn posn;
VImage trans = NULL;
VImage *dst_image;
VImageInfo *imageInfo;
int nobject = 0, ntimesteps = 0, nbands = 0, nrows = 0, ncols = 0;
VString ca, cp, extent, str;
int found = 0;
int j, dest_nbands;
char prg_name[100];
char ver[100];
getLipsiaVersion(ver, sizeof(ver));
sprintf(prg_name, "vfunctrans V%s", ver);
fprintf(stderr, "%s\n", prg_name);
/* Parse command line arguments: */
if(! VParseCommand(VNumber(options), options, & argc, argv) ||
! VIdentifyFiles(VNumber(options), options, "in", & argc, argv, 0) ||
! VIdentifyFiles(VNumber(options), options, "out", & argc, argv, -1))
goto Usage;
if(argc > 1) {
VReportBadArgs(argc, argv);
Usage:
VReportUsage(argv[0], VNumber(options), options, NULL);
exit(EXIT_FAILURE);
}
if(resolution <= 0)
VError(" 'resolution' must be an integer > 0");
/*
** Read the transformation matrix:
*/
fp = VOpenInputFile(trans_filename, TRUE);
list1 = VReadFile(fp, NULL);
if(! list1)
VError("Error reading image");
fclose(fp);
for(VFirstAttr(list1, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
if(VGetAttrRepn(& posn) != VImageRepn)
continue;
if(strncmp(VGetAttrName(&posn), "transform", 9) != 0)
continue;
VGetAttrValue(& posn, NULL, VImageRepn, & trans);
break;
}
if(trans == NULL)
VError("transformation matrix not found");
/*
** check attributes
*/
if(VGetAttr(VImageAttrList(trans), "ca", NULL,
VStringRepn, (VPointer) & ca) != VAttrFound)
VError(" attribute 'ca' missing in transformation matrix ");
if(VGetAttr(VImageAttrList(trans), "cp", NULL,
VStringRepn, (VPointer) & cp) != VAttrFound)
VError(" attribute 'cp' missing in transformation matrix ");
if(VGetAttr(VImageAttrList(trans), "extent", NULL,
VStringRepn, (VPointer) & extent) != VAttrFound)
VError(" attribute 'extent' missing in transformation matrix ");
/*
** open in-file
*/
if(in_files.number < 1 || in_files.number > 1)
VError(" incorrect number of input files: %d", in_files.number);
in_filename = ((VStringConst *) in_files.vector)[0];
if(strcmp(in_filename, "-") == 0)
in_file = stdin;
else {
in_file = fopen((char *)in_filename, "r");
if(! in_file)
VError("Failed to open input file %s", in_filename);
}
/*
** read file info
*/
if(! ReadHeader(in_file))
VError("error reading header");
if(!(list = ReadAttrList(in_file)))
VError("error reading attr list");
j = 0;
for(VFirstAttr(list, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
j++;
}
imageInfo = (VImageInfo *) VMalloc(sizeof(VImageInfo) * (j + 1));
nobject = nbands = found = 0;
for(VFirstAttr(list, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
str = VGetAttrName(&posn);
if(strncmp(str, "history", 7) == 0) {
nobject++;
continue;
}
VImageInfoIni(&imageInfo[nbands]);
if(! VGetImageInfo(in_file, list, nobject, &imageInfo[nbands]))
VError(" error reading image info");
if(imageInfo[nbands].repn == VShortRepn) {
found = 1;
nrows = imageInfo[nbands].nrows;
ncols = imageInfo[nbands].ncolumns;
ntimesteps = imageInfo[nbands].nbands;
nbands++;
}
nobject++;
}
fclose(in_file);
if(!found)
VError(" couldn't find functional data");
/*
** process each time step
*/
dst_image = VFunctrans(in_filename, imageInfo, nbands, trans, resolution,
ntimesteps, minval, compress, &dest_nbands);
/*
** output
*/
out_list = VCreateAttrList();
VHistory(VNumber(options), options, prg_name, &list, &out_list);
for(j = 0; j < dest_nbands; j++) {
VAppendAttr(out_list, "image", NULL, VImageRepn, dst_image[j]);
}
/* Open and write the output file: */
if(strcmp(out_filename, "-") == 0)
out_file = stdout;
else {
out_file = fopen(out_filename, "w");
if(! out_file)
VError("Failed to open output file %s", out_filename);
}
if(!VWriteFile(out_file, out_list) || fclose(out_file))
VSystemError("error writing output file");
fprintf(stderr, "\n%s: done.\n", argv[0]);
return (EXIT_SUCCESS);
}
int main(int argc, char *argv[]) {
static VArgVector in_files1;
static VArgVector in_files2;
static VArgVector mask_file;
static VArgVector report_file;
static VOptionDescRec options[] = {
{ "in1", VStringRepn, 0, & in_files1, VRequiredOpt, NULL, "Input files 1" },
{ "in2", VStringRepn, 0, & in_files2, VRequiredOpt, NULL, "Input files 2" },
{ "report", VStringRepn, 0, & report_file, VRequiredOpt, NULL, "Report file" },
{ "mask", VStringRepn, 0, & mask_file, VRequiredOpt, NULL, "Mask file(s)" }
};
FILE *fp = NULL;
VStringConst in_filename;
VAttrList list1, list2, list3;
VAttrListPosn posn;
VString str;
VImage src, *src1, *src2, *mask;
int i, nimages = 0, mimages = 0;
char prg_name[100];
char ver[100];
getLipsiaVersion(ver, sizeof(ver));
sprintf(prg_name, "vROIpaired_ttest V%s", ver);
fprintf(stderr, "%s\n", prg_name);
if(!VParseCommand(VNumber(options), options, & argc, argv)) {
VReportUsage(argv[0], VNumber(options), options, NULL);
exit(0);
}
/* get number of input images */
nimages = in_files1.number;
if(in_files2.number != nimages)
VError(" inconsistent number of files: in1: %d, in2: %d ",
nimages, in_files2.number);
mimages = mask_file.number;
if(nimages != mimages && mimages > 1)
VError(" inconsistent number of files, images: %d, masks: %d", nimages, mimages);
/* images 1 */
src1 = (VImage *) VMalloc(sizeof(VImage) * nimages);
for(i = 0; i < nimages; i++) {
src1[i] = NULL;
in_filename = ((VStringConst *) in_files1.vector)[i];
fp = VOpenInputFile(in_filename, TRUE);
if(!fp)
VError("Error opening file %s", in_filename);
list1 = VReadFile(fp, NULL);
if(! list1)
VError("Error reading file %s", in_filename);
fclose(fp);
for(VFirstAttr(list1, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
if(VGetAttrRepn(& posn) != VImageRepn)
continue;
VGetAttrValue(& posn, NULL, VImageRepn, & src);
if(VPixelRepn(src) != VFloatRepn)
continue;
if(VGetAttr(VImageAttrList(src), "modality", NULL, VStringRepn, &str) == VAttrFound) {
if(strcmp(str, "conimg") != 0)
continue;
}
src1[i] = src;
break;
}
if(src1[i] == NULL)
VError(" no contrast image found in %s", in_filename);
}
/* images 2 */
src2 = (VImage *) VMalloc(sizeof(VImage) * nimages);
for(i = 0; i < nimages; i++) {
src2[i] = NULL;
in_filename = ((VStringConst *) in_files2.vector)[i];
fp = VOpenInputFile(in_filename, TRUE);
if(!fp)
VError("Error opening file %s", in_filename);
list2 = VReadFile(fp, NULL);
if(! list2)
VError("Error reading file %s", in_filename);
fclose(fp);
for(VFirstAttr(list2, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
if(VGetAttrRepn(& posn) != VImageRepn)
continue;
VGetAttrValue(& posn, NULL, VImageRepn, & src);
if(VPixelRepn(src) != VFloatRepn)
continue;
if(VGetAttr(VImageAttrList(src), "modality", NULL, VStringRepn, &str) == VAttrFound) {
if(strcmp(str, "conimg") != 0)
continue;
}
src2[i] = src;
break;
}
if(src2[i] == NULL)
VError(" no contrast image found in %s", in_filename);
}
for(i = 0; i < nimages; i++) {
fprintf(stderr, "%3d: %s %s\n", i,
((VStringConst *) in_files1.vector)[i],
((VStringConst *) in_files2.vector)[i]);
}
fprintf(stderr, "\n");
/* mask images */
mask = (VImage *) VMalloc(sizeof(VImage) * mimages);
for(i = 0; i < mimages; i++) {
mask[i] = NULL;
in_filename = ((VStringConst *) mask_file.vector)[i];
fp = VOpenInputFile(in_filename, TRUE);
if(!fp)
VError("Error opening file %s", in_filename);
list3 = VReadFile(fp, NULL);
if(! list3)
VError("Error reading file", in_filename);
fclose(fp);
for(VFirstAttr(list3, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
if(VGetAttrRepn(& posn) != VImageRepn)
continue;
VGetAttrValue(& posn, NULL, VImageRepn, & src);
if(VPixelRepn(src) != VUByteRepn)
mask[i] = VConvertImageCopy(src, NULL, VAllBands, VUByteRepn);
else
mask[i] = src;
break;
}
if(mask[i] == NULL)
VError(" mask %d not found", i);
}
/* open report_file */
fp = NULL;
in_filename = ((VStringConst *) report_file.vector)[0];
fp = fopen(in_filename, "w");
if(!fp)
VError(" error opening file %s", in_filename);
/* paired t-test in ROIs */
VROIpaired_ttest(src1, src2, mask, nimages, mimages, fp);
exit(0);
}