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_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;
}
