VImage VImageManager::vtimestep( VAttrList list, VImage dest, int step )
{
VFillImage( dest, VAllBands, 0 );
VPointer src_pp = NULL;
VPointer dest_pp = NULL;
VAttrListPosn posn;
VShort *ptr1 = NULL;
VShort *ptr2 = NULL;
VString str;
VImage src;
int n = 0;
int npixels = 0;
bool revert = false;
for ( VFirstAttr ( list, & posn ); VAttrExists ( & posn ); VNextAttr ( & posn ) ) {
if ( VGetAttrRepn ( & posn ) != VImageRepn )
continue;
VGetAttrValue ( &posn, NULL, VImageRepn, &src );
if ( VPixelRepn( src ) != VShortRepn )
continue;
if ( ( VGetAttr ( VImageAttrList ( src ), "MPIL_vista_0", NULL,
VStringRepn, ( VPointer ) & str ) != VAttrFound ) &&
( VGetAttr ( VImageAttrList ( src ), "repetition_time", NULL,
VStringRepn, ( VPointer ) & str ) != VAttrFound ) )
continue;
/* doch nicht rumdrehen!
if (VGetAttr (VImageAttrList (src), "extent", NULL,
VStringRepn, (VPointer) & str) != VAttrFound)
revert = true;
*/
if ( n == 0 )
VCopyImageAttrs ( src, dest );
if ( VImageNRows( src ) > 1 ) {
if ( VSelectBand ( "vtimestep", src, step, &npixels, &src_pp ) == FALSE )
VError( "err reading data" );
int destBand = ( revert ) ? VImageNBands( dest ) - n - 1 : n;
dest_pp = VPixelPtr( dest, destBand, 0, 0 );
ptr1 = ( VShort * ) src_pp;
ptr2 = ( VShort * ) dest_pp;
memcpy ( ptr2, ptr1, npixels * sizeof( VShort ) );
}
n++;
}
return dest;
}
VBandInterp VImageColorInterp (VImage image)
{
VLong interp;
VGetAttrResult result;
if (VImageNBands (image) !=
(VImageNFrames (image) * VImageNViewpoints (image) *
VImageNColors (image) * VImageNComponents (image)))
VWarning ("VImageColorInterp: No. bands (%d) conflicts with no. "
"of frames, etc. (%d %d %d %d)",
VImageNBands (image), VImageNFrames (image),
VImageNViewpoints (image), VImageNColors (image),
VImageNComponents (image));
if (! VImageAttrList (image) ||
(result =
VGetAttr (VImageAttrList (image), VColorInterpAttr,
VBandInterpDict, VLongRepn, & interp)) == VAttrMissing)
return VImageNColors (image) > 1 ? VBandInterpOther : VBandInterpNone;
if (result == VAttrBadValue)
return VBandInterpOther;
switch (interp) {
case VBandInterpRGB:
if (VImageNColors (image) != 3) {
VWarning ("VBandColorInterp: RGB image has %d color dimension(s)",
VImageNColors (image));
return VBandInterpOther;
}
return VBandInterpRGB;
}
return VBandInterpOther;
}
/*
** read a 2nd level design file
*/
VImage
VRead2ndLevel(FILE *fp) {
VImage dest = NULL;
int i, j, nrows, ncols;
float val;
char buf[LEN], token[32];
nrows = ncols = 0;
while(!feof(fp)) {
memset(buf, 0, LEN);
if(!fgets(buf, LEN, fp))
break;
if(strlen(buf) < 1)
continue;
if(buf[0] == '%')
continue;
j = 0;
while(VStringToken(buf, token, j, 30)) {
if(!sscanf(token, "%f", &val))
VError("illegal input string: %s", token);
j++;
}
if(ncols == 0)
ncols = j;
if(j < 1)
continue;
else if(ncols != j)
VError(" inconsistent number of columns in row %d", nrows + 1);
nrows++;
}
rewind(fp);
dest = VCreateImage(1, nrows, ncols, VFloatRepn);
VFillImage(dest, VAllBands, 0);
VSetAttr(VImageAttrList(dest), "modality", NULL, VStringRepn, "X");
VSetAttr(VImageAttrList(dest), "name", NULL, VStringRepn, "X");
VSetAttr(VImageAttrList(dest), "ntimesteps", NULL, VLongRepn, (VLong)VImageNRows(dest));
VSetAttr(VImageAttrList(dest), "nsessions", NULL, VShortRepn, (VShort)1);
VSetAttr(VImageAttrList(dest), "designtype", NULL, VShortRepn, (VShort)2);
i = 0;
while(!feof(fp)) {
memset(buf, 0, LEN);
if(!fgets(buf, LEN, fp))
break;
if(strlen(buf) < 1)
continue;
if(buf[0] == '%')
continue;
j = 0;
while(VStringToken(buf, token, j, 30)) {
sscanf(token, "%f", &val);
VPixel(dest, 0, i, j, VFloat) = val;
j++;
}
if(j < 1)
continue;
i++;
}
return dest;
}
void FunctionalResize (VImage& Image, int Bands, int Rows, int Columns)
{
VImage zero; /* empty image */
/* resize image */
zero = VCreateImage (Bands, Rows, Columns, VShortRepn);
VImageAttrList (zero) = VCopyAttrList (VImageAttrList (Image));
VFillImage (zero, VAllBands, 0);
VDestroyImage (Image);
Image = zero;
} /* FunctionalResize */
/*
** concordance mapping
*/
VImage VCCM2(float *A1,float *A2,VImage map,int type)
{
VImage dest=NULL;
size_t b,r,c,i,j,k,kk,nvoxels;
int nslices=0,nrows=0,ncols=0;
double *arr1=NULL,*arr2=NULL,u;
nslices = VPixel(map,0,3,0,VShort);
nrows = VPixel(map,0,3,1,VShort);
ncols = VPixel(map,0,3,2,VShort);
nvoxels = VImageNColumns(map);
dest = VCreateImage(nslices,nrows,ncols,VFloatRepn);
VFillImage(dest,VAllBands,0);
VCopyImageAttrs (map, dest);
VSetAttr(VImageAttrList(dest),"modality",NULL,VStringRepn,"conimg");
arr1 = (double *) VCalloc(nvoxels,sizeof(double));
arr2 = (double *) VCalloc(nvoxels,sizeof(double));
fprintf(stderr," concordance mapping...\n");
for (i=0; i<nvoxels; i++) {
if (i%50 == 0) fprintf(stderr," %6d of %d\r",i,nvoxels);
b = (int)VPixel(map,0,0,i,VShort);
r = (int)VPixel(map,0,1,i,VShort);
c = (int)VPixel(map,0,2,i,VShort);
for (j=0; j<nvoxels; j++) arr1[j] = arr2[j] = 0;
kk = 0;
for (j=0; j<i; j++) {
k=j+i*(i+1)/2;
arr1[kk] = (double)A1[k];
arr2[kk] = (double)A2[k];
kk++;
}
for (j=i+1; j<nvoxels; j++) {
k=i+j*(j+1)/2;
arr1[kk] = (double)A1[k];
arr2[kk] = (double)A2[k];
kk++;
}
u = 0;
switch (type) {
case 0:
u = kendall(arr1,arr2,nvoxels);
break;
case 1:
u = CCC(arr1,arr2,nvoxels);
break;
default:
VError("illegal type");
}
VPixel(dest,b,r,c,VFloat) = (VFloat)u;
}
fprintf(stderr,"\n");
return dest;
}
const char *CVImage::getStringAttrib( const char *name, const VImage image )
{
char *value;
VGetAttrResult vresult = VGetAttr( VImageAttrList( image ), name, NULL, VStringRepn, &value );
if( vresult != VAttrFound )return NULL;
else return value;
}
const float CVImage::getFloatAttrib( const char *name, VImage image )
{
float value;
VGetAttrResult vresult = VGetAttr( VImageAttrList( image ), name, NULL, VFloatRepn, &value );
if( vresult != VAttrFound )return 0;
else return value;
}
const unsigned long CVImage::getNumberAttrib( const char *name, VImage image )
{
long value;
VGetAttrResult vresult = VGetAttr( VImageAttrList( image ), name, NULL, VLongRepn, &value );
if( vresult != VAttrFound )return 0;
else return value;
}
VImage
ConcatDesigns(VImage *design, int nimages) {
VImage dest = NULL;
VString buf = NULL;
VDouble x;
int i, r, c, row, col;
int nrows, ncols;
nrows = ncols = 0;
for(i = 0; i < nimages; i++) {
ncols += VImageNColumns(design[i]);
nrows += VImageNRows(design[i]);
}
dest = VCreateImage(1, nrows, ncols, VFloatRepn);
VFillImage(dest, VAllBands, 0);
VCopyImageAttrs(design[0], dest);
VSetAttr(VImageAttrList(dest), "nsessions", NULL, VShortRepn, (VShort)nimages);
buf = (VString) VMalloc(80);
buf[0] = '\0';
for(i = 0; i < nimages; i++)
sprintf(buf, "%s %d", buf, (int)VImageNRows(design[i]));
VSetAttr(VImageAttrList(dest), "session_lengths", NULL, VStringRepn, buf);
buf[0] = '\0';
for(i = 0; i < nimages; i++)
sprintf(buf, "%s %d", buf, (int)VImageNColumns(design[i]));
VSetAttr(VImageAttrList(dest), "session_covariates", NULL, VStringRepn, buf);
row = col = 0;
for(i = 0; i < nimages; i++) {
for(r = 0; r < VImageNRows(design[i]); r++) {
for(c = 0; c < VImageNColumns(design[i]); c++) {
x = VGetPixel(design[i], 0, r, c);
if(row + r >= VImageNRows(dest))
VError(" row: %d\n", row + r);
if(col + c >= VImageNColumns(dest))
VError(" column: %d\n", col + c);
VSetPixel(dest, 0, row + r, col + c, x);
}
}
row += VImageNRows(design[i]);
col += VImageNColumns(design[i]);
}
return dest;
}
VBoolean VSetBandInterp (VImage image,
VBandInterp frame_interp, int nframes,
VBandInterp viewpoint_interp, int nviewpoints,
VBandInterp color_interp, int ncolors,
VBandInterp component_interp, int ncomponents)
{
VBoolean result = TRUE;
VString str;
if (VImageNBands (image) !=
nframes * nviewpoints * ncolors * ncomponents) {
VWarning ("VSetBandInterp: No. bands (%d) conflicts with no. "
"of frames, etc. (%d %d %d %d)", VImageNBands (image),
nframes, nviewpoints, ncolors, ncomponents);
result = FALSE;
}
if (frame_interp == VBandInterpNone)
result &= VExtractAttr (VImageAttrList (image), VFrameInterpAttr,
NULL, VStringRepn, & str, FALSE);
else VSetAttr (VImageAttrList (image), VFrameInterpAttr,
VBandInterpDict, VLongRepn, (VLong) frame_interp);
VImageNFrames (image) = nframes;
if (viewpoint_interp == VBandInterpNone)
result &= VExtractAttr (VImageAttrList (image), VViewpointInterpAttr,
NULL, VStringRepn, & str, FALSE);
else VSetAttr (VImageAttrList (image), VViewpointInterpAttr,
VBandInterpDict, VLongRepn, (VLong) viewpoint_interp);
VImageNViewpoints (image) = nviewpoints;
if (color_interp == VBandInterpNone)
result &= VExtractAttr (VImageAttrList (image), VColorInterpAttr,
NULL, VStringRepn, & str, FALSE);
else VSetAttr (VImageAttrList (image), VColorInterpAttr,
VBandInterpDict, VLongRepn, (VLong) color_interp);
VImageNColors (image) = ncolors;
if (component_interp == VBandInterpNone)
result &= VExtractAttr (VImageAttrList (image), VComponentInterpAttr,
NULL, VStringRepn, & str, FALSE);
else VSetAttr (VImageAttrList (image), VComponentInterpAttr,
VBandInterpDict, VLongRepn, (VLong) component_interp);
VImageNComponents (image) = ncomponents;
return result;
}
static VAttrList VImageEncodeAttrMethod (VPointer value, size_t *lengthp)
{
VImage image = value;
VAttrList list;
size_t length;
#define OptionallyPrepend(value, name) \
if (value != 1) \
VPrependAttr (list, name, NULL, VLongRepn, (VLong) value)
/* Temporarily prepend several attributes to the image's attribute list: */
if ((list = VImageAttrList (image)) == NULL)
list = VImageAttrList (image) = VCreateAttrList ();
VPrependAttr (list, VRepnAttr, VNumericRepnDict,
VLongRepn, (VLong) VPixelRepn (image));
VPrependAttr (list, VNColumnsAttr, NULL,
VLongRepn, (VLong) VImageNColumns (image));
VPrependAttr (list, VNRowsAttr, NULL,
VLongRepn, (VLong) VImageNRows (image));
OptionallyPrepend (VImageNComponents (image), VNComponentsAttr);
OptionallyPrepend (VImageNColors (image), VNColorsAttr);
OptionallyPrepend (VImageNViewpoints (image), VNViewpointsAttr);
OptionallyPrepend (VImageNFrames (image), VNFramesAttr);
OptionallyPrepend (VImageNBands (image), VNBandsAttr);
/* Compute the file space needed for the image's binary data: */
length = VImageNPixels (image);
if (VPixelRepn (image) == VBitRepn)
length = (length + 7) / 8;
else length *= VPixelPrecision (image) / 8;
*lengthp = length;
return list;
#undef OptionallyPrepend
}
void VDestroyImage (VImage image)
{
if (image == NULL)
return;
if (! (image->flags & VImageSingleAlloc)) {
if (image->data != NULL) {
VFree (image->data);
}
if ((VPointer) image->row_index != NULL) {
VFree ((VPointer) image->row_index);
}
if ((VPointer) image->band_index != NULL) {
VFree ((VPointer) image->band_index);
}
}
if (VImageAttrList(image) != NULL) {
VDestroyAttrList (VImageAttrList (image));
}
if ((VPointer) image != NULL) {
VFree ((VPointer) image);
}
}
VImage
WriteOutput(VImage src,VImage map,int nslices,int nrows, int ncols, float *ev, int n)
{
VImage dest=NULL;
int i,b,r,c;
dest = VCreateImage(nslices,nrows,ncols,VFloatRepn);
VFillImage(dest,VAllBands,0);
VCopyImageAttrs (src, dest);
VSetAttr(VImageAttrList(dest),"modality",NULL,VStringRepn,"conimg");
for (i=0; i<n; i++) {
b = VPixel(map,0,0,i,VFloat);
r = VPixel(map,0,1,i,VFloat);
c = VPixel(map,0,2,i,VFloat);
if (b < 0 || r < 0 || c < 0) VError(" WriteOutput: illegal address %d %d %d",b,r,c);
VPixel(dest,b,r,c,VFloat) = ev[i];
}
return dest;
}
VAttrList
VNCM(VAttrList list,VImage mask,VShort minval,VShort first,VShort length,VFloat threshold)
{
VAttrList out_list=NULL;
VAttrListPosn posn;
VImage src[NSLICES],map=NULL;
VImage dest=NULL;
size_t b,r,c,i,j,i1,n,m,nt,last,ntimesteps,nrows,ncols,nslices;
gsl_matrix_float *mat=NULL;
float *A=NULL,*ev=NULL;
/*
** get image dimensions
*/
i = ntimesteps = nrows = ncols = 0;
for (VFirstAttr (list, & posn); VAttrExists (& posn); VNextAttr (& posn)) {
if (VGetAttrRepn (& posn) != VImageRepn) continue;
VGetAttrValue (& posn, NULL,VImageRepn, & src[i]);
if (VPixelRepn(src[i]) != VShortRepn) continue;
if (VImageNBands(src[i]) > ntimesteps) ntimesteps = VImageNBands(src[i]);
if (VImageNRows(src[i]) > nrows) nrows = VImageNRows(src[i]);
if (VImageNColumns(src[i]) > ncols) ncols = VImageNColumns(src[i]);
i++;
if (i >= NSLICES) VError(" too many slices");
}
nslices = i;
/* get time steps to include */
if (length < 1) length = ntimesteps-2;
last = first + length -1;
if (last >= ntimesteps) last = ntimesteps-1;
if (first < 0) first = 1;
nt = last - first + 1;
i1 = first+1;
if (nt < 2) VError(" not enough timesteps, nt= %d",nt);
fprintf(stderr,"# ntimesteps: %d, first= %d, last= %d, nt= %d\n",
(int)ntimesteps,(int)first,(int)last,(int)nt);
/* count number of voxels */
n = 0;
for (b=0; b<nslices; b++) {
if (VImageNRows(src[b]) < 2) continue;
for (r=0; r<nrows; r++) {
for (c=0; c<ncols; c++) {
if (VPixel(src[b],i1,r,c,VShort) < minval) continue;
if (VGetPixel(mask,b,r,c) < 0.5) continue;
n++;
}
}
}
fprintf(stderr," nvoxels: %ld\n",(long)n);
/*
** voxel addresses
*/
map = VCreateImage(1,5,n,VFloatRepn);
if (map == NULL) VError(" error allocating addr map");
VFillImage(map,VAllBands,0);
VPixel(map,0,3,0,VFloat) = nslices;
VPixel(map,0,3,1,VFloat) = nrows;
VPixel(map,0,3,2,VFloat) = ncols;
i = 0;
for (b=0; b<nslices; b++) {
if (VImageNRows(src[b]) < 2) continue;
for (r=0; r<nrows; r++) {
for (c=0; c<ncols; c++) {
if (VPixel(src[b],i1,r,c,VShort) < minval) continue;
if (VGetPixel(mask,b,r,c) < 0.5) continue;
VPixel(map,0,0,i,VFloat) = b;
VPixel(map,0,1,i,VFloat) = r;
VPixel(map,0,2,i,VFloat) = c;
i++;
}
}
}
/*
** avoid casting to float, copy data to matrix
*/
mat = gsl_matrix_float_calloc(n,nt);
for (i=0; i<n; i++) {
b = VPixel(map,0,0,i,VFloat);
r = VPixel(map,0,1,i,VFloat);
c = VPixel(map,0,2,i,VFloat);
float *ptr = gsl_matrix_float_ptr(mat,i,0);
int k;
j = 0;
for (k=first; k<=last; k++) {
if (j >= mat->size2) VError(" j= %d %d",j,mat->size2);
if (k >= VImageNBands(src[b])) VError(" k= %d %d",k, VImageNBands(src[b]));
*ptr++ = (float) VPixel(src[b],k,r,c,VShort);
j++;
}
}
/*
** compute similarity matrix
*/
m = (n*(n+1))/2;
fprintf(stderr," matrix computation, n= %ld...\n",(long)n);
A = (float *) calloc(m,sizeof(float));
if (!A) VError(" err allocating correlation matrix");
memset(A,0,m*sizeof(float));
size_t progress=0;
#pragma omp parallel for shared(progress) private(j) schedule(guided) firstprivate(mat,A)
for (i=0; i<n; i++) {
if (i%100 == 0) fprintf(stderr," %d00\r",(int)(++progress));
const float *arr1 = gsl_matrix_float_const_ptr(mat,i,0);
for (j=0; j<i; j++) {
const float *arr2 = gsl_matrix_float_const_ptr(mat,j,0);
const double v = Correlation(arr1,arr2,nt);
const size_t k=j+i*(i+1)/2;
if (k >= m) VError(" illegal addr k= %d, m= %d",k,m);
A[k] = (float)v;
}
}
fprintf(stderr," matrix done.\n");
gsl_matrix_float_free(mat);
/*
** eigenvector centrality
*/
ev = (float *) VCalloc(n,sizeof(float));
DegreeCentrality(A,ev,n,threshold);
dest = WriteOutput(src[0],map,nslices,nrows,ncols,ev,n);
VSetAttr(VImageAttrList(dest),"name",NULL,VStringRepn,"DegreeCM");
out_list = VCreateAttrList();
VAppendAttr(out_list,"image",NULL,VImageRepn,dest);
return out_list;
}
VAttrList
VGetContrast(VAttrList list, gsl_vector_float *con, VShort type) {
VAttrList out_list;
int nbands = 0, nrows = 0, ncols = 0, band, row, col;
VImage src = NULL, dest = NULL, std_image = NULL;
VImage beta_images[MBETA], res_image = NULL, bcov_image = NULL;
VString buf = NULL;
VAttrListPosn posn;
VString str;
int i, nbeta;
float t = 0, s = 0, tsigma = 0, z = 0, zmax = 0, zmin = 0;
float sigma, var, sum, df;
float *ptr1, *ptr2;
char *constring = NULL;
gsl_vector_float *beta = NULL, *tmp = NULL;
gsl_matrix_float *bcov = NULL;
i = 0;
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, "BETA") == 0) {
beta_images[i++] = VCopyImage(src, NULL, VAllBands);
} else if(strcmp(str, "RES/trRV") == 0) {
res_image = VCopyImage(src, NULL, VAllBands);
} else if(strcmp(str, "BCOV") == 0) {
bcov_image = VCopyImage(src, NULL, VAllBands);
}
}
nbeta = VImageNRows(bcov_image);
nbands = VImageNBands(beta_images[0]);
nrows = VImageNRows(beta_images[0]);
ncols = VImageNColumns(beta_images[0]);
if(VGetAttr(VImageAttrList(beta_images[0]), "df", NULL, VFloatRepn, &df) != VAttrFound)
VError(" attribute 'df' not found");
if(nbeta > MBETA) {
fprintf(stderr, " number of betas: %d, maximum number of betas: %d\n", nbeta, MBETA);
VError(" maximum number of betas is exceeded");
}
/*
** read contrast vector
*/
if(nbeta != con->size)
VError("contrast vector has bad length (%d), correct length is %d", con->size, nbeta);
fprintf(stderr, " contrast vector:\n");
char str1[10];
constring = (char *)VMalloc(sizeof(char) * 10 * nbeta);
constring[0] = '\0';
for(i = 0; i < nbeta; i++) {
fprintf(stderr, " %.2f", fvget(con, i));
sprintf(str1, "%1.2f ", fvget(con, i));
strcat((char *)constring, (const char *)str1);
}
fprintf(stderr, "\n");
/* get variance estimation */
bcov = gsl_matrix_float_alloc(nbeta, nbeta);
ptr1 = VImageData(bcov_image);
ptr2 = bcov->data;
for(i = 0; i < nbeta * nbeta; i++)
*ptr2++ = *ptr1++;
gsl_matrix_float_transpose(bcov);
tmp = fmat_x_vector(bcov, con, tmp);
var = fskalarproduct(tmp, con);
sigma = sqrt(var);
/*
** create output data structs
*/
out_list = VCreateAttrList();
dest = VCreateImage(nbands, nrows, ncols, VFloatRepn);
VFillImage(dest, VAllBands, 0);
VCopyImageAttrs(beta_images[0], dest);
switch(type) {
case 0: /* conimg */
buf = VNewString("conimg");
break;
case 1: /* t-image */
buf = VNewString("tmap");
break;
case 2: /* zmap */
buf = VNewString("zmap");
break;
default:
VError(" illegal type");
}
fprintf(stderr, " output type: %s\n", buf);
VSetAttr(VImageAttrList(dest), "modality", NULL, VStringRepn, buf);
VSetAttr(VImageAttrList(dest), "name", NULL, VStringRepn, buf);
VSetAttr(VImageAttrList(dest), "contrast", NULL, VStringRepn, constring);
VAppendAttr(out_list, "image", NULL, VImageRepn, dest);
if(type == 0) {
std_image = VCreateImage(nbands, nrows, ncols, VFloatRepn);
VFillImage(std_image, VAllBands, 0);
VCopyImageAttrs(beta_images[0], std_image);
VSetAttr(VImageAttrList(std_image), "modality", NULL, VStringRepn, "std_dev");
VSetAttr(VImageAttrList(std_image), "name", NULL, VStringRepn, "std_dev");
VAppendAttr(out_list, "image", NULL, VImageRepn, std_image);
}
/*
** loop thru image
*/
zmax = zmin = 0;
beta = gsl_vector_float_alloc(nbeta);
for(band = 0; band < nbands; band++) {
for(row = 0; row < nrows; row++) {
for(col = 0; col < ncols; col++) {
t = z = sum = 0;
ptr1 = beta->data;
for(i = 0; i < nbeta; i++) {
*ptr1++ = VPixel(beta_images[i], band, row, col, VFloat);
}
sum = fskalarproduct(beta, con);
if(ABS(sum) < 1.0e-10)
continue;
s = VPixel(res_image, band, row, col, VFloat);
tsigma = sqrt(s) * sigma;
if(tsigma > 0.00001)
t = sum / tsigma;
else
t = 0;
if(isnan(t) || isinf(t))
t = 0;
switch(type) {
case 0: /* conimg */
z = sum;
break;
case 1: /* t-image */
z = t;
break;
case 2: /* zmap */
z = t2z_approx(t, df);
if(z > 30)
z = 30;
if(sum < 0)
z = -z;
break;
default:
;
}
if(isnan(z) || isinf(z))
z = 0;
if(z > zmax)
zmax = z;
if(z < zmin)
zmin = z;
VPixel(dest, band, row, col, VFloat) = z;
if(type == 0)
VPixel(std_image, band, row, col, VFloat) = tsigma;
}
}
}
fprintf(stderr, " min= %.3f, max= %.3f\n", zmin, zmax);
return out_list;
}
void VImageManager::init( VAttrList list )
{
VAttrListPosn posn;
int nbands = 0;
int nrows = 0;
int ncols = 0;
int timeSlices = 2;
VImage src;
VString str;
for ( VFirstAttr ( list, & posn ); VAttrExists ( & posn ); VNextAttr ( & posn ) ) {
if ( VGetAttrRepn ( & posn ) != VImageRepn )
continue;
VGetAttrValue ( &posn, NULL, VImageRepn, &src );
if ( VPixelRepn( src ) != VShortRepn )
continue;
// check if we have a functional data image
if ( ( VGetAttr ( VImageAttrList ( src ), "MPIL_vista_0", NULL,
VStringRepn, ( VPointer ) & str ) == VAttrFound ) ||
( VGetAttr ( VImageAttrList ( src ), "repetition_time", NULL,
VStringRepn, ( VPointer ) & str ) == VAttrFound ) ) {
if ( VImageNRows( src ) > nrows )
nrows = VImageNRows( src );
if ( VImageNColumns( src ) > ncols )
ncols = VImageNColumns( src );
if ( VImageNBands( src ) > timeSlices )
timeSlices = VImageNBands( src );
nbands++;
}
}
if ( nbands == 0 )
VError( "No raw data found" );
// now loading the vimages
int currentTimeSlice = 0; // curr slice
for ( currentTimeSlice = 0; currentTimeSlice < timeSlices; currentTimeSlice++ ) {
VImage dest = VCreateImage( nbands, nrows, ncols, VShortRepn );
vtimestep( list, dest, currentTimeSlice );
m_imageList.append( dest );
}
prepareScaleValue();
// creating data arrays
int size = ncols * nbands;
m_coronarData = new unsigned char[size];
memset( m_coronarData, 0, size * sizeof( unsigned char ) );
size = ncols * nrows;
m_axialData = new unsigned char[size];
memset( m_axialData, 0, size * sizeof( unsigned char ) );
size = nbands * nrows;
m_sagittalData = new unsigned char[size];
memset( m_sagittalData, 0, size * sizeof( unsigned char ) );
}
VImage
VDoTrans(VImage src, VImage dest, VImage transform, VFloat resolution, VLong type) {
VImage src1 = NULL, dest_cor = NULL, dest_sag = NULL, trans = NULL;
int i, nbands1 = 0, nrows1 = 0, ncols1 = 0;
int xdim, ydim, zdim;
int orient = AXIAL;
float b0, r0, c0;
float scaleb, scaler, scalec;
float scale[3], shift[3];
VString str, str1, str2, str3, str4, str5, str6;
VShort buf;
VDouble u;
float transResX = 1.0, transResY = 1.0, transResZ = 1.0;
VString _transResString;
if(VGetAttr(VImageAttrList(transform), "voxel", NULL, VStringRepn, (VPointer) &_transResString) == VAttrFound) {
sscanf(_transResString, "%f %f %f", &transResX, &transResY, &transResZ);
}
/*
** get matrix size
*/
xdim = 160;
ydim = 200;
zdim = 160;
if(VGetAttr(VImageAttrList(transform), "zdim", NULL,
VShortRepn, (VPointer) & buf) == VAttrFound) {
zdim = buf;
}
if(VGetAttr(VImageAttrList(transform), "ydim", NULL,
VShortRepn, (VPointer) & buf) == VAttrFound) {
ydim = buf;
}
if(VGetAttr(VImageAttrList(transform), "xdim", NULL,
VShortRepn, (VPointer) & buf) == VAttrFound) {
xdim = buf;
}
/*
** get slice orientation
*/
if(VGetAttr(VImageAttrList(src), "orientation", NULL,
VStringRepn, (VPointer) & str) != VAttrFound)
VError(" attribute 'orientation' missing in input file.");
if(strcmp(str, "coronal") == 0) {
orient = CORONAL;
nbands1 = ydim;
nrows1 = zdim;
ncols1 = xdim;
} else if(strcmp(str, "axial") == 0) {
orient = AXIAL;
nbands1 = zdim;
nrows1 = ydim;
ncols1 = xdim;
} else if(strcmp(str, "sagittal") == 0) {
orient = SAGITTAL;
nbands1 = zdim;
nrows1 = xdim;
ncols1 = ydim;
} else
VError("orientation must be axial or coronal");
nbands1 /= (resolution / transResX);
nrows1 /= (resolution / transResY);
ncols1 /= (resolution / transResZ);
/*
** scale to size
*/
if(VGetAttr(VImageAttrList(src), "voxel", NULL,
VStringRepn, (VPointer) & str) != VAttrFound)
VError(" attribute 'voxel' missing in input file.");
sscanf(str, "%f %f %f", &scalec, &scaler, &scaleb);
scaleb /= (resolution / transResX);
scaler /= (resolution / transResY);
scalec /= (resolution / transResZ);
scale[0] = scaleb;
scale[1] = scaler;
scale[2] = scalec;
shift[0] = 0;
shift[1] = (float)nrows1 * 0.5 - scaler * (float)VImageNRows(src) * 0.5;
shift[2] = (float)ncols1 * 0.5 - scalec * (float)VImageNColumns(src) * 0.5;
src1 = VShuffleSlices(src, NULL);
switch(type) {
case 0:
src = VTriLinearScale3d(src1, NULL, nbands1, nrows1, ncols1, shift, scale);
break;
case 1:
src = VNNScale3d(src1, NULL, nbands1, nrows1, ncols1, shift, scale);
break;
default:
VError(" illegal resampling type");
}
/*
** resample image
*/
trans = VCopyImage(transform, NULL, VAllBands);
for(i = 0; i < 3; i++) {
u = VPixel(trans, 0, i, 0, VDouble);
u /= resolution;
VPixel(trans, 0, i, 0, VDouble) = u;
}
b0 = (float)nbands1 * 0.5;
r0 = (float)nrows1 * 0.5;
c0 = (float)ncols1 * 0.5;
switch(type) {
case 0:
dest = VTriLinearSample3d(src, dest, trans, b0, r0, c0, nbands1, nrows1, ncols1);
break;
case 1:
dest = VNNSample3d(src, dest, trans, b0, r0, c0, nbands1, nrows1, ncols1);
break;
}
/*
** update header
*/
float _cax, _cay, _caz, _cpx, _cpy, _cpz;
float _fixpointx, _fixpointy, _fixpointz;
str1 = str2 = str3 = str4 = NULL;
str1 = (VString) VMalloc(80);
sprintf(str1, "%.2f %.2f %.2f", resolution, resolution, resolution);
if(VGetAttr(VImageAttrList(trans), "ca", NULL,
VStringRepn, (VPointer) & str2) != VAttrFound) {
str2 = NULL;
} else {
sscanf(str2, "%f %f %f", &_cax, &_cay, &_caz);
_cax /= (resolution / transResX);
_cay /= (resolution / transResY);
_caz /= (resolution / transResZ);
sprintf(str2, "%.2f %.2f %.2f", _cax, _cay, _caz);
}
if(VGetAttr(VImageAttrList(trans), "cp", NULL,
VStringRepn, (VPointer) & str3) != VAttrFound) {
str3 = NULL;
} else {
sscanf(str3, "%f %f %f", &_cpx, &_cpy, &_cpz);
_cpx /= (resolution / transResX);
_cpy /= (resolution / transResY);
_cpz /= (resolution / transResZ);
sprintf(str3, "%.2f %.2f %.2f", _cpx, _cpy, _cpz);
}
if(VGetAttr(VImageAttrList(trans), "extent", NULL,
VStringRepn, (VPointer) & str4) != VAttrFound)
str4 = NULL;
if(VGetAttr(VImageAttrList(trans), "fixpoint", NULL,
VStringRepn, (VPointer) & str5) != VAttrFound) {
str5 = NULL;
} else {
sscanf(str5, "%f %f %f", &_fixpointx, &_fixpointy, &_fixpointz);
_fixpointx /= (resolution / transResX);
_fixpointy /= (resolution / transResY);
_fixpointz /= (resolution / transResZ);
sprintf(str5, "%.2f %.2f %.2f", _fixpointx, _fixpointy, _fixpointz);
}
if(VGetAttr(VImageAttrList(trans), "talairach", NULL,
VStringRepn, (VPointer) & str6) != VAttrFound) {
str6 = NULL;
}
if(orient == CORONAL) {
dest_cor = VAxial2Coronal(dest, NULL);
VDestroyImage(dest);
VCopyImageAttrs(src, dest_cor);
VSetAttr(VImageAttrList(dest_cor), "voxel", NULL, VStringRepn, str1);
if(str2)
VSetAttr(VImageAttrList(dest_cor), "ca", NULL, VStringRepn, str2);
if(str3)
VSetAttr(VImageAttrList(dest_cor), "cp", NULL, VStringRepn, str3);
if(str4)
VSetAttr(VImageAttrList(dest_cor), "extent", NULL, VStringRepn, str4);
if(str5)
VSetAttr(VImageAttrList(dest_cor), "fixpoint", NULL, VStringRepn, str5);
if(str6)
VSetAttr(VImageAttrList(dest_cor), "talairach", NULL, VStringRepn, str6);
return dest_cor;
} else if(orient == SAGITTAL) {
dest_sag = VAxial2Sagittal(dest, NULL);
VDestroyImage(dest);
VCopyImageAttrs(src, dest_sag);
VSetAttr(VImageAttrList(dest_sag), "voxel", NULL, VStringRepn, str1);
if(str2)
VSetAttr(VImageAttrList(dest_sag), "ca", NULL, VStringRepn, str2);
if(str3)
VSetAttr(VImageAttrList(dest_sag), "cp", NULL, VStringRepn, str3);
if(str4)
VSetAttr(VImageAttrList(dest_sag), "extent", NULL, VStringRepn, str4);
if(str5)
VSetAttr(VImageAttrList(dest_sag), "fixpoint", NULL, VStringRepn, str5);
if(str6)
VSetAttr(VImageAttrList(dest_sag), "talairach", NULL, VStringRepn, str6);
return dest_sag;
} else {
VCopyImageAttrs(src, dest);
VSetAttr(VImageAttrList(dest), "voxel", NULL, VStringRepn, str1);
if(str2)
VSetAttr(VImageAttrList(dest), "ca", NULL, VStringRepn, str2);
if(str3)
VSetAttr(VImageAttrList(dest), "cp", NULL, VStringRepn, str3);
if(str4)
VSetAttr(VImageAttrList(dest), "extent", NULL, VStringRepn, str4);
if(str5)
VSetAttr(VImageAttrList(dest), "fixpoint", NULL, VStringRepn, str5);
if(str6)
VSetAttr(VImageAttrList(dest), "talairach", NULL, VStringRepn, str6);
return dest;
}
}
VImage
SimilarityMatrix(VAttrList list, VImage mask, VShort minval, VShort fisher) {
VAttrListPosn posn;
VImage src[NSLICES], dest = NULL, map = NULL;
int b, r, c, i, j, n, ntimesteps, nrows, ncols, nslices;
double u, x, y, smin, smax, tiny = 1.0e-6;
gsl_matrix_float *mat = NULL;
/*
** get image dimensions
*/
i = ntimesteps = nrows = ncols = 0;
for(VFirstAttr(list, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
if(VGetAttrRepn(& posn) != VImageRepn)
continue;
VGetAttrValue(& posn, NULL, VImageRepn, & src[i]);
if(VPixelRepn(src[i]) != VShortRepn)
continue;
if(VImageNBands(src[i]) > ntimesteps)
ntimesteps = VImageNBands(src[i]);
if(VImageNRows(src[i]) > nrows)
nrows = VImageNRows(src[i]);
if(VImageNColumns(src[i]) > ncols)
ncols = VImageNColumns(src[i]);
i++;
if(i >= NSLICES)
VError(" too many slices");
}
nslices = i;
n = 0;
for(b = 0; b < nslices; b++) {
if(VImageNRows(src[b]) < 2)
continue;
for(r = 0; r < nrows; r++) {
for(c = 0; c < ncols; c++) {
if(VPixel(src[b], 0, r, c, VShort) < minval)
continue;
if(VGetPixel(mask, b, r, c) < 0.1)
continue;
n++;
}
}
}
fprintf(stderr, " n: %d\n", n);
/*
** voxel addresses
*/
map = VCreateImage(1, 5, n, VFloatRepn);
VFillImage(map, VAllBands, 0);
VPixel(map, 0, 3, 0, VFloat) = nslices;
VPixel(map, 0, 3, 1, VFloat) = nrows;
VPixel(map, 0, 3, 2, VFloat) = ncols;
i = 0;
for(b = 0; b < nslices; b++) {
if(VImageNRows(src[b]) < 2)
continue;
for(r = 0; r < nrows; r++) {
for(c = 0; c < ncols; c++) {
if(VPixel(src[b], 0, r, c, VShort) < minval)
continue;
if(VGetPixel(mask, b, r, c) < 0.1)
continue;
VPixel(map, 0, 0, i, VFloat) = b;
VPixel(map, 0, 1, i, VFloat) = r;
VPixel(map, 0, 2, i, VFloat) = c;
i++;
}
}
}
/* ini output image */
if(n < 8000)
dest = VCreateImage(1, n, n, VFloatRepn);
else if(n >= 8000 && n < 10000)
dest = VCreateImage(1, n, n, VShortRepn);
else
dest = VCreateImage(1, n, n, VSByteRepn);
VFillImage(dest, VAllBands, 0);
smin = VPixelMinValue(dest);
smax = VPixelMaxValue(dest);
/*
** avoid casting to float, copy data to matrix
*/
mat = gsl_matrix_float_calloc(n, ntimesteps);
for(i = 0; i < n; i++) {
b = VPixel(map, 0, 0, i, VFloat);
r = VPixel(map, 0, 1, i, VFloat);
c = VPixel(map, 0, 2, i, VFloat);
float *ptr = gsl_matrix_float_ptr(mat, i, 0);
int k;
j = 0;
for(k = 0; k < ntimesteps; k++) {
if(j >= mat->size2)
VError(" j= %d %d", j, mat->size2);
if(k >= VImageNBands(src[b]))
VError(" k= %d %d", k, VImageNBands(src[b]));
*ptr++ = (float) VPixel(src[b], k, r, c, VShort);
j++;
}
}
/*
** main process loop
*/
for(i = 0; i < n; i++) {
if(i % 50 == 0)
fprintf(stderr, " i: %4d\r", i);
const float *arr1 = gsl_matrix_float_const_ptr(mat, i, 0);
for(j = 0; j <= i; j++) {
const float *arr2 = gsl_matrix_float_const_ptr(mat, j, 0);
u = Correlation(arr1, arr2, ntimesteps);
/* Fisher r-to-z transform */
if(fisher) {
x = 1 + u;
y = 1 - u;
if(x < tiny)
x = tiny;
if(y < tiny)
y = tiny;
u = 0.5 * log(x / y);
}
if(VPixelRepn(dest) != VFloatRepn) {
u *= smax;
if(u < smin)
u = smin;
if(u > smax)
u = smax;
}
VSetPixel(dest, 0, i, j, u);
VSetPixel(dest, 0, j, i, u);
}
}
VCopyImageAttrs(src[0], dest);
VSetAttr(VImageAttrList(dest), "similarity_metric", NULL, VStringRepn, "corr_pearson");
VSetAttr(VImageAttrList(dest), "name", NULL, VStringRepn, "similarity_matrix");
VSetAttr(VImageAttrList(dest), "map", NULL, VImageRepn, map);
return dest;
}
/*
** slicetime correction for non-constant TR
*/
void
VSlicetime_NC(VAttrList list, VShort minval, VFloat tdel,
VBoolean slicetime_correction, float *onset_array, VString filename) {
FILE *fp = NULL;
VImage src;
VAttrListPosn posn;
VString buf, str;
int b, r, c, i, j, nt = 0, mt = 0, val, del = 0;
double xmin, xmax, sum, nx, estim_tr = 0;
double *xx = NULL, *yy = NULL, xi, yi, slicetime = 0, u = 0;
gsl_interp_accel *acc = NULL;
gsl_spline *spline = NULL;
xmin = (VShort) VRepnMinValue(VShortRepn);
xmax = (VShort) VRepnMaxValue(VShortRepn);
buf = VMalloc(LEN);
/*
** read scan times from file, non-constant TR
*/
if(strlen(filename) > 2) {
fp = fopen(filename, "r");
if(!fp)
VError(" error opening file %s", filename);
i = 0;
while(!feof(fp)) {
for(j = 0; j < LEN; j++)
buf[j] = '\0';
fgets(buf, LEN, fp);
if(buf[0] == '%' || buf[0] == '#')
continue;
if(strlen(buf) < 2)
continue;
i++;
}
rewind(fp);
nt = i;
fprintf(stderr, " num timesteps: %d\n", nt);
xx = (double *) VCalloc(nt, sizeof(double));
yy = (double *) VCalloc(nt, sizeof(double));
i = 0;
sum = 0;
while(!feof(fp)) {
for(j = 0; j < LEN; j++)
buf[j] = '\0';
fgets(buf, LEN, fp);
if(buf[0] == '%' || buf[0] == '#')
continue;
if(strlen(buf) < 2)
continue;
if(sscanf(buf, "%lf", &u) != 1)
VError(" line %d: illegal input format", i + 1);
xx[i] = u * 1000.0; /* convert to millisec */
if(i > 1)
sum += xx[i] - xx[i - 1];
i++;
}
fclose(fp);
estim_tr = sum / (double)(nt - 2);
fprintf(stderr, " average scan interval = %.3f sec\n", estim_tr / 1000.0);
}
/*
** process data
*/
b = -1;
for(VFirstAttr(list, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
if(VGetAttrRepn(& posn) != VImageRepn)
continue;
VGetAttrValue(& posn, NULL, VImageRepn, & src);
if(VPixelRepn(src) != VShortRepn)
continue;
VSetAttr(VImageAttrList(src), "repetition_time", NULL, VLongRepn, (VLong)estim_tr);
VExtractAttr(VImageAttrList(src), "MPIL_vista_0", NULL, VStringRepn, &str, FALSE);
b++;
if(VImageNRows(src) < 2)
continue;
/*
** get header info
*/
if(VGetAttr(VImageAttrList(src), "slice_time", NULL,
VDoubleRepn, (VPointer) & slicetime) != VAttrFound && slicetime_correction && onset_array == NULL)
VError(" 'slice_time' info missing");
if(onset_array != NULL)
slicetime = onset_array[b];
if(nt != VImageNBands(src))
VError(" inconsistent number of time steps, %d %d",
nt, VImageNBands(src));
if(acc == NULL && slicetime_correction) {
acc = gsl_interp_accel_alloc();
spline = gsl_spline_alloc(gsl_interp_akima, nt);
for(i = 0; i < 5; i++) {
if(xx[i] / 1000.0 > tdel)
break;
}
del = i;
fprintf(stderr, " The first %.2f secs (%d timesteps) will be replaced.\n", tdel, del);
}
/*
** loop through all voxels in current slice
*/
if(slicetime_correction)
fprintf(stderr, " slice: %3d, %10.3f ms\r", b, slicetime);
for(r = 0; r < VImageNRows(src); r++) {
for(c = 0; c < VImageNColumns(src); c++) {
if(VPixel(src, 0, r, c, VShort) < minval)
continue;
/* replace first few time steps by average */
if(del > 0) {
mt = del + 10;
if(mt > nt)
mt = nt;
sum = nx = 0;
for(i = del; i < mt; i++) {
sum += VPixel(src, i, r, c, VShort);
nx++;
}
if(nx < 1)
continue;
val = sum / nx;
for(i = 0; i < del; i++) {
VPixel(src, i, r, c, VShort) = val;
}
}
if(!slicetime_correction)
continue;
/* correct for slicetime offsets using cubic spline interpolation */
for(i = 0; i < nt; i++) {
yy[i] = VPixel(src, i, r, c, VShort);
}
gsl_spline_init(spline, xx, yy, nt);
for(i = 1; i < nt; i++) {
xi = xx[i] - slicetime;
yi = gsl_spline_eval(spline, xi, acc);
val = (int)(yi + 0.49);
if(val > xmax)
val = xmax;
if(val < xmin)
val = xmin;
VPixel(src, i, r, c, VShort) = val;
}
}
}
}
fprintf(stderr, "\n");
}
int main(int argc, char *argv[]) {
static VLong objnr = -1;
static VString name = "";
static VString value = "";
static VOptionDescRec options[] = {
{
"obj", VLongRepn, 1, (VPointer) &objnr,
VOptionalOpt, NULL, "object number, all objects (-1)"
},
{
"name", VStringRepn, 1, (VPointer) &name,
VRequiredOpt, NULL, "attribute name"
},
{
"value", VStringRepn, 1, (VPointer) &value,
VRequiredOpt, NULL, "attribute value"
}
};
FILE *in_file, *out_file;
VAttrList list, olist;
VAttrListPosn posn;
VImage isrc;
VGraph gsrc;
Volumes vsrc;
VString buf;
int nobj;
char prg_name[100];
char ver[100];
getLipsiaVersion(ver, sizeof(ver));
sprintf(prg_name, "vattredit V%s", ver);
fprintf(stderr, "%s\n", prg_name);
/* Parse command line arguments and identify files: */
VParseFilterCmd(VNumber(options), options, argc, argv,
&in_file, & out_file);
/* Read source image(s): */
if(!(list = VReadFile(in_file, NULL)))
exit(1);
/* Process each image: */
nobj = 0;
for(VFirstAttr(list, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
olist = NULL;
if(nobj == objnr || objnr < 0) {
if(VGetAttrRepn(& posn) == VImageRepn) {
VGetAttrValue(& posn, NULL, VImageRepn, & isrc);
olist = VImageAttrList(isrc);
} else if(VGetAttrRepn(& posn) == VGraphRepn) {
VGetAttrValue(& posn, NULL, VGraphRepn, & gsrc);
olist = VGraphAttrList(gsrc);
} else if(VGetAttrRepn(& posn) == VolumesRepn) {
VGetAttrValue(& posn, NULL, VolumesRepn, & vsrc);
olist = VolumesAttrList(vsrc);
}
if(olist != NULL) {
if(VGetAttr(olist, name, NULL, VStringRepn, &buf) == VAttrFound)
fprintf(stderr, " object %3d, old value: %s\n", nobj, buf);
VSetAttr(olist, name, NULL, VStringRepn, value);
fprintf(stderr, " object %3d, new value: %s\n", nobj, value);
}
}
nobj++;
}
/* Make History */
VHistory(VNumber(options), options, prg_name, &list, &list);
/* Write out the results: */
if(! VWriteFile(out_file, list))
exit(1);
fprintf(stderr, "%s: done.\n", argv[0]);
return 0;
}
VImage
VCerebellum(VImage src) {
VImage coronal, label_coronal;
VImage sagital, label_sagital;
VImage axial, label_axial;
VImage bin0_image, bin1_image, label_image;
VBit *bin0_pp, *src_pp;
VUByte *ubyte_pp;
int i, nbands, nrows, ncols, npixels, nl = 0;
float x0, x1, x2;
VString str;
int b, r, c, cp, rp, bp, slice_extent, slice_origin, b0;
nbands = VImageNBands(src);
nrows = VImageNRows(src);
ncols = VImageNColumns(src);
npixels = nbands * nrows * ncols;
str = VMalloc(80);
if(VGetAttr(VImageAttrList(src), "cp", NULL, VStringRepn, (VPointer) &str) != VAttrFound)
VError(" attribute 'cp' not found");
sscanf(str, "%f %f %f", &x0, &x1, &x2);
bp = (int) VRint((double) x2);
rp = (int) VRint((double) x1);
cp = (int) VRint((double) x0);
if(VGetAttr(VImageAttrList(src), "extent", NULL, VStringRepn, (VPointer) &str) != VAttrFound)
VError(" attribute 'extent' not found");
sscanf(str, "%f %f %f", &x0, &x1, &x2);
slice_extent = (int) VRint((double) x2);
if(VGetAttr(VImageAttrList(src), "origin", NULL, VStringRepn, (VPointer) &str) != VAttrFound)
VError(" attribute 'origin' not found");
sscanf(str, "%f %f %f", &x0, &x1, &x2);
slice_origin = (int) VRint((double) x2);
/* erode */
bin1_image = VDTErode(src, NULL, (VDouble) 2.0);
/* readdress to coronal slices and remove small 2D components */
coronal = VCreateImage(1, nbands, ncols, VBitRepn);
label_coronal = VCreateImage(1, nbands, ncols, VUByteRepn);
ubyte_pp = (VUByte *) VImageData(label_coronal);
for(i = 0; i < (nbands * ncols); i++)
*ubyte_pp++ = 0;
for(r = rp; r < nrows; r++) {
bin0_pp = (VBit *) VImageData(coronal);
for(i = 0; i < (nbands * ncols); i++)
*bin0_pp++ = 0;
for(b = 0; b < nbands; b++) {
for(c = 0; c < ncols; c++) {
VPixel(coronal, 0, b, c, VBit) = VPixel(bin1_image, b, r, c, VBit);
}
}
label_coronal = VLabelImage2d(coronal, label_coronal, 8, VUByteRepn, &nl);
VDeleteCereb(label_coronal, &coronal, 110, (int) 0);
for(b = 0; b < nbands; b++) {
for(c = 0; c < ncols; c++) {
if(VPixel(coronal, 0, b, c, VBit) == 0)
VPixel(bin1_image, b, r, c, VBit) = 0;
}
}
}
/* readdress to sagital slices and remove small 2D components */
sagital = VCreateImage(1, nbands, nrows, VBitRepn);
label_sagital = VCreateImage(1, nbands, nrows, VUByteRepn);
ubyte_pp = (VUByte *) VImageData(label_sagital);
for(i = 0; i < (nbands * nrows); i++)
*ubyte_pp++ = 0;
for(c = 0; c < ncols; c++) {
if(ABS(c - 80) < 10)
continue;
bin0_pp = (VBit *) VImageData(sagital);
for(i = 0; i < (nbands * nrows); i++)
*bin0_pp++ = 0;
for(b = 0; b < nbands; b++) {
for(r = 0; r < nrows; r++) {
VPixel(sagital, 0, b, r, VBit) = VPixel(bin1_image, b, r, c, VBit);
}
}
label_sagital = VLabelImage2d(sagital, label_sagital, (int) 8, VUByteRepn, &nl);
VDeleteCereb(label_sagital, &sagital, 115, cp);
for(b = 0; b < nbands; b++) {
for(r = 0; r < nrows; r++) {
if(VPixel(sagital, 0, b, r, VBit) == 0)
VPixel(bin1_image, b, r, c, VBit) = 0;
}
}
}
/* readdress to axial slices and remove small 2D components */
axial = VCreateImage(1, nrows, ncols, VBitRepn);
label_axial = VCreateImage(1, nrows, ncols, VUByteRepn);
ubyte_pp = (VUByte *) VImageData(label_axial);
for(i = 0; i < (nrows * ncols); i++)
*ubyte_pp++ = 0;
/* for (b=bp; b<nbands; b++) { */
for(b = 105; b < nbands; b++) {
bin0_pp = (VBit *) VImageData(axial);
for(i = 0; i < (nrows * ncols); i++)
*bin0_pp++ = 0;
for(r = 0; r < nrows; r++) {
for(c = 0; c < ncols; c++) {
VPixel(axial, 0, r, c, VBit) = VPixel(bin1_image, b, r, c, VBit);
}
}
label_sagital = VLabelImage2d(axial, label_axial, (int) 8, VUByteRepn, &nl);
VDeleteCereb(label_axial, &axial, 0, 0);
for(r = 0; r < nrows; r++) {
for(c = 0; c < ncols; c++) {
if(VPixel(axial, 0, r, c, VBit) == 0)
VPixel(bin1_image, b, r, c, VBit) = 0;
}
}
}
/* remove everything below slice extent */
b0 = slice_extent + slice_origin;
npixels = nrows * ncols;
for(b = b0; b < nbands; b++) {
bin0_pp = (VBit *) VPixelPtr(bin1_image, b, 0, 0);
for(i = 0; i < npixels; i++)
*bin0_pp++ = 0;
}
/* dilate */
bin0_image = VDTDilate(bin1_image, NULL, (VDouble) 3.0);
npixels = nrows * ncols;
for(b = 0; b < bp; b++) {
bin0_pp = (VBit *) VPixelPtr(bin0_image, b, 0, 0);
src_pp = (VBit *) VPixelPtr(src, b, 0, 0);
for(i = 0; i < npixels; i++)
*bin0_pp++ = *src_pp++;
}
for(b = bp; b < nbands; b++) {
bin0_pp = (VBit *) VPixelPtr(bin0_image, b, 0, 0);
src_pp = (VBit *) VPixelPtr(src, b, 0, 0);
for(i = 0; i < npixels; i++) {
if(*src_pp == 0)
*bin0_pp = 0;
src_pp++;
bin0_pp++;
}
}
/*
** remove small remaining components
*/
label_image = VLabelImage3d(bin0_image, NULL, (int) 26, VShortRepn, &nl);
bin0_image = VSelectBig(label_image, bin0_image);
VImageAttrList(bin0_image) = VCopyAttrList(VImageAttrList(src));
return bin0_image;
}
int main(int argc, char *argv[]) {
static VFloat reso = -1.0;
static VLong itype = 0;
static VBoolean flip = TRUE;
static VBoolean reorder = TRUE;
static VOptionDescRec options[] = {
{
"reso", VFloatRepn, 1, (VPointer) &reso,
VOptionalOpt, NULL, "New voxel resolution in mm, def: -1 means min(1.0,\"best source resolution\")"
},
{
"flip", VBooleanRepn, 1, (VPointer) &flip,
VOptionalOpt, NULL, "Whether to flip to natural convention"
},
{
"reorder", VBooleanRepn, 1, (VPointer) &reorder,
VOptionalOpt, NULL, "Whether to reorder axial slices from axial source image"
},
{
"interpolation", VLongRepn, 1, & itype, VOptionalOpt, ITYPDict,
"Type of interpolation (0: linear, 1: nearest neighbour, 2: cubic spline)"
}
};
FILE *in_file, *out_file;
VAttrList list;
VAttrListPosn posn;
int nobjects = 0;
VImage src = NULL, dest = NULL, result = NULL;
int i, b, r, c, nbands, nrows, ncols;
VString str, newstr, fixpointString, caString, cpString;
float fix_c, fix_r, fix_b;
float ca_c, ca_r, ca_b;
float cp_c, cp_r, cp_b;
float x, y, z, min;
VDouble v, scale_band, scale_row, scale_col;
float scale[3], shift[3];
/* print information */
char prg_name[100];
char ver[100];
getLipsiaVersion(ver, sizeof(ver));
sprintf(prg_name, "visotrop V%s", ver);
fprintf(stderr, "%s\n", prg_name);
fflush(stderr);
/* Parse command line arguments: */
VParseFilterCmd(VNumber(options), options, argc, argv,
& in_file, & out_file);
/* Read source image(s): */
if(!(list = VReadFile(in_file, NULL)))
exit(EXIT_FAILURE);
/* Scale each object: */
for(VFirstAttr(list, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
switch(VGetAttrRepn(& posn)) {
case VImageRepn:
VGetAttrValue(& posn, NULL, VImageRepn, & src);
if(VGetAttr(VImageAttrList(src), "voxel", NULL,
VStringRepn, (VPointer) & str) == VAttrFound) {
sscanf(str, "%f %f %f", &x, &y, &z);
fprintf(stderr, " voxel: %f %f %f\n", x, y, z);
min = x < y ? x : y;
min = z < min ? z : min;
/* if resolution is not set, use default value 1 or
smaler value if the image resolution is better */
if(reso < 0.0)
reso = min < 1.0 ? min : 1.0;
if(reso <= 0.0)
exit(EXIT_FAILURE);
fprintf(stderr, " new resolution: %f \n", reso);
scale_col = x / reso;
scale_row = y / reso;
scale_band = z / reso;
nbands = VImageNBands(src) * scale_band;
nrows = VImageNRows(src) * scale_row;
ncols = VImageNColumns(src) * scale_col;
if(VImageNBands(src) == nbands
&& VImageNRows(src) == nrows
&& VImageNColumns(src) == ncols) {
itype = 0;
}
fprintf(stderr, " interpolation type: %s\n", ITYPDict[itype].keyword);
fprintf(stderr, " old dim: %3d %3d %3d\n",
VImageNBands(src), VImageNRows(src), VImageNColumns(src));
for(i = 0; i < 3; i++)
shift[i] = scale[i] = 0;
scale[0] = scale_band;
scale[1] = scale_row;
scale[2] = scale_col;
switch(itype) {
/* trilinear interpolation resampling */
case 0:
dest = VTriLinearScale3d(src, NULL, (int)nbands, (int)nrows, (int)ncols,
shift, scale);
break;
/* nearest neightbour resampling */
case 1:
dest = VNNScale3d(src, NULL, (int)nbands, (int)nrows, (int)ncols,
shift, scale);
break;
/* cubic spline */
case 2:
dest = VCubicSplineScale3d(src, NULL, (int)nbands, (int)nrows, (int)ncols,
shift, scale);
break;
case 3: /* no interpolation, just reshuffle */
dest = VCopyImage(src, NULL, VAllBands);
break;
default:
VError(" unknown resampling type %d", itype);
}
if(! dest)
exit(EXIT_FAILURE);
/*aa 2003/09/11 added function not to rotate siemens data*/
if(! VGetAttr(VImageAttrList(src), "orientation", NULL,
VStringRepn, (VPointer) & str) == VAttrFound)
VError(" attribute 'orientation' missing");
if(strcmp(str, "axial") == 0) {
fprintf(stderr, " new dim: %3d %3d %3d\n", nbands, nrows, ncols);
result = VCreateImage(nbands, nrows, ncols, VPixelRepn(src));
VFillImage(result, VAllBands, 0);
for(b = 0; b < nbands; b++)
for(r = 0; r < nrows; r++)
for(c = 0; c < ncols; c++) {
v = VGetPixel(dest, b, r, c);
if((flip == FALSE) && (reorder == FALSE))
VSetPixel(result, b, r, ncols - c - 1, v);
else if((flip == TRUE) && (reorder == FALSE))
VSetPixel(result, b, r, c, v);
else if((flip == FALSE) && (reorder == TRUE))
VSetPixel(result, nbands - b - 1, r, ncols - c - 1, v);
else if((flip == TRUE) && (reorder == TRUE))
VSetPixel(result, nbands - b - 1, r, c, v);
}
} else if(strcmp(str, "sagittal") == 0) {
/* re-arrange from sagittal to axial orientation */
fprintf(stderr, " new dim: %3d %3d %3d\n", nrows, ncols, nbands);
result = VCreateImage(nrows, ncols, nbands, VPixelRepn(src));
VFillImage(result, VAllBands, 0);
for(b = 0; b < nbands; b++)
for(r = 0; r < nrows; r++)
for(c = 0; c < ncols; c++) {
v = VGetPixel(dest, b, r, c);
if(flip == FALSE)
VSetPixel(result, r, c, nbands - b - 1, v);
else
VSetPixel(result, r, c, b, v);
}
} else if(strcmp(str, "coronal") == 0) {
/* re-arrange from coronal to axial orientation */
fprintf(stderr, " new dim: %3d %3d %3d\n", nrows, nbands, ncols);
result = VCreateImage(nrows, nbands, ncols, VPixelRepn(src));
VFillImage(result, VAllBands, 0);
for(b = 0; b < nbands; b++)
for(r = 0; r < nrows; r++)
for(c = 0; c < ncols; c++) {
v = VGetPixel(dest, b, r, c);
if(flip == FALSE)
VSetPixel(result, r, b, ncols - c - 1, v);
else
VSetPixel(result, r, b, c, v);
}
} else {
VError(" unknown resampling type %d", itype);
exit(EXIT_FAILURE);
}
/* copy attributes from source image */
VCopyImageAttrs(src, result);
// [TS] 08/03/27
// correct 'fixpoint', 'ca' and 'cp' if they exist in the source image
//
// NOTE:
// this is only done when no flipping or reordering is requested :-(
// (WARNING!!!!) '-flip true' actually means that no flipping is done (WHAAAAT ????)
// and therefore we test for reorder = false and flip = true
fixpointString = VMalloc(80);
caString = VMalloc(80);
cpString = VMalloc(80);
VBoolean _issueWarning = FALSE;
if(VGetAttr(VImageAttrList(src), "fixpoint", NULL, VStringRepn, (VPointer)&fixpointString) == VAttrFound) {
if(reorder == FALSE && flip == TRUE) {
sscanf(fixpointString, "%f %f %f", &fix_c, &fix_r, &fix_b);
fix_c *= scale_col;
fix_r *= scale_row;
fix_b *= scale_band;
sprintf((char *)fixpointString, "%f %f %f", fix_c, fix_r, fix_b);
VSetAttr(VImageAttrList(result), "fixpoint", NULL, VStringRepn, fixpointString);
} else {
_issueWarning = TRUE;
}
}
if(VGetAttr(VImageAttrList(src), "ca", NULL, VStringRepn, (VPointer)&caString) == VAttrFound) {
if(reorder == FALSE && flip == TRUE) {
sscanf(caString, "%f %f %f", &ca_c, &ca_r, &ca_b);
ca_c *= scale_col;
ca_r *= scale_row;
ca_b *= scale_band;
sprintf((char *)caString, "%f %f %f", ca_c, ca_r, ca_b);
VSetAttr(VImageAttrList(result), "ca", NULL, VStringRepn, caString);
} else {
_issueWarning = TRUE;
}
}
if(VGetAttr(VImageAttrList(src), "cp", NULL, VStringRepn, (VPointer)&cpString) == VAttrFound) {
if(reorder == FALSE && flip == TRUE) {
sscanf(cpString, "%f %f %f", &cp_c, &cp_r, &cp_b);
cp_c *= scale_col;
cp_r *= scale_row;
cp_b *= scale_band;
sprintf((char *)cpString, "%f %f %f", cp_c, cp_r, cp_b);
VSetAttr(VImageAttrList(result), "cp", NULL, VStringRepn, cpString);
} else {
_issueWarning = TRUE;
}
}
if(_issueWarning) {
VWarning("Attributes 'fixpoint', 'ca' and 'cp' exist but were not corrected and are therefore likely to be wrong");
VWarning("This was caused by setting -flip to false or -reorder to true");
VWarning("Please correct the values manually using vattredit");
}
/* set the attributes to the changed values */
newstr = VMalloc(80);
sprintf((char *)newstr, "%f %f %f", reso, reso, reso);
VSetAttr(VImageAttrList(result), "voxel", NULL, VStringRepn, newstr);
VSetAttr(VImageAttrList(result), "orientation", NULL, VStringRepn, "axial");
if(flip)
VSetAttr(VImageAttrList(result), "convention", NULL, VStringRepn, "natural");
else
VSetAttr(VImageAttrList(result), "convention", NULL, VStringRepn, "radiologic");
}
VSetAttrValue(& posn, NULL, VImageRepn, result);
VDestroyImage(src);
break;
default:
continue;
}
nobjects++;
}
/* Make History */
VHistory(VNumber(options), options, prg_name, &list, &list);
/* Write the results to the output file: */
if(! VWriteFile(out_file, list))
exit(EXIT_FAILURE);
fprintf(stderr, "%s: done.\n", argv[0]);
return EXIT_SUCCESS;
}
VImage
PairedTest(VImage *src1, VImage *src2, VImage dest, int n, VShort type) {
int i, j, k, b, r, c, nslices, nrows, ncols;
float ave1, ave2, var1, var2, nx, u;
float sum, smooth = 0;
float t, z, df, sd, cov, *data1 = NULL, *data2 = NULL;
float tiny = 1.0e-10;
nslices = VImageNBands(src1[0]);
nrows = VImageNRows(src1[0]);
ncols = VImageNColumns(src1[0]);
gsl_set_error_handler_off();
dest = VCopyImage(src1[0], NULL, VAllBands);
VFillImage(dest, VAllBands, 0);
VSetAttr(VImageAttrList(dest), "num_images", NULL, VShortRepn, (VShort)n);
VSetAttr(VImageAttrList(dest), "patient", NULL, VStringRepn, "paired_ttest");
if(type == 0)
VSetAttr(VImageAttrList(dest), "modality", NULL, VStringRepn, "tmap");
else
VSetAttr(VImageAttrList(dest), "modality", NULL, VStringRepn, "zmap");
VSetAttr(VImageAttrList(dest), "df", NULL, VShortRepn, (VShort)(n - 1));
/* get smoothness estimates */
sum = nx = 0;
for(i = 0; i < n; i++) {
if(VGetAttr(VImageAttrList(src1[i]), "smoothness", NULL, VFloatRepn, &smooth) == VAttrFound) {
sum += smooth;
nx++;
}
}
for(i = 0; i < n; i++) {
if(VGetAttr(VImageAttrList(src2[i]), "smoothness", NULL, VFloatRepn, &smooth) == VAttrFound) {
sum += smooth;
nx++;
}
}
if(nx > 1) {
VSetAttr(VImageAttrList(dest), "smoothness", NULL, VFloatRepn, sum / nx);
}
data1 = (float *) VMalloc(n * sizeof(float));
data2 = (float *) VMalloc(n * sizeof(float));
df = n - 1;
nx = (float)n;
for(b = 0; b < nslices; b++) {
for(r = 0; r < nrows; r++) {
for(c = 0; c < ncols; c++) {
k = 0;
for(i = 0; i < n; i++) {
data1[i] = VPixel(src1[i], b, r, c, VFloat);
data2[i] = VPixel(src2[i], b, r, c, VFloat);
if(ABS(data1[i]) > tiny && ABS(data2[i]) > tiny)
k++;
}
if(k < n - 3)
continue;
avevar(data1, n, &ave1, &var1);
avevar(data2, n, &ave2, &var2);
if(var1 < tiny || var2 < tiny)
continue;
z = t = 0;
cov = 0;
for(j = 0; j < n; j++)
cov += (data1[j] - ave1) * (data2[j] - ave2);
cov /= df;
u = (var1 + var2 - 2.0 * cov);
if(u < tiny)
continue;
sd = sqrt(u / nx);
if(sd < tiny)
continue;
t = (ave1 - ave2) / sd;
if(isnan(t) || isinf(t))
continue;
switch(type) {
case 0:
VPixel(dest, b, r, c, VFloat) = t;
break;
case 1:
/* z = t2z_approx(t,df); */
z = t2z((double)t, (double)df);
if(t < 0)
z = -z;
VPixel(dest, b, r, c, VFloat) = z;
break;
default:
VError(" illegal type");
}
}
}
}
return dest;
}
VImage
PairedWilcoxTest(VImage *src1, VImage *src2, VImage dest, int n) {
int i, m, k, b, r, c, nslices, nrows, ncols;
int sumpos, sumneg, w;
double wx, u, v, z, p, tiny = 1.0e-10;
double *ptr1, *ptr2;
float *table = NULL;
gsl_vector *vec1 = NULL, *vec2 = NULL;
gsl_permutation *perm = NULL, *rank = NULL;
extern void gsl_sort_vector_index(gsl_permutation *, gsl_vector *);
nslices = VImageNBands(src1[0]);
nrows = VImageNRows(src1[0]);
ncols = VImageNColumns(src1[0]);
dest = VCopyImage(src1[0], NULL, VAllBands);
VFillImage(dest, VAllBands, 0);
VSetAttr(VImageAttrList(dest), "num_images", NULL, VShortRepn, (VShort)n);
VSetAttr(VImageAttrList(dest), "patient", NULL, VStringRepn, "paired_wilcoxtest");
VSetAttr(VImageAttrList(dest), "modality", NULL, VStringRepn, "zmap");
m = 0;
for(i = 1; i <= n; i++)
m += i;
if(n > 18) {
table = getTable(n);
for(i = 0; i < m; i++) {
p = table[i];
p *= 0.5;
if(p < tiny)
p = tiny;
z = p2z(p);
if(z < 0)
z = 0;
table[i] = z;
}
} else {
table = (float *) VMalloc(sizeof(float) * m);
for(i = 0; i < m; i++) {
for(i = 0; i < m; i++) {
wx = i;
p = LevelOfSignificanceWXMPSR(wx, (long int)n);
p *= 0.5;
z = p2z(p);
table[i] = z;
}
}
}
vec1 = gsl_vector_calloc(n);
vec2 = gsl_vector_calloc(n);
perm = gsl_permutation_alloc(n);
rank = gsl_permutation_alloc(n);
for(b = 0; b < nslices; b++) {
for(r = 0; r < nrows; r++) {
for(c = 0; c < ncols; c++) {
k = 0;
ptr1 = vec1->data;
ptr2 = vec2->data;
for(i = 0; i < n; i++) {
u = VPixel(src1[i], b, r, c, VFloat);
v = VPixel(src2[i], b, r, c, VFloat);
if(ABS(u) > tiny && ABS(v) > tiny)
k++;
*ptr1++ = ABS(u - v);
*ptr2++ = u - v;
}
if(k < n / 2)
continue;
gsl_sort_vector_index(perm, vec1);
gsl_permutation_inverse(rank, perm);
sumpos = sumneg = 0;
ptr2 = vec2->data;
for(i = 0; i < n; i++) {
u = *ptr2++;
if(u > 0)
sumpos += rank->data[i];
else if(u < 0)
sumneg += rank->data[i];
}
w = sumpos;
if(sumpos > sumneg)
w = sumneg;
if(w >= m)
z = 0;
else
z = table[w];
if(sumneg > sumpos)
z = -z;
VPixel(dest, b, r, c, VFloat) = z;
}
}
}
return dest;
}
/*
** general linear regression
*/
VAttrList
VRegression(ListInfo *linfo, int nlists, VShort minval, VImage design, VFloat sigma, VLong itr) {
VAttrList out_list;
VImageInfo *xinfo;
int nbands = 0, nslices = 0, nrows = 0, ncols = 0, slice, row, col, nr, nc;
VImage src[NSLICES], res_image = NULL;
VImage beta_image[MBETA], BCOV = NULL, KX_image = NULL;
VImage res_map[ETMP];
float smooth_fwhm = 0, vx = 0, vy = 0, vz = 0;
VFloat *float_pp, df;
VRepnKind repn;
float d, err;
int i, k, l, n, m = 0, nt, fd = 0, npix = 0;
int i0 = 0, i1 = 0;
double u, sig, trace = 0, trace2 = 0, var = 0, sum = 0, nx = 0, mean = 0, sum2;
float *ptr1, *ptr2;
double x;
gsl_matrix_float *X = NULL, *XInv = NULL, *SX = NULL;
gsl_vector_float *y, *z, *beta, *ys;
gsl_vector *kernel;
gsl_matrix_float *S = NULL, *Vc = NULL, *F = NULL, *P = NULL, *Q = NULL;
gsl_matrix_float *R = NULL, *RV = NULL;
VBoolean smooth = TRUE; /* no smoothness estimation */
gsl_set_error_handler_off();
/*
** read input data
*/
nslices = nbands = nrows = ncols = 0;
for(k = 0; k < nlists; k++) {
n = linfo[k].nslices;
nr = linfo[k].nrows;
nc = linfo[k].ncols;
nt = linfo[k].ntimesteps;
nbands += nt;
if(nslices == 0)
nslices = n;
else if(nslices != n)
VError(" inconsistent image dimensions, slices: %d %d", n, nslices);
if(nrows == 0)
nrows = nr;
else if(nrows != nr)
VError(" inconsistent image dimensions, rows: %d %d", nr, nrows);
if(ncols == 0)
ncols = nc;
else if(ncols != nc)
VError(" inconsistent image dimensions, cols: %d %d", nc, ncols);
}
fprintf(stderr, " num images: %d, image dimensions: %d x %d x %d\n",
nlists, nslices, nrows, ncols);
/*
** get design dimensions
*/
m = VImageNRows(design); /* number of timesteps */
n = VImageNColumns(design); /* number of covariates */
fprintf(stderr, " ntimesteps=%d, num covariates=%d\n", m, n);
if(n >= MBETA)
VError(" too many covariates (%d), max is %d", n, MBETA);
if(m != nbands)
VError(" design dimension inconsistency: %d %d", m, nbands);
fprintf(stderr, " working...\n");
/*
** read design matrix
*/
X = gsl_matrix_float_alloc(m, n);
for(k = 0; k < m; k++) {
for(l = 0; l < n; l++) {
x = VGetPixel(design, 0, k, l);
fmset(X, k, l, (float)x);
}
}
/*
** pre-coloring, set up K-matrix, S=K, V = K*K^T with K=S
*/
S = gsl_matrix_float_alloc(m, m);
GaussMatrix((double)sigma, S);
Vc = fmat_x_matT(S, S, NULL);
/*
** compute pseudoinverse
*/
SX = fmat_x_mat(S, X, NULL);
XInv = fmat_PseudoInv(SX, NULL);
/*
** get variance estimate
*/
Q = fmat_x_mat(XInv, Vc, Q);
F = fmat_x_matT(Q, XInv, F);
BCOV = VCreateImage(1, n, n, VFloatRepn);
float_pp = VImageData(BCOV);
ptr1 = F->data;
for(i = 0; i < n * n; i++)
*float_pp++ = *ptr1++;
gsl_matrix_float_free(Q);
gsl_matrix_float_free(F);
/*
** get effective degrees of freedom
*/
R = gsl_matrix_float_alloc(m, m);
P = fmat_x_mat(SX, XInv, P);
gsl_matrix_float_set_identity(R);
gsl_matrix_float_sub(R, P);
RV = fmat_x_mat(R, Vc, NULL);
trace = 0;
for(i = 0; i < m; i++)
trace += fmget(RV, i, i);
P = fmat_x_mat(RV, RV, P);
trace2 = 0;
for(i = 0; i < m; i++)
trace2 += fmget(P, i, i);
df = (trace * trace) / trace2;
fprintf(stderr, " df= %.3f\n", df);
/*
** create output images
*/
xinfo = linfo[0].info;
out_list = VCreateAttrList();
res_image = VCreateImage(nslices, nrows, ncols, VFloatRepn);
VFillImage(res_image, VAllBands, 0);
VSetAttr(VImageAttrList(res_image), "name", NULL, VStringRepn, "RES/trRV");
VSetAttr(VImageAttrList(res_image), "modality", NULL, VStringRepn, "RES/trRV");
VSetAttr(VImageAttrList(res_image), "df", NULL, VFloatRepn, df);
VSetAttr(VImageAttrList(res_image), "patient", NULL, VStringRepn, xinfo->patient);
VSetAttr(VImageAttrList(res_image), "voxel", NULL, VStringRepn, xinfo->voxel);
VSetAttr(VImageAttrList(res_image), "repetition_time", NULL, VLongRepn, itr);
VSetAttr(VImageAttrList(res_image), "talairach", NULL, VStringRepn, xinfo->talairach);
/* neu */
VSetAttr(VImageAttrList(res_image),"indexOrigin",NULL,VStringRepn,xinfo->indexOrigin);
VSetAttr(VImageAttrList(res_image),"columnVec",NULL,VStringRepn,xinfo->columnVec);
VSetAttr(VImageAttrList(res_image),"rowVec",NULL,VStringRepn,xinfo->rowVec);
VSetAttr(VImageAttrList(res_image),"sliceVec",NULL,VStringRepn,xinfo->sliceVec);
VSetAttr(VImageAttrList(res_image),"FOV",NULL,VStringRepn,xinfo->FOV);
/*--------*/
if(xinfo->fixpoint[0] != 'N')
VSetAttr(VImageAttrList(res_image), "fixpoint", NULL, VStringRepn, xinfo->fixpoint);
if(xinfo->ca[0] != 'N') {
VSetAttr(VImageAttrList(res_image), "ca", NULL, VStringRepn, xinfo->ca);
VSetAttr(VImageAttrList(res_image), "cp", NULL, VStringRepn, xinfo->cp);
VSetAttr(VImageAttrList(res_image), "extent", NULL, VStringRepn, xinfo->extent);
}
VAppendAttr(out_list, "image", NULL, VImageRepn, res_image);
for(i = 0; i < n; i++) {
beta_image[i] = VCreateImage(nslices, nrows, ncols, VFloatRepn);
VFillImage(beta_image[i], VAllBands, 0);
VSetAttr(VImageAttrList(beta_image[i]), "patient", NULL, VStringRepn, xinfo->patient);
VSetAttr(VImageAttrList(beta_image[i]), "voxel", NULL, VStringRepn, xinfo->voxel);
VSetAttr(VImageAttrList(beta_image[i]), "repetition_time", NULL, VLongRepn, itr);
VSetAttr(VImageAttrList(beta_image[i]), "talairach", NULL, VStringRepn, xinfo->talairach);
/* neu */
VSetAttr(VImageAttrList(beta_image[i]),"indexOrigin",NULL,VStringRepn,xinfo->indexOrigin);
VSetAttr(VImageAttrList(beta_image[i]),"columnVec",NULL,VStringRepn,xinfo->columnVec);
VSetAttr(VImageAttrList(beta_image[i]),"rowVec",NULL,VStringRepn,xinfo->rowVec);
VSetAttr(VImageAttrList(beta_image[i]),"sliceVec",NULL,VStringRepn,xinfo->sliceVec);
VSetAttr(VImageAttrList(beta_image[i]),"FOV",NULL,VStringRepn,xinfo->FOV);
/*--------*/
if(xinfo->fixpoint[0] != 'N')
VSetAttr(VImageAttrList(beta_image[i]), "fixpoint", NULL, VStringRepn, xinfo->fixpoint);
if(xinfo->ca[0] != 'N') {
VSetAttr(VImageAttrList(beta_image[i]), "ca", NULL, VStringRepn, xinfo->ca);
VSetAttr(VImageAttrList(beta_image[i]), "cp", NULL, VStringRepn, xinfo->cp);
VSetAttr(VImageAttrList(beta_image[i]), "extent", NULL, VStringRepn, xinfo->extent);
}
VSetAttr(VImageAttrList(beta_image[i]), "name", NULL, VStringRepn, "BETA");
VSetAttr(VImageAttrList(beta_image[i]), "modality", NULL, VStringRepn, "BETA");
VSetAttr(VImageAttrList(beta_image[i]), "beta", NULL, VShortRepn, i + 1);
VSetAttr(VImageAttrList(beta_image[i]), "df", NULL, VFloatRepn, df);
VAppendAttr(out_list, "image", NULL, VImageRepn, beta_image[i]);
}
VSetAttr(VImageAttrList(design), "name", NULL, VStringRepn, "X");
VSetAttr(VImageAttrList(design), "modality", NULL, VStringRepn, "X");
VAppendAttr(out_list, "image", NULL, VImageRepn, design);
KX_image = Mat2Vista(SX);
VSetAttr(VImageAttrList(KX_image), "name", NULL, VStringRepn, "KX");
VSetAttr(VImageAttrList(KX_image), "modality", NULL, VStringRepn, "KX");
VAppendAttr(out_list, "image", NULL, VImageRepn, KX_image);
VSetAttr(VImageAttrList(BCOV), "name", NULL, VStringRepn, "BCOV");
VSetAttr(VImageAttrList(BCOV), "modality", NULL, VStringRepn, "BCOV");
VAppendAttr(out_list, "image", NULL, VImageRepn, BCOV);
/*
** create temporary images for smoothness estimation
*/
/* smoothness estim only for 3D images, i.e. CA/CP known */
/* if(xinfo->ca[0] == 'N')
smooth = FALSE;*/
if(smooth) {
i0 = 20;
i1 = i0 + 30;
if(i1 > m)
i1 = m;
for(i = i0; i < i1; i++) {
if(i - i0 >= ETMP)
VError(" too many tmp images");
res_map[i - i0] = VCreateImage(nslices, nrows, ncols, VFloatRepn);
VFillImage(res_map[i - i0], VAllBands, 0);
}
}
/*
** process
*/
ys = gsl_vector_float_alloc(m);
y = gsl_vector_float_alloc(m);
z = gsl_vector_float_alloc(m);
beta = gsl_vector_float_alloc(n);
kernel = GaussKernel((double)sigma);
for(k = 0; k < nlists; k++) {
src[k] = VCreateImage(linfo[k].ntimesteps, nrows, ncols, linfo[k].repn);
VFillImage(src[k], VAllBands, 0);
}
npix = 0;
for(slice = 0; slice < nslices; slice++) {
if(slice % 5 == 0)
fprintf(stderr, " slice: %3d\r", slice);
for(k = 0; k < nlists; k++) {
if(linfo[k].zero[slice] == 0)
goto next1;
fd = open(linfo[k].filename, O_RDONLY);
if(fd == -1)
VError("could not open file %s", linfo[k].filename);
nt = linfo[k].ntimesteps;
if(! VReadBandDataFD(fd, &linfo[k].info[slice], 0, nt, &src[k]))
VError(" error reading data");
close(fd);
}
repn = linfo[0].repn;
for(row = 0; row < nrows; row++) {
for(col = 0; col < ncols; col++) {
for(k = 0; k < nlists; k++)
if(VPixel(src[k], 0, row, col, VShort) < minval + 1)
goto next;
npix++;
/* read time series data */
sum = sum2 = nx = 0;
ptr1 = y->data;
for(k = 0; k < nlists; k++) {
nt = VImageNBands(src[k]);
for(i = 0; i < nt; i++) {
u = VPixel(src[k], i, row, col, VShort);
(*ptr1++) = u;
sum += u;
sum2 += u * u;
nx++;
}
}
mean = sum / nx;
sig = sqrt((double)((sum2 - nx * mean * mean) / (nx - 1.0)));
if(sig < 0.001)
continue;
/* centering and scaling, Seber, p.330 */
ptr1 = y->data;
for(i = 0; i < m; i++) {
u = ((*ptr1) - mean) / sig;
(*ptr1++) = u + 100.0;
}
/* S x y */
ys = VectorConvolve(y, ys, kernel);
/* compute beta's */
fmat_x_vector(XInv, ys, beta);
/* residuals */
fmat_x_vector(SX, beta, z);
err = 0;
ptr1 = ys->data;
ptr2 = z->data;
for(i = 0; i < m; i++) {
d = ((*ptr1++) - (*ptr2++));
err += d * d;
}
/* sigma^2 */
var = err / trace;
/* write residuals output */
VPixel(res_image, slice, row, col, VFloat) = (VFloat)var;
/* save residuals of several timesteps for smoothness estimation */
if(smooth) {
ptr1 = ys->data;
ptr2 = z->data;
err = 0;
for(i = i0; i < i1; i++) {
d = ((*ptr1++) - (*ptr2++));
err += d * d;
VPixel(res_map[i - i0], slice, row, col, VFloat) = d;
}
if (err > 0) err = sqrt(err);
for(i = i0; i < i1; i++) {
d = VPixel(res_map[i - i0], slice, row, col, VFloat);
if (err > 1.0e-6) d /= err;
else d = 0;
VPixel(res_map[i - i0], slice, row, col, VFloat) = d / err;
}
}
/* write beta output */
ptr1 = beta->data;
for(i = 0; i < n; i++)
VPixel(beta_image[i], slice, row, col, VFloat) = (VFloat)(*ptr1++);
next:
;
}
}
next1:
;
}
/*
** Smoothness estimation based on residual images
*/
if(smooth) {
smooth_fwhm = VSmoothnessEstim(res_map, i1 - i0);
sscanf(xinfo->voxel, "%f %f %f", &vx, &vy, &vz);
vx = (vx + vy + vz) / 3.0; /* voxels should be isotropic */
smooth_fwhm *= vx;
fprintf(stderr, " smoothness: %f\n", smooth_fwhm);
VSetAttr(VImageAttrList(res_image), "smoothness", NULL, VFloatRepn, smooth_fwhm);
for(i = 0; i < n; i++) {
VSetAttr(VImageAttrList(beta_image[i]), "smoothness", NULL, VFloatRepn, smooth_fwhm);
}
for(i = 0; i < i1 - i0; i++)
VDestroyImage(res_map[i]);
}
ende:
if(npix == 0)
VError(" no voxels above threshold %d found", minval);
return out_list;
}
/*
** slicetime correction with constant TR
*/
void
VSlicetime(VAttrList list, VShort minval, VFloat tdel,
VBoolean slicetime_correction, float *onset_array) {
VImage src;
VAttrListPosn posn;
VString str, buf;
int b, r, c, i, nt, mt, val, del = 0;
double xmin, xmax, sum, nx;
double *xx = NULL, *yy = NULL, xi, yi, tr = 0, xtr = 0, slicetime = 0;
gsl_interp_accel *acc = NULL;
gsl_spline *spline = NULL;
xmin = (VShort) VRepnMinValue(VShortRepn);
xmax = (VShort) VRepnMaxValue(VShortRepn);
buf = VMalloc(256);
/*
** process data
*/
b = -1;
for(VFirstAttr(list, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
if(VGetAttrRepn(& posn) != VImageRepn)
continue;
VGetAttrValue(& posn, NULL, VImageRepn, & src);
if(VPixelRepn(src) != VShortRepn)
continue;
b++;
if(VImageNRows(src) < 2)
continue;
/*
** get header info
*/
if(VGetAttr(VImageAttrList(src), "slice_time", NULL,
VDoubleRepn, (VPointer) & slicetime) != VAttrFound && slicetime_correction && onset_array == NULL)
VError(" 'slice_time' info missing");;
if(onset_array != NULL)
slicetime = onset_array[b];
tr = 0;
if(VGetAttr(VImageAttrList(src), "repetition_time", NULL,
VDoubleRepn, (VPointer) & tr) != VAttrFound) {
tr = 0;
if(VGetAttr(VImageAttrList(src), "MPIL_vista_0", NULL,
VStringRepn, (VPointer) & str) == VAttrFound) {
sscanf(str, " repetition_time=%lf %s", &tr, buf);
}
}
if(tr < 1)
VError(" attribute 'repetition_time' missing");
xtr = tr / 1000.0;
del = (int)(tdel / xtr + 0.5); /* num timesteps to be ignored */
nt = VImageNBands(src);
if(acc == NULL) {
acc = gsl_interp_accel_alloc();
spline = gsl_spline_alloc(gsl_interp_akima, nt);
xx = (double *) VCalloc(nt, sizeof(double));
yy = (double *) VCalloc(nt, sizeof(double));
fprintf(stderr, " The first %.2f secs (%d timesteps) will be replaced.\n", tdel, del);
}
/*
** loop through all voxels in current slice
*/
if(slicetime_correction)
fprintf(stderr, " slice: %3d, %10.3f ms, TR: %.3f\r", b, slicetime, xtr);
for(r = 0; r < VImageNRows(src); r++) {
for(c = 0; c < VImageNColumns(src); c++) {
if(VPixel(src, 0, r, c, VShort) < minval)
continue;
/* replace first few time steps by average */
if(del > 0) {
mt = del + 10;
if(mt > nt)
mt = nt;
sum = nx = 0;
for(i = del; i < mt; i++) {
sum += VPixel(src, i, r, c, VShort);
nx++;
}
if(nx < 1)
continue;
val = sum / nx;
for(i = 0; i < del; i++) {
VPixel(src, i, r, c, VShort) = val;
}
}
if(!slicetime_correction)
continue;
/* correct for slicetime offsets using cubic spline interpolation */
for(i = 0; i < nt; i++) {
xi = i;
xx[i] = xi * tr;
yy[i] = VPixel(src, i, r, c, VShort);
}
gsl_spline_init(spline, xx, yy, nt);
for(i = 1; i < nt; i++) {
xi = xx[i] - slicetime;
yi = gsl_spline_eval(spline, xi, acc);
val = (int)(yi + 0.49);
if(val > xmax)
val = xmax;
if(val < xmin)
val = xmin;
VPixel(src, i, r, c, VShort) = val;
}
}
}
}
fprintf(stderr, "\n");
}
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;
}
VImage
VDoMulticomp3d(VImage src, VImage multicomp, VBoolean verbose) {
VString str;
Volumes volumes;
Volume vol;
VImage tmp = NULL, label_image = NULL, dest = NULL;
VFloat *src_pp, *dst_pp, u, zthr = 0, zmax = 0, voxsize = 1, sym = 0;
VBit *bin_pp;
int i, nl, size, nbands, nrows, ncols, npixels;
int b, r, c, b0, r0, c0;
int nflag, pflag;
float x0, x1, x2;
float sign = 1;
float voxel[3], ca[3], extent[3];
/*
** read multicomp file header
*/
voxsize = 1;
if(VGetAttr(VImageAttrList(multicomp), "voxel_size", NULL,
VFloatRepn, (VPointer) & voxsize) != VAttrFound)
VError(" attribute 'voxel_size' not found");
if(VGetAttr(VImageAttrList(multicomp), "zthr", NULL, VFloatRepn, (VPointer) &zthr) != VAttrFound)
VError(" attribute 'zthr' not found");
/*
** read src header
*/
if(verbose) {
if(VGetAttr(VImageAttrList(src), "voxel", NULL,
VStringRepn, (VPointer) & str) != VAttrFound)
VError(" attribute 'voxel' not found");
sscanf(str, "%f %f %f", &x0, &x1, &x2);
if(ABS(x0 * x1 * x2 - voxsize) > 0.01)
VError(" voxel sizes do not match %.3f %.3f %.3f", x0, x1, x2);
voxel[0] = x0;
voxel[1] = x1;
voxel[2] = x2;
if(VGetAttr(VImageAttrList(src), "ca", NULL,
VStringRepn, (VPointer) & str) != VAttrFound)
VError(" attribute 'ca' not found");
sscanf(str, "%f %f %f", &x0, &x1, &x2);
ca[0] = x0;
ca[1] = x1;
ca[2] = x2;
if(VGetAttr(VImageAttrList(src), "extent", NULL,
VStringRepn, (VPointer) & str) != VAttrFound)
VError(" attribute 'extent' not found");
sscanf(str, "%f %f %f", &x0, &x1, &x2);
extent[0] = x0;
extent[1] = x1;
extent[2] = x2;
}
nbands = VImageNBands(src);
nrows = VImageNRows(src);
ncols = VImageNColumns(src);
npixels = VImageNPixels(src);
tmp = VCreateImage(nbands, nrows, ncols, VBitRepn);
dest = VCopyImage(src, NULL, VAllBands);
VFillImage(dest, VAllBands, 0);
/*
** positive threshold
*/
nflag = pflag = 0;
src_pp = VImageData(src);
bin_pp = VImageData(tmp);
for(i = 0; i < npixels; i++) {
*bin_pp = 0;
u = *src_pp;
if(u > 0 && u >= zthr)
*bin_pp = 1;
src_pp++;
bin_pp++;
}
label_image = VLabelImage3d(tmp, label_image, (int)26, VShortRepn, &nl);
if(nl < 1 && pflag == 0) {
VWarning(" no voxels above threshold %.3f", zthr);
goto next;
} else
pflag++;
volumes = VImage2Volumes(label_image);
for(vol = volumes->first; vol != NULL; vol = vol->next) {
sign = 1;
size = VolumeSize(vol);
zmax = VolumeZMax(vol, src, (float)1, &b, &r, &c);
sym = VolumeSym(vol, src, sign, zthr);
if(CheckValueSymm(multicomp, size, zmax, sym) == FALSE) {
VolumeZero(vol, tmp);
} else {
if(verbose) {
VPixel2Tal(ca, voxel, extent, b, r, c, &x0, &x1, &x2);
c0 = VRint(x0);
r0 = VRint(x1);
b0 = VRint(x2);
fprintf(stderr, " nvoxels: %5d, zmax: %7.3f, sym: %.3f, addr: %3d %3d %3d\n",
size, zmax, sym, c0, r0, b0);
}
}
}
src_pp = VImageData(src);
dst_pp = VImageData(dest);
bin_pp = VImageData(tmp);
for(i = 0; i < npixels; i++) {
if(*bin_pp > 0)
*dst_pp = *src_pp;
src_pp++;
dst_pp++;
bin_pp++;
}
/*
** negative threshold
*/
next:
src_pp = VImageData(src);
bin_pp = VImageData(tmp);
for(i = 0; i < npixels; i++) {
*bin_pp = 0;
u = *src_pp;
if(u < 0 && -u >= zthr)
*bin_pp = 1;
src_pp++;
bin_pp++;
}
label_image = VLabelImage3d(tmp, label_image, (int)26, VShortRepn, &nl);
if(nl < 1 && nflag == 0) {
/* VWarning(" no voxels below negative threshold %.3f",-zthr); */
goto ende;
} else
nflag++;
volumes = VImage2Volumes(label_image);
for(vol = volumes->first; vol != NULL; vol = vol->next) {
sign = -1;
size = VolumeSize(vol);
zmax = VolumeZMax(vol, src, sign, &b, &r, &c);
sym = VolumeSym(vol, src, sign, zthr);
if(CheckValueSymm(multicomp, size, zmax, sym) == FALSE) {
VolumeZero(vol, tmp);
} else {
if(verbose) {
VPixel2Tal(ca, voxel, extent, b, r, c, &x0, &x1, &x2);
c0 = VRint(x0);
r0 = VRint(x1);
b0 = VRint(x2);
fprintf(stderr, " nvoxels: %5d, zmax: %7.3f, sym: %.3f, addr: %3d %3d %3d\n",
size, zmax, sym, c0, r0, b0);
}
}
}
src_pp = VImageData(src);
dst_pp = VImageData(dest);
bin_pp = VImageData(tmp);
for(i = 0; i < npixels; i++) {
if(*bin_pp > 0)
*dst_pp = *src_pp;
src_pp++;
dst_pp++;
bin_pp++;
}
ende:
if(nflag == 0 && pflag == 0)
VError(" no voxels passed threshold");
return dest;
}
VImage
VCovariates(VString cfile, VFloat tr, VBoolean normalize) {
VImage dest = NULL;
FILE *fp = NULL;
char buf[LEN], token[80];
int i, j, nt, m, ncols, nrows;
float x;
double u, sum1, sum2, nx, mean, sigma, tiny = 1.0e-4;
fp = fopen(cfile, "r");
if(fp == NULL)
VError(" err opening file %s", cfile);
nrows = ncols = 0;
while(!feof(fp)) {
for(j = 0; j < LEN; j++)
buf[j] = '\0';
fgets(buf, LEN, fp);
if(buf[0] == '#' || buf[0] == '%')
continue;
if(strlen(buf) < 3)
continue;
j = 0;
while(VStringToken(buf, token, j, 30)) {
sscanf(token, "%f", &x);
if(j >= NCOV)
VError(" too many additional covariates (%d), max is %d", j, NCOV - 1);
j++;
}
if(j > ncols)
ncols = j;
nrows++;
}
fprintf(stderr, "# num rows: %d, num cols: %d\n", nrows, ncols);
dest = VCreateImage(1, nrows, ncols + 1, VFloatRepn);
VSetAttr(VImageAttrList(dest), "modality", NULL, VStringRepn, "X");
VSetAttr(VImageAttrList(dest), "name", NULL, VStringRepn, "X");
VSetAttr(VImageAttrList(dest), "repetition_time", NULL, VLongRepn, (VLong)(tr * 1000.0));
VSetAttr(VImageAttrList(dest), "ntimesteps", NULL, VLongRepn, (VLong)nrows);
VSetAttr(VImageAttrList(dest), "derivatives", NULL, VShortRepn, (VFloat) 0);
VSetAttr(VImageAttrList(dest), "delay", NULL, VFloatRepn, (VFloat) 0);
VSetAttr(VImageAttrList(dest), "undershoot", NULL, VFloatRepn, (VFloat) 0);
VSetAttr(VImageAttrList(dest), "understrength", NULL, VFloatRepn, (VFloat) 0);
VSetAttr(VImageAttrList(dest), "nsessions", NULL, VShortRepn, (VShort)1);
VSetAttr(VImageAttrList(dest), "designtype", NULL, VShortRepn, (VShort)1);
VFillImage(dest, VAllBands, 0);
for(j = 0; j < nrows; j++)
VPixel(dest, 0, j, ncols, VFloat) = 1;
rewind(fp);
i = 0;
while(!feof(fp)) {
for(j = 0; j < LEN; j++)
buf[j] = '\0';
fgets(buf, LEN, fp);
if(buf[0] == '#' || buf[0] == '%')
continue;
if(strlen(buf) < 3)
continue;
if(i > nrows)
VError(" too many rows in file (%d), max is %d", i, nrows);
j = 0;
while(VStringToken(buf, token, j, 30)) {
sscanf(token, "%f", &x);
if(j >= NCOV)
VError(" too many additional covariates (%d), max is %d", j, NCOV - 1);
VPixel(dest, 0, i, j, VFloat) = x;
j++;
}
if(j < 1)
continue;
if(i >= nrows)
continue;
i++;
}
fclose(fp);
if(i != nrows)
VError(" file: inconsistent number of rows: %d %d", i, nrows);
if(!normalize)
return dest;
nt = VImageNRows(dest);
m = VImageNColumns(dest);
for(i = 0; i < m; i++) {
sum1 = sum2 = nx = 0;
for(j = 0; j < nt; j++) {
u = VPixel(dest, 0, j, i, VFloat);
sum1 += u;
sum2 += u * u;
nx++;
}
mean = sum1 / nx;
sigma = sqrt((sum2 - nx * mean * mean) / (nx - 1.0));
if(sigma < tiny)
continue;
for(j = 0; j < nt; j++) {
u = VPixel(dest, 0, j, i, VFloat);
u = (u - mean) / sigma;
VPixel(dest, 0, j, i, VFloat) = u;
}
}
return dest;
}
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);
}
