int
tes1_read_vol(Tes &ts,Cube &cb,int t)
{
gzFile fp;
string keyword;
tokenlist args;
int cnt;
// Tes::ReadHeader should already have read the header, which
// includes the mask
if (!ts.header_valid)
return (100);
if (t<0 || t>ts.dimt-1)
return 101;
fp=gzopen(ts.GetFileName().c_str(),"r");
if (!fp)
return (100);
// skip the header and mask and advance to our image position
gzseek(fp,ts.offset+(t*ts.datasize),SEEK_SET);
cb.SetVolume(ts.dimx,ts.dimy,ts.dimz,ts.datatype);
if (!cb.data)
return 102;
int index=0;
for (int k=0; k<ts.dimz; k++) {
for (int j=0; j<ts.dimy; j++) {
for (int i=0; i<ts.dimx; i++) {
if (ts.mask[index]) {
cnt=gzread(fp,cb.data+(ts.datasize*index),ts.datasize);
if (cnt!=ts.datasize) {
gzclose(fp);
return 103;
}
gzseek(fp,ts.datasize*(ts.dimt-1),SEEK_CUR);
}
index++;
}
}
}
gzclose(fp);
if (my_endian() != ts.filebyteorder)
cb.byteswap();
if (ts.f_scaled) {
if (ts.datatype==vb_byte || ts.datatype==vb_short || ts.datatype==vb_long)
cb.convert_type(vb_float);
cb*=ts.scl_slope;
cb+=ts.scl_inter;
}
return(0); // no error!
}
void
Extractor::init(tokenlist &args)
{
// defaults
xvflag=0;
newdim[0]=41;
newdim[1]=51;
newdim[2]=27;
newcube.voxsize[0]=3.75;
newcube.voxsize[1]=3.75;
newcube.voxsize[2]=5.00;
newcube.origin[0]=21;
newcube.origin[1]=31;
newcube.origin[2]=10;
original.ReadFile(args[0]);
if (args.size()==1)
newcube.SetFileName((string)"m"+original.GetFileName());
if (args.size()==2 || args.size()==3) {
newcube.SetFileName(args[1]);
if (args.size()==3) {
xval=strtol(args[2]);
xvflag=1;
}
}
if (args.size()==11 || args.size()==12) {
newcube.SetFileName(args[1]);
newdim[0]=strtol(args[2]);
newdim[1]=strtol(args[3]);
newdim[2]=strtol(args[4]);
newcube.voxsize[0]=strtod(args[5]);
newcube.voxsize[1]=strtod(args[6]);
newcube.voxsize[2]=strtod(args[7]);
newcube.origin[0]=strtol(args[8]);
newcube.origin[1]=strtol(args[9]);
newcube.origin[2]=strtol(args[10]);
if (args.size()==12) {
xval=strtol(args[11]);
xvflag=1;
}
}
newcube.SetVolume(newdim[0],newdim[1],newdim[2],original.datatype);
}
void
do_sumrfx(const string &fname,const string &mname,double thresh,vector<VBRegion> &rlist)
{
int i,j,k;
Tes rfx;
Cube mask;
rfx.ReadFile(fname);
if (!rfx.data_valid) {
printf("sumrfx: invalid 4D file %s.\n",fname.c_str());
return;
}
// specified mask, intersect with tes mask
if (mname.size()) {
mask.ReadFile(mname);
for (i=0; i<mask.dimx; i++)
for (j=0; j<mask.dimy; j++)
for (k=0; k<mask.dimz; k++)
if (rfx.GetMaskValue(i,j,k)<0.5)
mask.SetValue(i,j,k,0);
}
// default mask
else {
mask.SetVolume(rfx.dimx,rfx.dimy,rfx.dimz,vb_byte);
for (i=0; i<mask.dimx; i++)
for (j=0; j<mask.dimy; j++)
for (k=0; k<mask.dimz; k++)
mask.SetValue(i,j,k,rfx.GetMaskValue(i,j,k));
}
if (!mask.data_valid) {
printf("sumrfx: invalid mask file %s.\n",mname.c_str());
return;
}
if (mask.dimx != rfx.dimx || mask.dimy != rfx.dimy || mask.dimz != rfx.dimz) {
printf("sumrfx: mask and rfx volume dimensions don't match\n");
return;
}
printf("sumrfx: thresh %.2f mask file: %s\n",thresh,mname.c_str());
for (i=0; i<rfx.dimt; i++) {
Cube mycube;
rfx.getCube(i,mycube);
if (!mycube.data_valid) continue;
do_sumcube(rfx.GetFileName(),i,mycube,mask,thresh,rlist);
}
}
int
main(int argc,char *argv[])
{
if (argc<2) {
vbcmap_help();
exit(0);
}
tokenlist args;
vector<string>filelist;
string dvname,ivname,outfile,maskfile,pfile,pmapname;
args.Transfer(argc-1,argv+1);
int part=1,nparts=1;
string perm_mat;
int perm_index=-1;
int minlesions=2;
bool f_yates=0;
bool f_fisher=0;
bool f_zscore=0;
bool f_flip=0;
bool f_fdr=0;
bool f_twotailed=0;
bool f_nodup=0;
float q=0;
for (size_t i=0; i<args.size(); i++) {
if (args[i]=="-v")
vbcmap_version();
else if (args[i]=="-h")
vbcmap_help();
else if (args[i]=="-2")
f_twotailed=1;
else if (args[i]=="-z")
f_zscore=1;
else if (args[i]=="-f")
f_flip=1;
else if (args[i]=="-x")
f_fisher=1;
else if (args[i]=="-y")
f_yates=1;
else if (args[i]=="-nodup")
f_nodup=1;
else if (args[i]=="-pfile" && i<args.size()-1) {
pfile=args[++i];
}
else if (args[i]=="-pmap" && i<args.size()-1) {
pmapname=args[++i];
}
else if (args[i]=="-m" && i<args.size()-1) {
maskfile=args[++i];
}
else if (args[i]=="-q" && i<args.size()-1) {
f_fdr=1;
q=strtod(args[++i]);
}
else if (args[i]=="-n" && i<args.size()-1) {
minlesions=strtol(args[++i]);
if (minlesions<2) minlesions=2;
}
else if (args[i]=="-op" && i<args.size()-2) {
perm_mat=args[++i];
perm_index=strtol(args[++i]);
}
else if (args[i]=="-p" && i<args.size()-2) {
part=strtol(args[++i]);
nparts=strtol(args[++i]);
}
else
filelist.push_back(args[i]);
}
if (filelist.size()!=3) {
vbcmap_help();
exit(112);
}
ivname=filelist[0];
dvname=filelist[1];
outfile=filelist[2];
Cube tmap,mask;
Tes ts;
VB_Vector depvar;
if (ts.ReadFile(ivname)) {
printf("[E] vbcmap: couldn't get grouping info from %s\n",ivname.c_str());
exit(101);
}
if (depvar.ReadFile(dvname)) {
printf("[E] vbcmap: couldn't get dependent variable info from %s\n",dvname.c_str());
exit(102);
}
// build our mask
ts.ExtractMask(mask);
if (maskfile.size()) {
Cube tmask;
if (tmask.ReadFile(maskfile)) {
printf("[E] vbcmap: couldn't read mask file %s\n",maskfile.c_str());
exit(103);
}
if (!(tmask.dimsequal(mask))) {
printf("[E] vbcmap: lesion maps and mask files have inconsistent dimensions\n");
exit(104);
}
mask.intersect(tmask);
}
// permute order of dv if requested
VB_Vector perm_order;
if (perm_index>-1) {
VBMatrix vm(perm_mat,0,0,perm_index,perm_index);
perm_order=vm.GetColumn(0);
VB_Vector tmp(depvar.size());
for (uint32 i=0; i<depvar.size(); i++)
tmp[i]=depvar[(int)perm_order[i]];
depvar=tmp;
}
// convert dv to bitmask
bitmask dvbm;
dvbm.resize(depvar.size());
dvbm.clear();
for (size_t i=0; i<depvar.size(); i++) {
if (!f_flip && fabs(depvar[i])>FLT_MIN)
dvbm.set(i);
if (f_flip && !(fabs(depvar[i])>FLT_MIN))
dvbm.set(i);
}
string partstring;
if (nparts>1)
partstring="_part_"+strnum(part);
bitmask bm;
bm.resize(ts.dimt);
map<bitmask,x2val> statlookup;
map<bitmask,x2val>::iterator iter;
Cube statmap(ts.dimx,ts.dimy,ts.dimz,vb_float);
Cube pmap;
Tes cimap;
x2val res;
Cube fdrmask;
if (f_fdr || pmapname.size()) {
pmap.SetVolume(ts.dimx,ts.dimy,ts.dimz,vb_float);
fdrmask=mask;
fdrmask.zero();
}
vector<double> pvals; // all p vals used in fdr calculation
bool f_non1=0;
int16 val;
for (int i=0; i<ts.dimx; i++) {
for (int j=0; j<ts.dimy; j++) {
for (int k=0; k<ts.dimz; k++) {
if (!mask.testValue(i,j,k))
continue;
for (int m=0; m<ts.dimt; m++) {
val=ts.getValue<int16>(i,j,k,m);
if (val) {
bm.set(m);
if (val!=1) f_non1=1;
}
else
bm.unset(m);
}
if (bm.count()<minlesions)
continue;
if (ts.dimt-bm.count()<2)
continue;
iter=statlookup.find(bm);
if (iter==statlookup.end()) {
// this is a new pattern
if (f_fdr)
fdrmask.SetValue(i,j,k,1);
if (f_fisher)
res=calc_fisher(bm,dvbm);
else
res=calc_chisquared(bm,dvbm,f_yates);
if (f_twotailed)
res.p*=2.0;
// FIXME??? if we need the p value or z score, get it
// if doing fdr, stash the p value
if (f_fdr || pmapname.size()) {
pmap.SetValue(i,j,k,res.p);
pvals.push_back(res.p);
}
// if doing confidence intervals, stash that
if (f_zscore)
statmap.SetValue(i,j,k,res.z);
else
statmap.SetValue(i,j,k,res.x2);
statlookup[bm]=res;
}
else {
// this is a previously encountered pattern
if (f_fdr && !f_nodup) {
fdrmask.SetValue(i,j,k,1);
pvals.push_back(iter->second.p);
}
statmap.SetValue(i,j,k,iter->second.x2);
if (f_fdr || pmapname.size())
pmap.SetValue(i,j,k,iter->second.p);
}
}
}
}
if (f_non1) {
cout << "[W] vbcmap: non-0/1 values found in lesion map" << endl;
}
if (f_fdr) {
vector<fdrstat> ffs=calc_multi_fdr_thresh(statmap,pmap,fdrmask,q);
if (ffs.size()) {
cout << (format("[I] vbcmap: FDR calculation included %d voxels with p values from %.4f to %.4f\n")
%ffs[0].nvoxels%ffs[0].low%ffs[0].high).str();
statmap.AddHeader("# the following thresholds must be exceeded for FDR control");
vbforeach(fdrstat ff,ffs) {
if (ff.maxind>=0)
cout << (format("[I] vbcmap: FDR threhsold for q=%.2f is %.4f\n")%ff.q%ff.statval).str();
else
cout << (format("[I] vbcmap: no FDR threhsold could be identified for q=%.2f\n")%ff.q).str();
string tmps=(format("fdrthresh: %g %g")%ff.q%ff.statval).str().c_str();
statmap.AddHeader(tmps);
}
}
}
int
VBSim::Go(int argc,char *argv[])
{
tokenlist args;
rng=NULL;
dimx=0;
dimy=0;
dimz=0;
dimt=0;
n_mean=10.0;
n_variance=5.0;
n_fwhm=0.0;
float vx=1.0;
float vy=1.0;
float vz=1.0;
float vt=2000;
uint32 rngseed=VBRandom();
args.Transfer(argc,argv);
if (args.size() == 0) {
vbsim_help();
exit(0);
}
for (size_t i=0; i<args.size(); i++) {
// -d x y z for dims
if (args[i]=="-d" && i<args.size()-4) {
dimx=strtol(args[i+1]);
dimy=strtol(args[i+2]);
dimz=strtol(args[i+3]);
dimt=strtol(args[i+4]);
i+=4;
}
// -c for loading anatomy
else if (args[i]=="-c" && i<args.size()-1) {
anatname=args[i+1];
i++;
}
// -z for voxel sizes
else if (args[i]=="-z" && i<args.size()-3) {
vx=strtod(args[++i]);
vy=strtod(args[++i]);
vz=strtod(args[++i]);
vt=strtod(args[++i]);
}
// -n for per-volume noise
else if (args[i]=="-n" && i<args.size()-3) {
n_mean=strtod(args[i+1]);
n_variance=strtod(args[i+2]);
n_fwhm=strtod(args[i+3]);
i+=3;
}
else if (args[i]=="-s" && i<args.size()-1)
rngseed=strtol(args[++i]);
else if (args[i]=="-o" && i<args.size()-1) {
outfile=args[i+1];
i++;
}
else {
printf("[E] vbsim: unrecognized argument %s\n",args(i));
return 140;
}
}
if (dimx<1 || dimy<0 || dimz<0 || dimt<0) {
printf("[E] vbsim: bad dimensions\n");
return 110;
}
// initialize RNG
rng=gsl_rng_alloc(gsl_rng_mt19937);
assert(rng);
gsl_rng_set(rng,rngseed);
// FIXME tell the user here what we're doing
// CREATE ANATOMY (constant image)
if (anatname.size()) {
if (anat.ReadFile(anatname)) {
printf("[E] vbsim: couldn't read %s\n",anatname.c_str());
return 101;
}
if (anat.dimx!=dimx || anat.dimy!=dimy || anat.dimz != dimz) {
printf("[E] vbsim: %s doesn't match your dimensions\n",anatname.c_str());
return 102;
}
}
else {
// create volume according to dimensions, add random noise if requested
anat.SetVolume(dimx,dimy,dimz,vb_float);
}
// SPECIAL CASE-- vecs if dimy=dimz=dimt==0
if (dimt==0 && dimy==0 && dimz==0) {
printf("[I] vbsim: creating a vector with %d elements with N(%g,%g)\n",dimx,
n_mean,sqrt(n_variance));
if (outfile=="")
outfile="data.ref";
VB_Vector vv(dimx);
if (!(isnan(n_mean))) {
for (int32 i=0; i<dimx; i++)
vv[i]=n_mean+gaussian_random(sqrt(abs(n_variance)));
}
if (vv.WriteFile(outfile)) {
printf("[E] vbsim: error writing 1D file %s\n",outfile.c_str());
exit(120);
}
printf("[I] vbsim: wrote 1D file %s\n",outfile.c_str());
exit(0);
}
// SPECIAL CASE-- cubes if dimt==0
if (dimt==0) {
printf("[I] vbsim: creating a %dx%dx%d 3D volume with N(%g,%g)\n",dimx,dimy,dimz,
n_mean,sqrt(n_variance));
if (outfile=="")
outfile="data.cub";
Cube vol(dimx,dimy,dimz,vb_float);
if (!(isnan(n_mean)))
AddGaussian(vol,n_mean,n_variance,n_fwhm,n_fwhm,n_fwhm);
vol+=anat;
vol.setVoxSizes(vx,vy,vz,vt);
if (vol.WriteFile(outfile)) {
printf("[E] vbsim: error writing 3D volume %s\n",outfile.c_str());
exit(120);
}
printf("[I] vbsim: wrote 3D volume %s\n",outfile.c_str());
exit(0);
}
printf("[I] vbsim: creating a %dx%dx%dx%d 4D volume with N(%g,%g)\n",dimx,dimy,dimz,dimt,
n_mean,sqrt(n_variance));
if (outfile=="")
outfile="data.tes";
// CREATE FUNCTIONALS (variable images, one per time point)
mytes.SetVolume(dimx,dimy,dimz,dimt,vb_float);
for (int i=0; i<dimt; i++) {
Cube vol(dimx,dimy,dimz,vb_float);
if (!(isnan(n_mean)))
AddGaussian(vol,n_mean,n_variance,n_fwhm,n_fwhm,n_fwhm);
vol+=anat;
mytes.SetCube(i,vol);
}
mytes.setVoxSizes(vx,vy,vz,vt);
if (mytes.WriteFile(outfile)) {
printf("[E] vbsim: error writing 4D volume %s\n",outfile.c_str());
return 120;
}
printf("[I] vbsim: wrote 4D volume %s\n",outfile.c_str());
return 0;
}
