From 2f156f3df33cf3cc4a2a5e6556c23257ea91f2d0 Mon Sep 17 00:00:00 2001
From: Tim Behrens <behrens@fmrib.ox.ac.uk>
Date: Wed, 1 Sep 2004 18:08:03 +0000
Subject: [PATCH] *** empty log message ***
---
make_dyadic_vectors.cc | 67 +++++++++++++++++++++++++++---------------
old_bedpost | 2 ++
2 files changed, 45 insertions(+), 24 deletions(-)
diff --git a/make_dyadic_vectors.cc b/make_dyadic_vectors.cc
index 2fd0934..0d0e594 100644
--- a/make_dyadic_vectors.cc
+++ b/make_dyadic_vectors.cc
@@ -7,16 +7,28 @@ using namespace NEWIMAGE;
int main ( int argc, char **argv ){
if(argc<4){
- cerr<<"usage: make_dyadic_vectors <theta_vol> <phi_vol> <output>"<<endl;
+ cerr<<"usage: make_dyadic_vectors <theta_vol> <phi_vol> [mask] <output>"<<endl;
+ cerr<<"[mask] is optional"<<endl;
exit(0);
}
+
volume4D<float> ths,phs;
volumeinfo tempinfo;
read_volume4D(ths,argv[1],tempinfo);
read_volume4D(phs,argv[2]);
+ volume<float> mask;
+ string oname;
+ if(argc==5){
+ oname=argv[4];
+ read_volume(mask,argv[3]);
+ }
+ else{
+ mask=ths[0]*0+1;
+ oname=argv[3];
+ }
volume4D<float> dyadic_vecs(ths.xsize(),ths.ysize(),ths.zsize(),3);
dyadic_vecs=0;
- copybasicproperties(ths,dyadic_vecs);
+ copybasicproperties(ths[0],dyadic_vecs[0]);
SymmetricMatrix dyad(3);dyad=0;
ColumnVector dir(3);
@@ -26,35 +38,42 @@ int main ( int argc, char **argv ){
for(int k=ths.minz();k<=ths.maxz();k++){
for(int j=ths.miny();j<=ths.maxy();j++){
for(int i=ths.minx();i<=ths.maxx();i++){
- dyad=0;
- for(int s=ths.mint();s<=ths.maxt();s++){
- float th=ths(i,j,k,s);
- float ph=phs(i,j,k,s);
- dir(1)=sin(th)*cos(ph);
- dir(2)=sin(th)*sin(ph);
- dir(3)=cos(th);
- dyad << dyad+dir*dir.t();
- }
-
- EigenValues(dyad,dyad_D,dyad_V);
- int maxeig;
- if(dyad_D(1)>dyad_D(2)){
- if(dyad_D(1)>dyad_D(3)) maxeig=1;
- else maxeig=3;
+ if(mask(i,j,k)>0){
+ dyad=0;
+ for(int s=ths.mint();s<=ths.maxt();s++){
+
+ float th=ths(i,j,k,s);
+ float ph=phs(i,j,k,s);
+ dir(1)=sin(th)*cos(ph);
+ dir(2)=sin(th)*sin(ph);
+ dir(3)=cos(th);
+ dyad << dyad+dir*dir.t();
+ }
+
+ EigenValues(dyad,dyad_D,dyad_V);
+ int maxeig;
+ if(dyad_D(1)>dyad_D(2)){
+ if(dyad_D(1)>dyad_D(3)) maxeig=1;
+ else maxeig=3;
+ }
+ else{
+ if(dyad_D(2)>dyad_D(3)) maxeig=2;
+ else maxeig=3;
+ }
+ dyadic_vecs(i,j,k,0)=dyad_V(1,maxeig);
+ dyadic_vecs(i,j,k,1)=dyad_V(2,maxeig);
+ dyadic_vecs(i,j,k,2)=dyad_V(3,maxeig);
}
else{
- if(dyad_D(2)>dyad_D(3)) maxeig=2;
- else maxeig=3;
+ dyadic_vecs(i,j,k,0)=0;
+ dyadic_vecs(i,j,k,1)=0;
+ dyadic_vecs(i,j,k,2)=0;
}
- dyadic_vecs(i,j,k,0)=dyad_V(1,maxeig);
- dyadic_vecs(i,j,k,1)=dyad_V(2,maxeig);
- dyadic_vecs(i,j,k,2)=dyad_V(3,maxeig);
}
-
}
}
- save_volume4D(dyadic_vecs,argv[3],tempinfo);
+ save_volume4D(dyadic_vecs,oname,tempinfo);
}
diff --git a/old_bedpost b/old_bedpost
index 7d5b306..75c03fb 100755
--- a/old_bedpost
+++ b/old_bedpost
@@ -197,6 +197,8 @@ ${FSLDIR}/bin/avwmaths ${subjdir}.bedpost/merged_thsamples -Tmean ${subjdir}.bed
${FSLDIR}/bin/avwmaths ${subjdir}.bedpost/merged_phsamples -Tmean ${subjdir}.bedpost/mean_phsamples
${FSLDIR}/bin/avwmaths ${subjdir}.bedpost/merged_fsamples -Tmean ${subjdir}.bedpost/mean_fsamples
+${FSLDIR}/bin/make_dyadic_vectors ${subjdir}.bedpost/merged_thsamples ${subjdir}.bedpost/merged_phsamples ${subjdir}.bedpost/nodif_brain_mask ${subjdir}.bedpost/dyadic_vectors
+
if [ ${finished} -eq 1 ];then
if [ `imtest ${subjdir}.bedpost/merged_thsamples` -eq 1 ];then
if [ `imtest ${subjdir}.bedpost/merged_phsamples` -eq 1 ];then
--
GitLab