diff --git a/old_bedpost b/old_bedpost
index 7b4ff61421b462d553f3ce27452e3d6f2f225fe4..27c85b74410fe69607e0e8bbda17d945c7be8843 100755
--- a/old_bedpost
+++ b/old_bedpost
@@ -20,9 +20,9 @@ Clean_Exit(){
for j in ${i};do
host=`echo $j | awk -F _fdt_ '{print $1}'`
pid=`echo $j | awk -F _fdt_ '{print $2}'`
- if [ "x${FSL_MACHINE_LIST}" != "x" ]; then
-# ${FSL_REMOTE_CALL} $host "kill -KILL $pid" #this leaves one child process per processor - what can you do?
- $FSL_REMOTE_CALL $host "if [ -r /etc/fslconf/fsl.sh ];then . /etc/fslconf/fsl.sh; elif [ -r /usr/local/etc/fslconf/fsl.sh ];then . /usr/local/etc/fslconf/fsl.sh; elif [ -r \${HOME}/.fslconf/fsl.sh ]; then . \${HOME}/.fslconf/fsl.sh; fi; if [ x\${FSLDIR} != "x" ];then \${FSLDIR}/bin/bedpost_kill_pid ${pid} >/dev/null 2>&1; else echo FSLDIR not set in any default location on machine `hostname`;fi" >/dev/null 2>&1 &
+ if [ "x${FSLMACHINELIST}" != "x" ]; then
+# ${FSLREMOTECALL} $host "kill -KILL $pid" #this leaves one child process per processor - what can you do?
+ $FSLREMOTECALL $host "if [ -r /usr/local/etc/fslconf/fsl.sh ];then . /usr/local/etc/fslconf/fsl.sh;fi; if [ -r /etc/fslconf/fsl.sh ];then . /etc/fslconf/fsl.sh;fi; if [ -r \${HOME}/.fslconf/fsl.sh ]; then . \${HOME}/.fslconf/fsl.sh; fi; if [ x\${FSLDIR} != "x" ];then \${FSLDIR}/bin/bedpost_kill_pid ${pid} >/dev/null 2>&1; else echo FSLDIR not set in any default location on machine `hostname`;fi" >/dev/null 2>&1 &
else
${FSLDIR}/bin/bedpost_kill_pid ${pid}
fi
@@ -33,14 +33,14 @@ Clean_Exit(){
}
Lock(){
- if [ "x${FSL_LOCK_DIR}" != "x" ];then
- touch ${FSL_LOCK_DIR}/.bedpost.lock
+ if [ "x${FSLLOCKDIR}" != "x" ];then
+ touch ${FSLLOCKDIR}/.bedpost.lock
fi
}
ExitUnlock(){
- if [ -e ${FSL_LOCK_DIR}/.bedpost.lock ];then
- rm ${FSL_LOCK_DIR}/.bedpost.lock
+ if [ -e ${FSLLOCKDIR}/.bedpost.lock ];then
+ rm ${FSLLOCKDIR}/.bedpost.lock
fi
#clean up slices
@@ -58,9 +58,9 @@ ExitUnlock(){
}
LockTest(){
- if [ "x${FSL_LOCK_DIR}" = "x" ];then
+ if [ "x${FSLLOCKDIR}" = "x" ];then
echo 1;
- elif [ ! -e ${FSL_LOCK_DIR}/.bedpost.lock ];then
+ elif [ ! -e ${FSLLOCKDIR}/.bedpost.lock ];then
echo 1;
else
echo 0;
@@ -148,21 +148,20 @@ ${FSLDIR}/bin/avwslice ${subjdir}/data
${FSLDIR}/bin/avwslice ${subjdir}/nodif_brain_mask
#for parallel processing, the following need to be setup elsewhere
-#FSL_MACHINE_LIST="list of machines (can be duplicated for two processors etc.)"
-#FSL_REMOTE_CALL="ssh (or rsh or whatever you want to use)"
+#FSLMACHINELIST="list of machines (can be duplicated for two processors etc.)"
+#FSLREMOTECALL="ssh (or rsh or whatever you want to use)"
-if [ "x$FSL_MACHINE_LIST" = "x" ] ; then
+if [ "x$FSLMACHINELIST" = "x" ] ; then
echo "processing data on local host"
${FSLDIR}/bin/bedpost_proc $subjdir $nslices ${subjdir}.bedpost/logs/pid_${$} &
else
- echo "processing data on hosts: $FSL_MACHINE_LIST"
- for machine in $FSL_MACHINE_LIST; do
- $FSL_REMOTE_CALL $machine "if [ -r /etc/fslconf/fsl.sh ];then . /etc/fslconf/fsl.sh; elif [ -r /usr/local/etc/fslconf/fsl.sh ];then . /usr/local/etc/fslconf/fsl.sh; elif [ -r \${HOME}/.fslconf/fsl.sh ]; then . \${HOME}/.fslconf/fsl.sh; fi; if [ x\${FSLDIR} != "x" ];then \${FSLDIR}/bin/bedpost_proc $subjdir $nslices ${subjdir}.bedpost/logs/pid_${$}; else echo FSLDIR not set in any default location on machine `hostname`;fi" &
+ echo "processing data on hosts: $FSLMACHINELIST"
+ for machine in $FSLMACHINELIST; do
+ $FSLREMOTECALL $machine "if [ -r /usr/local/etc/fslconf/fsl.sh ];then . /usr/local/etc/fslconf/fsl.sh;fi; if [ -r /etc/fslconf/fsl.sh ];then . /etc/fslconf/fsl.sh;fi; if [ -r \${HOME}/.fslconf/fsl.sh ]; then . \${HOME}/.fslconf/fsl.sh; fi; if [ x\${FSLDIR} != "x" ];then \${FSLDIR}/bin/bedpost_proc $subjdir $nslices ${subjdir}.bedpost/logs/pid_${$}; else echo FSLDIR not set in any default location on machine `hostname`;fi" &
done
fi
-
b=0
finished=0;
while [ $finished -eq 0 ];do
@@ -191,6 +190,19 @@ ${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
+if [ ${finished} -eq 1 ];then
+ if [ `imtest ${subjdir}.bedpost/merged_thsamples` -eq 1 ];then
+ if [ `imtest ${subjdir}.bedpost/merged_phsamples` -eq 1 ];then
+ if [ `imtest ${subjdir}.bedpost/merged_fsamples` -eq 1 ];then
+ rm -rf ${subjdir}.bedpost/diff_slices
+ rm -f ${subjdir}/data_slice_*
+ rm -f ${subjdir}/nodif_brain_mask_slice_*
+ fi
+ fi
+ fi
+fi
+
+
mkdir -p ${subjdir}.bedpost/xfms
xfmdir=${subjdir}.bedpost/xfms
@@ -200,7 +212,6 @@ echo 0 0 1 0 >> ${xfmdir}/eye.mat
echo 0 0 0 1 >> ${xfmdir}/eye.mat
echo "DONE"
-
ExitUnlock()
diff --git a/old_bedpost_cleanup b/old_bedpost_cleanup
index 1243fef6af6ea83dc1949f49545ff798620bb2ca..bd07090d698b9c95272927caa7535ec01be98043 100755
--- a/old_bedpost_cleanup
+++ b/old_bedpost_cleanup
@@ -1,12 +1,12 @@
#!/bin/sh
-if [ "$FSL_MACHINE_LIST" = "" ] ; then
+if [ "x$FSLMACHINELIST" = "x" ] ; then
${FSLDIR}/bin/bedpost_kill_all
else
- unique_machines=`echo $FSL_MACHINE_LIST |tr " " \\\n |sort -u`
+ unique_machines=`echo $FSLMACHINELIST |tr " " \\\n |sort -u`
echo $unique_machines;
for machine in $unique_machines; do
- $FSL_REMOTE_CALL $machine "if [ -r /etc/fslconf/fsl.sh ];then . /etc/fslconf/fsl.sh; elif [ -r /usr/local/etc/fslconf/fsl.sh ];then . /usr/local/etc/fslconf/fsl.sh; elif [ -r \${HOME}/.fslconf/fsl.sh ]; then . \${HOME}/.fslconf/fsl.sh; fi; if [ x\${FSLDIR} != "x" ];then \${FSLDIR}/bin/bedpost_kill_all; else echo FSLDIR not set in any default location on machine `hostname`;fi" &
+ $FSLREMOTECALL $machine "if [ -r /usr/local/etc/fslconf/fsl.sh ];then . /usr/local/etc/fslconf/fsl.sh;fi; if [ -r /etc/fslconf/fsl.sh ];then . /etc/fslconf/fsl.sh;fi; if [ -r \${HOME}/.fslconf/fsl.sh ]; then . \${HOME}/.fslconf/fsl.sh; fi; if [ x\${FSLDIR} != "x" ];then \${FSLDIR}/bin/bedpost_kill_all; else echo FSLDIR not set in any default location on machine `hostname`;fi" &
done
fi
diff --git a/probtrackOptions.cc b/probtrackOptions.cc
index 91ee23e86c58e364941951d0f8f894444ddf0256..b7cee78103624fdf7f4ad1394b67e69f3614879e 100644
--- a/probtrackOptions.cc
+++ b/probtrackOptions.cc
@@ -175,9 +175,14 @@ probtrackOptions* probtrackOptions::gopt = NULL;
void probtrackOptions::modehelp()
{
- cout<<"tracking mode - Options are:\n\n simple (default)\n Input is text file defining start point.\n Output is dti space volume with connectivity values at each voxel.\n Note-everything in simple mode is in\n diffusion space.\n\n seeds_to_targets\n Inputs are a volume with ones at all seed points\n (requires a matrix taking it to DTI space (--xfm))\n and a text file with the name of a single target mask\n on each new line (--targetmasks).\n Output is a single volume for each target mask where the value of each\n volume within the seed mask corresponds to the number of particles \n seeded from this voxel reaching this target mask.\n\n seedmask\n Input is a volume with ones at all seed points\n (requires a matrix taking it to DTI space (--xfm))\n Output is seed space volume with connectivity values at each voxel\n summed from every seed.\n\n twomasks_symm\n Input is a binary volume for first mask (-x)\n also requires a binary volume for second mask (--mask2)\n (requires a matrix taking both seeds to DTI space (--xfm))\n Output is the sum of all paths the from first mask which pass\n through the second and vice-versa i.e. only paths\n which pass through both masks are retained.\n\n waypoints\n Input is a binary volume for seed mask (-x)\n also requires a binary waypoint mask or ascii list\n of waypoint masks (--mask2)\n (requires a matrix taking both seeds to DTI space (--xfm))\n Output is a volume containing all the paths from the\n seedmask which pass through ALL of the waypoint masks. \n\n matrix1\n Input is a volume with ones at all seed points\n (requires a matrix taking it to DTI space (--xfm))\n Output is an avw format nseeds x nseeds matrix \n where element ij contains the number of particles leaving seed \n voxel i and passing through seed voxel j. \n Second output is an nsees x 3 matrix containing the \n anatomical locations in Seed space of each matrix node.\n\n matrix2\n Inputs are a volume with ones at all seed points\n (requires a matrix taking it to DTI space (--xfm))\n and a low resolution binary mask in register with the\n seed volume (--lrmask)\n Output is a matrix of size nseeds x nlowres \n which contains the connectivity distributions from every seed voxel.\n Auxiliary outputs are index matrices for each axis \n of this matrix containing the anatomical location of each\n node in seed space (x-axis) and low res space (y-axis)\n\n maskmatrix\n Input is volume with integers in each seed location\n Integer values distinguish different clusters\n (e.g. output of Feat clustering)\n (requires a matrix taking it to DTI space (--xfm))\n Output is two matrices whose ij^th element is the\n mean and max number of particles seeded from cluster i which pass \n through cluster j\n"<<endl;
- }
+ cout<<"tracking mode - Options are:\n\n simple (default)\n Input is text file defining start point.\n Output is dti space volume with connectivity values at each voxel.\n Note-everything in simple mode is in\n diffusion space.\n\n seeds_to_targets\n Inputs are a volume with ones at all seed points\n (requires a matrix taking it to DTI space (--xfm))\n and a text file with the name of a single target mask\n on each new line (--targetmasks).\n Output is a single volume for each target mask where the value of each\n volume within the seed mask corresponds to the number of particles \n seeded from this voxel reaching this target mask.\n\n seedmask\n Input is a volume with ones at all seed points\n (requires a matrix taking it to DTI space (--xfm))\n Output is seed space volume with connectivity values at each voxel\n summed from every seed.\n\n twomasks_symm\n Input is a binary volume for first mask (-x)\n also requires a binary volume for second mask (--mask2)\n (requires a matrix taking both seeds to DTI space (--xfm))\n Output is the sum of all paths the from first mask which pass\n through the second and vice-versa i.e. only paths\n which pass through both masks are retained.\n\n waypoints\n Input is a binary volume for seed mask (-x)\n also requires a binary waypoint mask or ascii list\n of waypoint masks (--mask2)\n (requires a matrix taking both seeds to DTI space (--xfm))\n Output is a volume containing all the paths from the\n seedmask which pass through ALL of the waypoint masks.\n"<<endl;
+ if ( getenv("FSLINFMRIB"))
+ matrixmodehelp();
+ }
+ void probtrackOptions::matrixmodehelp(){
+ cout<<" matrix1\n Input is a volume with ones at all seed points\n (requires a matrix taking it to DTI space (--xfm))\n Output is an avw format nseeds x nseeds matrix \n where element ij contains the number of particles leaving seed \n voxel i and passing through seed voxel j. \n Second output is an nsees x 3 matrix containing the \n anatomical locations in Seed space of each matrix node.\n\n matrix2\n Inputs are a volume with ones at all seed points\n (requires a matrix taking it to DTI space (--xfm))\n and a low resolution binary mask in register with the\n seed volume (--lrmask)\n Output is a matrix of size nseeds x nlowres \n which contains the connectivity distributions from every seed voxel.\n Auxiliary outputs are index matrices for each axis \n of this matrix containing the anatomical location of each\n node in seed space (x-axis) and low res space (y-axis)\n\n maskmatrix\n Input is volume with integers in each seed location\n Integer values distinguish different clusters\n (e.g. output of Feat clustering)\n (requires a matrix taking it to DTI space (--xfm))\n Output is two matrices whose ij^th element is the\n mean and max number of particles seeded from cluster i which pass \n through cluster j\n"<<endl;
+ }
void probtrackOptions::status()
diff --git a/probtrackOptions.h b/probtrackOptions.h
index 658bbe0afd2a00633688db9eaff72550ebab57ca..8d05930063b89974f0dd1e8f39c0d0bfcf590ea6 100644
--- a/probtrackOptions.h
+++ b/probtrackOptions.h
@@ -37,11 +37,11 @@ class probtrackOptions {
Option<string> outfile;
Option<string> rubbishfile;
Option<string> seeds_to_dti;
- Option<string> skipmask;
+ FmribOption<string> skipmask;
Option<string> seedref;
Option<string> mask2;
Option<string> meshfile;
- Option<string> lrmask;
+ FmribOption<string> lrmask;
Option<string> logdir;
Option<bool> forcedir;
Option<int> nparticles;
@@ -55,6 +55,7 @@ class probtrackOptions {
void parse_command_line(int argc, char** argv,Log& logger);
void modecheck();
void modehelp();
+ void matrixmodehelp();
void status();
private:
probtrackOptions();
@@ -112,7 +113,7 @@ class probtrackOptions {
string("Reference vol to define seed space in simple mode - diffusion space assumed if absent"),
false, requires_argument),
mask2(string("--mask2"), string(""),
- string("second mask in both 2 mask modes."),
+ string("second mask in twomask_symm mode. Waypoint mask or ascii list of masks in wapoints mode."),
false, requires_argument),
meshfile(string("--mesh"), string(""),
string(""),
diff --git a/reord_OM.cc b/reord_OM.cc
index 92795536b011ed247471663559bc508a61f15529..6c63d0194423a19f584891b45d54c90da55b5a71 100644
--- a/reord_OM.cc
+++ b/reord_OM.cc
@@ -311,15 +311,10 @@ int main ( int argc, char **argv ){
}
// write_ascii_matrix(newOMmat.t(),"preprecock");
//Checking for and loading up Seed Coordinates
- string coordname="coords_for_"+ip+".hdr";
- ifstream coordfile(coordname.c_str());
- if(!coordfile){
- string coordname="coords_for_"+ip+".hdr.gz";
- ifstream coordfile(coordname.c_str());
- }
- if(coordfile){
- coordfile.close();
- read_volume(coordvol,"coords_for_"+ip);
+
+ string coordname="coords_for_"+ip;
+ if(fsl_imageexists(coordname)){
+ read_volume(coordvol,coordname);
coordbool=true;
mycoordmat.ReSize(coordvol.xsize(),coordvol.ysize());
for(int j=0;j<coordvol.ysize();j++){
@@ -333,15 +328,9 @@ int main ( int argc, char **argv ){
}
//Checking For and Loading Up Tract coordinates
- string trcoordname="tract_space_coords_for_"+ip+".hdr";
- ifstream trcoordfile(trcoordname.c_str());
- if(!trcoordfile){
- string trcoordname="tract_space_coords_for_"+ip+".hdr.gz";
- ifstream trcoordfile(trcoordname.c_str());
- }
- if(trcoordfile){
- trcoordfile.close();
- read_volume(tractcoordvol,"tract_space_coords_for_"+ip);
+ string trcoordname="tract_space_coords_for_"+ip;
+ if(fsl_imageexists(trcoordname)){
+ read_volume(tractcoordvol,trcoordname);
tractcoordbool=true;
mytractcoordmat.ReSize(tractcoordvol.xsize(),tractcoordvol.ysize());
for(int j=0;j<tractcoordvol.ysize();j++){