From dd8d829a91dd675a011549c6115237c7c43b1326 Mon Sep 17 00:00:00 2001
From: Saad Jbabdi <saad@fmrib.ox.ac.uk>
Date: Mon, 6 Aug 2007 20:12:10 +0000
Subject: [PATCH] small modifs
---
fdt.tcl | 22 ++++++++++++----------
probtrackOptions.cc | 6 +++---
probtrackxOptions.h | 2 +-
3 files changed, 16 insertions(+), 14 deletions(-)
diff --git a/fdt.tcl b/fdt.tcl
index 3b12703..b1703f4 100644
--- a/fdt.tcl
+++ b/fdt.tcl
@@ -688,7 +688,7 @@ proc fdt:apply { w dialog } {
exec mkdir -p $probtrack(output)
}
- set filebase $probtrack(output)/fdtx
+ set filebase $probtrack(output)/fdt
set logfile "${filebase}_log.tcl"
set log [open "$logfile" w]
puts $log "set tool $probtrack(tool)"
@@ -738,15 +738,17 @@ proc fdt:apply { w dialog } {
set flags "--mode=simple --seedref=$probtrack(reference) -o $probtrack(output) -x ${filebase}_coordinates.txt $flags"
}
seedmask {
- if { $probtrack(bcyn) } {
- fdt_monitor_short $w "${FSLDIR}/bin/convert_xfm -omat $probtrack(output)/tmp_xfm_mat -inverse $probtrack(xfm)"
- fdt_monitor_short $w "${FSLDIR}/bin/flirt -in $probtrack(bedpost_dir)/nodif_brain_mask -ref $probtrack(reference) -applyxfm -init $probtrack(output)/tmp_xfm_mat -out $probtrack(output)/tmp_brain_mask"
- fdt_monitor_short $w "${FSLDIR}/bin/flirt -in $probtrack(output)/tmp_brain_mask -ref $probtrack(output)/tmp_brain_mask -applyisoxfm $probtrack(scale) -out $probtrack(output)/lowresmask"
- fdt_monitor_short $w "${FSLDIR}/bin/fslmaths $probtrack(output)/lowresmask -thr 0.5 -bin $probtrack(output)/lowresmask"
- set flags "$flags --lrmask=$probtrack(output)/lowresmask --omatrix2"
- fdt_monitor_short $w "${FSLDIR}/bin/imrm $probtrack(output)/tmp_brain_mask"
- fdt_monitor_short $w "/bin/rm $probtrack(output)/tmp_xfm_mat"
- }
+ if { [ file exists /usr/local/fsl/bin/reord_OM ] } {
+ if { $probtrack(bcyn) } {
+ fdt_monitor_short $w "${FSLDIR}/bin/convert_xfm -omat $probtrack(output)/tmp_xfm_mat -inverse $probtrack(xfm)"
+ fdt_monitor_short $w "${FSLDIR}/bin/flirt -in $probtrack(bedpost_dir)/nodif_brain_mask -ref $probtrack(reference) -applyxfm -init $probtrack(output)/tmp_xfm_mat -out $probtrack(output)/tmp_brain_mask"
+ fdt_monitor_short $w "${FSLDIR}/bin/flirt -in $probtrack(output)/tmp_brain_mask -ref $probtrack(output)/tmp_brain_mask -applyisoxfm $probtrack(scale) -out $probtrack(output)/lowresmask"
+ fdt_monitor_short $w "${FSLDIR}/bin/fslmaths $probtrack(output)/lowresmask -thr 0.5 -bin $probtrack(output)/lowresmask"
+ set flags "$flags --lrmask=$probtrack(output)/lowresmask --omatrix2"
+ fdt_monitor_short $w "${FSLDIR}/bin/imrm $probtrack(output)/tmp_brain_mask"
+ fdt_monitor_short $w "/bin/rm $probtrack(output)/tmp_xfm_mat"
+ }
+ }
set flags "--mode=seedmask -x $probtrack(reference) $flags"
}
network {
diff --git a/probtrackOptions.cc b/probtrackOptions.cc
index 784ddff..abc642e 100644
--- a/probtrackOptions.cc
+++ b/probtrackOptions.cc
@@ -42,9 +42,9 @@ probtrackOptions* probtrackOptions::gopt = NULL;
modecheck(); // check all the correct options are set for this mode.
if(mode.value()!="simple"){
if(forcedir.value())
- logger.setthenmakeDir(logdir.value(),"probtrackx.log");
+ logger.setthenmakeDir(logdir.value(),"probtrack.log");
else
- logger.makeDir(logdir.value(),"probtrackx.log");
+ logger.makeDir(logdir.value(),"probtrack.log");
cout << "Log directory is: " << logger.getDir() << endl;
@@ -60,7 +60,7 @@ probtrackOptions* probtrackOptions::gopt = NULL;
}
catch(X_OptionError& e){
cerr<<e.what()<<endl;
- cerr<<"try: probtrackx --help"<<endl;
+ cerr<<"try: probtrack --help"<<endl;
exit(0);
}
diff --git a/probtrackxOptions.h b/probtrackxOptions.h
index f7e6ae9..92a89a0 100644
--- a/probtrackxOptions.h
+++ b/probtrackxOptions.h
@@ -187,7 +187,7 @@ class probtrackxOptions {
string("Use anisotropy to constrain tracking"),
false, no_argument),
randfib(string("--randfib"), false,
- string("Select randomly from the first two fibres when seeding"),
+ string("Select randomly from one of the fibres"),
false, no_argument),
modeuler(string("--modeuler"), false,
string("Use modified euler streamlining"),
--
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