From fa0425e123b17156700cb1e1742d62324fc29f48 Mon Sep 17 00:00:00 2001
From: Matthew Webster <mwebster@fmrib.ox.ac.uk>
Date: Mon, 30 Apr 2007 15:27:23 +0000
Subject: [PATCH] saad fixes
---
fdtx.tcl | 50 +++++++++++++++++++++-----------------------------
1 file changed, 21 insertions(+), 29 deletions(-)
diff --git a/fdtx.tcl b/fdtx.tcl
index 5dc92e3..c63c94d 100644
--- a/fdtx.tcl
+++ b/fdtx.tcl
@@ -650,7 +650,7 @@ proc fdt:apply { w dialog } {
global probtrack
set errorStr ""
if { $probtrack(bedpost_dir) == "" } { set errorStr "You must specify the bedpost directory!" }
- if { $probtrack(reference) == "" } { set errorStr "$errorStr You must specify a reference image" }
+ if { $probtrack(mode) != "network" && $probtrack(reference) == "" } { set errorStr "$errorStr You must specify a reference image" }
if { $probtrack(exclude_yn) && $probtrack(exclude) == "" } { set errorStr "$errorStr You must specify the exclusion mask!" }
if { $probtrack(terminate_yn) && $probtrack(stop) == ""} { set errorStr "$errorStr You must specify the termination mask!" }
if { $probtrack(output) == "" } { set errorStr "$errorStr You must specify the output basename!" }
@@ -686,6 +686,20 @@ proc fdt:apply { w dialog } {
puts $log "set probtrack(stop) $probtrack(stop)"
}
+ if { $errorStr != "" } {
+ MxPause $errorStr
+ return
+ }
+ set canwrite 1
+ if { [ file exists $probtrack(output) ] } {
+ set canwrite [ YesNoWidget "Overwrite $probtrack(output)?" Yes No ]
+ }
+ if { $canwrite } {
+ puts "rm -rf $probtrack(output)"
+ exec rm -rf $probtrack(output)
+ puts "mkdir -p $probtrack(output)"
+ exec mkdir -p $probtrack(output)
+ }
set flags "$flags --forcedir --opd -s $probtrack(bedpost_dir)/merged -m $probtrack(bedpost_dir)/nodif_brain_mask --dir=$probtrack(output)"
foreach entry {bedpost_dir xfm mode exclude_yn usereference_yn verbose_yn loopcheck_yn modeuler_yn curvature nsteps steplength nparticles} {
@@ -713,44 +727,22 @@ proc fdt:apply { w dialog } {
puts $log "set probtrack(y) $probtrack(y)"
puts $log "set probtrack(z) $probtrack(z)"
puts $log "set probtrack(units) $probtrack(units)"
- set flags "$flags --seedref=$probtrack(reference) -o $probtrack(output)"
- set probtrack(reference2) ${filebase}_coordinates.txt
+ set flags "--mode=single --seedref=$probtrack(reference) -o $probtrack(output) -x ${filebase}_coordinates.txt $flags"
}
seedmask {
if { $probtrack(bcyn) } {
- fdt_monitor_short $w "${FSLDIR}/bin/flirt -in seed_brain_mask -ref seed_brain_mask -applyisoxfm 5 -out lowresmask"
- fdt_monitor_short $w "${FSLDIR}/bin/avwmaths lowresmask -ككthr 0.5 -bin lowresmask"
+ fdt_monitor_short $w "${FSLDIR}/bin/flirt -in $probtrack(bedpost_dir)/seed_brain_mask -ref $probtrack(bedpost_dir)/seed_brain_mask -applyisoxfm 5 -out $probtrack(bedpost_dir)/lowresmask"
+ fdt_monitor_short $w "${FSLDIR}/bin/avwmaths lowresmask -thr 0.5 -bin lowresmask"
set flags "$flags --lrmask=lowresmask --omatrix2"
}
-
- set probtrack(reference2) $probtrack(reference)
+ set flags "--mode=seedmask -x $probtrack(reference) $flags"
}
network {
- set flags "$flags --network"
- set probtrack(mode) seedmask
fdt_exp w $w.data.seed.targets $probtrack(output)/masks.txt
- set probtrack(reference2) $probtrack(output)/masks.txt
+ set flags "--network --mode=seedmask -x $probtrack(output)/masks.txt $flags"
}
}
- if { $errorStr != "" } {
- MxPause $errorStr
- return
- }
- set canwrite 1
- if { [ file exists $probtrack(output) ] } {
- set canwrite [ YesNoWidget "Overwrite $probtrack(output)?" Yes No ]
- }
- if { $canwrite } {
- puts "here"
- puts "rm -rf $probtrack(output)"
- exec rm -rf $probtrack(output)
- puts "mkdir -p $probtrack(output)"
- exec mkdir -p $probtrack(output)
- }
-
- puts $probtrack(output)
-
if { $canwrite } {
set copylog "fdt.log"
@@ -763,7 +755,7 @@ proc fdt:apply { w dialog } {
set flags "$flags --targetmasks=$probtrack(output)/targets.txt --os2t "
}
- fdt_monitor_short $w "$FSLDIR/bin/probtrackx --mode=$probtrack(mode) -x $probtrack(reference2) $flags"
+ fdt_monitor_short $w "$FSLDIR/bin/probtrackx $flags"
if { $probtrack(classify_yn) == 1 } {
fdt_monitor_short $w "$FSLDIR/bin/find_the_biggest ${logdir}/seeds_to_* biggest >> ${logdir}/fdt_seed_classification.txt"
}
--
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