From 5500520495893ac2e965999c282ffad6c6e826bd Mon Sep 17 00:00:00 2001
From: Saad Jbabdi <saad@fmrib.ox.ac.uk>
Date: Mon, 3 Sep 2012 14:03:14 +0000
Subject: [PATCH] Now uses probtrackx2 + many more options
---
fdt.tcl | 57 ++++++++++++++++++++++++++++-----------------------------
1 file changed, 28 insertions(+), 29 deletions(-)
diff --git a/fdt.tcl b/fdt.tcl
index 822799f..f28f05f 100644
--- a/fdt.tcl
+++ b/fdt.tcl
@@ -237,7 +237,7 @@ proc fdt:dialog { w tclstartupfile } {
$w.probtrack insert 1 options -text "Options"
#-------- Mode specific option --------
frame $w.data
- FileEntry $w.data.directory -textvariable probtrack(bedpost_dir) -label "BEDPOSTX directory" -title "Choose BEDPOSTX directory" -filetypes * -command "probtrack_update_files $w"
+ FileEntry $w.data.directory -textvariable probtrack(bedpost_dir) -label "BEDPOSTX directory" -title "Choose BEDPOSTX directory" -filetypes { } -command "probtrack_update_files $w"
TitleFrame $w.data.seed -text "Seed Space"
@@ -272,7 +272,7 @@ proc fdt:dialog { w tclstartupfile } {
optionMenu2 $w.data.seed.ssf.typelabel.type probtrack(meshspace) caret "Caret" freesurfer "FreeSurfer" first "FIRST" vox "Voxel"
FileEntry $w.data.seed.ssf.surfref -textvariable probtrack(surfref) -label "Surface Reference Image" -title "Select surface reference volume" -filetypes IMAGE
- FileEntry $w.data.seed.ssf.reference -textvariable probtrack(reference) -label "Seed reference image:" -title "Choose reference image" -filetypes { *.nii *.nii.gz *.gii }
+ FileEntry $w.data.seed.ssf.reference -textvariable probtrack(reference) -label "Seed Image/Surface" -title "Choose Image/Surface" -filetypes "{*.nii,*.nii.gz,*.gii}"
pack $w.data.seed.ssf.ssd -side top -anchor nw
pack $w.data.seed.voxel.x $w.data.seed.voxel.y $w.data.seed.voxel.z $w.data.seed.voxel.vox $w.data.seed.voxel.mm -side left -padx 2
pack $w.data.seed.voxel $w.data.seed.ssf -in $w.data.seed.f -side left -anchor w -pady 2
@@ -283,7 +283,7 @@ proc fdt:dialog { w tclstartupfile } {
listbox $w.data.seed.targets -height 6 -width 50 -yscrollcommand "$w.data.seed.sb set"
scrollbar $w.data.seed.sb -command "$w.data.seed.targets yview "
frame $w.data.seed.tb
- button $w.data.seed.tb.add -text "Add Image" -command "feat_file:setup_dialog $w a a a [namespace current] { *.nii *.nii.gz *.gii } {Select File} {fdt_add $w $w.data.seed.targets} {}"
+ button $w.data.seed.tb.add -text "Add Image" -command "feat_file:setup_dialog $w a a a [namespace current] {{*.nii,*.nii.gz,*.gii}} {Select File} {fdt_add $w $w.data.seed.targets} {}"
button $w.data.seed.tb.del -text "Remove Image" -command "fdt_sub $w $w.data.seed.targets"
button $w.data.seed.tb.imp -text "Load List" -command "feat_file:setup_dialog $w a a a [namespace current] * {Select File} {fdt_imp $w $w.data.seed.targets} {}"
button $w.data.seed.tb.exp -text "Save List" -command "feat_file:setup_dialog $w a a a [namespace current] * {Select File} {fdt_exp $w $w.data.seed.targets} {}"
@@ -336,7 +336,7 @@ proc fdt:dialog { w tclstartupfile } {
listbox $w.data.targets.wf.tf.targets -height 6 -width 50 -yscrollcommand "$w.data.targets.wf.tf.sb set"
scrollbar $w.data.targets.wf.tf.sb -command "$w.data.targets.wf.tf.targets yview "
frame $w.data.targets.wf.tf.tb
- button $w.data.targets.wf.tf.tb.add -text "Add Image" -command "feat_file:setup_dialog $w a a a [namespace current] { *.nii *.nii.gz *.gii } {Select File} {fdt_add $w $w.data.targets.wf.tf.targets} {}"
+ button $w.data.targets.wf.tf.tb.add -text "Add Image" -command "feat_file:setup_dialog $w a a a [namespace current] {{*.nii,*.nii.gz,*.gii}} {Select File} {fdt_add $w $w.data.targets.wf.tf.targets} {}"
button $w.data.targets.wf.tf.tb.del -text "Remove Image" -command "fdt_sub $w $w.data.targets.wf.tf.targets"
button $w.data.targets.wf.tf.tb.imp -text "Load List" -command "feat_file:setup_dialog $w a a a [namespace current] * {Select File} {fdt_imp $w $w.data.targets.wf.tf.targets} {}"
button $w.data.targets.wf.tf.tb.exp -text "Save List" -command "feat_file:setup_dialog $w a a a [namespace current] * {Select File} {fdt_exp $w $w.data.targets.wf.tf.targets} {}"
@@ -350,12 +350,12 @@ proc fdt:dialog { w tclstartupfile } {
option add *targets*Checkbutton*anchor w
frame $w.data.targets.ef
checkbutton $w.data.targets.ef.srt -text "Exclusion mask" -variable probtrack(exclude_yn) -command " pack forget $w.data.targets.ef.rubbish ; if { \$probtrack(exclude_yn) } { pack $w.data.targets.ef.rubbish } ; $w.probtrack compute_size"
- FileEntry $w.data.targets.ef.rubbish -textvariable probtrack(exclude) -title "Select exclusion image" -filetypes { *.nii *.nii.gz *.gii }
+ FileEntry $w.data.targets.ef.rubbish -textvariable probtrack(exclude) -title "Select exclusion image" -filetypes "{*.nii,*.nii.gz,*.gii}"
pack $w.data.targets.ef.srt -side left
frame $w.data.targets.sf
checkbutton $w.data.targets.sf.sst -text "Termination mask" -variable probtrack(terminate_yn) -command " pack forget $w.data.targets.sf.stop ; if { \$probtrack(terminate_yn) } { pack $w.data.targets.sf.stop } ; $w.probtrack compute_size"
- FileEntry $w.data.targets.sf.stop -textvariable probtrack(stop) -title "Select termination image" -filetypes { *.nii *.nii.gz *.gii }
+ FileEntry $w.data.targets.sf.stop -textvariable probtrack(stop) -title "Select termination image" -filetypes "{*.nii,*.nii.gz,*.gii}"
pack $w.data.targets.sf.sst -side left
frame $w.data.targets.cf
@@ -364,7 +364,7 @@ proc fdt:dialog { w tclstartupfile } {
listbox $w.data.targets.cf.tf.targets -height 6 -width 50 -yscrollcommand "$w.data.targets.cf.tf.sb set"
scrollbar $w.data.targets.cf.tf.sb -command "$w.data.targets.cf.tf.targets yview "
frame $w.data.targets.cf.tf.tb
- button $w.data.targets.cf.tf.tb.add -text "Add Image" -command "feat_file:setup_dialog $w a a a [namespace current] { *.nii *.nii.gz *.gii } {Select File} {fdt_add $w $w.data.targets.cf.tf.targets} {}"
+ button $w.data.targets.cf.tf.tb.add -text "Add Image" -command "feat_file:setup_dialog $w a a a [namespace current] {{*.nii,*.nii.gz,*.gii}} {Select File} {fdt_add $w $w.data.targets.cf.tf.targets} {}"
button $w.data.targets.cf.tf.tb.del -text "Remove Image" -command "fdt_sub $w $w.data.targets.cf.tf.targets"
button $w.data.targets.cf.tf.tb.imp -text "Load List" -command "feat_file:setup_dialog $w a a a [namespace current] * {Select File} {fdt_imp $w $w.data.targets.cf.tf.targets} {}"
button $w.data.targets.cf.tf.tb.exp -text "Save List" -command "feat_file:setup_dialog $w a a a [namespace current] * {Select File} {fdt_exp $w $w.data.targets.cf.tf.targets} {}"
@@ -394,7 +394,7 @@ proc fdt:dialog { w tclstartupfile } {
}
}
- FileEntry $w.data.dir -textvariable probtrack(output) -label "Output directory:" -title "Name the output directory" -filetypes *
+ FileEntry $w.data.dir -textvariable probtrack(output) -label "Output directory:" -title "Name the output directory" -filetypes { }
pack $w.data.directory $w.data.seed $w.data.targets $w.data.dir -padx 3 -pady 3 -anchor nw
@@ -463,12 +463,12 @@ proc fdt:dialog { w tclstartupfile } {
set probtrack(omatrix2_yn) 0
checkbutton $w.matadvanced.omatrix2_yn -text "Output Seed x Mask2 Matrix" -variable probtrack(omatrix2_yn) -command "fdt:matrix_mode $w"
- FileEntry $w.matadvanced.omatrix2_mask -textvariable probtrack(mask22) -label "Tract space mask" -title "Select tract space mask" -filetypes { *.nii *.nii.gz *.gii }
+ FileEntry $w.matadvanced.omatrix2_mask -textvariable probtrack(mask22) -label "Tract space mask" -title "Select tract space mask" -filetypes "{*.nii,*.nii.gz,*.gii}"
set probtrack(omatrix3_yn) 0
checkbutton $w.matadvanced.omatrix3_yn -text "Output Mask1 x Mask2 Matrix" -variable probtrack(omatrix3_yn) -command "fdt:matrix_mode $w"
- FileEntry $w.matadvanced.omatrix3_mask1 -textvariable probtrack(mask31) -label "Row space mask" -title "Select row space mask" -filetypes { *.nii *.nii.gz *.gii }
- FileEntry $w.matadvanced.omatrix3_mask2 -textvariable probtrack(mask32) -label "Column space mask" -title "Select column space mask" -filetypes { *.nii *.nii.gz *.gii }
+ FileEntry $w.matadvanced.omatrix3_mask1 -textvariable probtrack(mask31) -label "Row space mask" -title "Select row space mask" -filetypes "{*.nii,*.nii.gz,*.gii}"
+ FileEntry $w.matadvanced.omatrix3_mask2 -textvariable probtrack(mask32) -label "Column space mask" -title "Select column space mask" -filetypes "{*.nii,*.nii.gz,*.gii}"
pack \
$w.options.nparticles \
@@ -587,7 +587,7 @@ proc fdt:probtrack_mode { w } {
seedmask {
pack forget $w.data.seed.ssf.ssd
pack $w.data.targets.cf -in $w.data.targets.f -anchor w
- $w.data.seed.ssf.reference configure -label "Seed image/surface:" -title "Choose mask image"
+ $w.data.seed.ssf.reference configure -label "Seed Image/Surface:" -title "Choose Image/Surface"
pack $w.data.seed.ssf.reference $w.data.seed.ssf.ssd -side top -anchor w -pady 2
if { $probtrack(usereference_yn) } { pack $w.data.seed.ssf.nonlinear $w.data.seed.ssf.xfm -side top -anchor w -pady 2 }
@@ -817,11 +817,11 @@ proc fdt:apply { w dialog } {
if { $probtrack(wayorder_yn) == 1 } { set flags "$flags --wayorder" }
if { $probtrack(omatrix1_yn) == 1 } { set flags "$flags --omatrix1" }
- if { $probtrack(omatrix2_yn) && && $probtrack(mask22) == "" } { set errorStr "$errorStr You must specify a tract space mask!" }
+ if { $probtrack(omatrix2_yn) && $probtrack(mask22) == "" } { set errorStr "$errorStr You must specify a tract space mask!" }
if { $probtrack(omatrix2_yn) == 1 } { set flags "$flags --omatrix2 --target2=$probtrack(mask22)" }
- if { $probtrack(omatrix3_yn) && && $probtrack(mask31) == "" } { set errorStr "$errorStr You must specify a row space mask!" }
- if { $probtrack(omatrix3_yn) && && $probtrack(mask32) == "" } { set errorStr "$errorStr You must specify a column space mask!" }
- if { $probtrack(omatrix3_yn) == 1 } { set flags "$flags --omatrix3 --target3=$probtrack(mask31) --lrtarget3=$probtrackx(mask32)" }
+ if { $probtrack(omatrix3_yn) && $probtrack(mask31) == "" } { set errorStr "$errorStr You must specify a row space mask!" }
+ if { $probtrack(omatrix3_yn) && $probtrack(mask32) == "" } { set errorStr "$errorStr You must specify a column space mask!" }
+ if { $probtrack(omatrix3_yn) == 1 } { set flags "$flags --omatrix3 --target3=$probtrack(mask31) --lrtarget3=$probtrack(mask32)" }
if { $probtrack(pd) } { set flags "$flags --pd" }
set flags "$flags -c $probtrack(curvature) -S $probtrack(nsteps) --steplength=$probtrack(steplength) -P $probtrack(nparticles)"
@@ -870,7 +870,7 @@ proc fdt:apply { w dialog } {
}
if { $probtrack(useSurface) } {
set flags "$flags --meshspace=$probtrack(meshspace) --seedref=$probtrack(surfref)"
- puts $log "set probtrack(useSurface) $probtrack(surface)"
+ puts $log "set probtrack(useSurface) $probtrack(useSurface)"
puts $log "set probtrack(meshspace) $probtrack(meshspace)"
puts $log "set probtrack(surfref) $probtrack(surfref)"
}
@@ -955,31 +955,30 @@ proc fdt:apply { w dialog } {
exec chmod 777 ${filebase}_script.sh
puts $script "#!/bin/sh"
puts $script "cd $probtrack(output)"
- #puts $script "$FSLDIR/bin/probtrackx2 $flags"
- puts $script "~saad/fsl/src/ptx2/probtrackx2 $flags"
+ puts $script "$FSLDIR/bin/probtrackx2 $flags"
if { $probtrack(classify_yn) == 1 } {
- puts $script "$FSLDIR/bin/find_the_biggest seeds_to_* biggest >> fdt_seed_classification.txt"
- }
- if { $probtrack(mode) == "simple" } {
- puts $script "rm ${filebase}_coordinates.txt"
+ puts $script "$FSLDIR/bin/find_the_biggest seeds_to_* $probtrack(output)/biggest >> fdt_seed_classification.txt"
}
+ #if { $probtrack(mode) == "simple" } {
+ #puts $script "rm ${filebase}_coordinates.txt"
+ #}
puts $script "mv $logfile $copylog"
puts $script "rm ${filebase}_script.sh"
close $script
exec $FSLDIR/bin/fsl_sub -q long.q ${filebase}_script.sh
} else {
- fdt_monitor_short $w "~saad/fsl/src/ptx2/probtrackx2 $flags"
+ fdt_monitor_short $w "$FSLDIR/bin/probtrackx2 $flags"
if { $probtrack(classify_yn) == 1 } {
- exec sh -c "$FSLDIR/bin/find_the_biggest $probtrack(output)/seeds_to_* biggest >> $probtrack(output)/fdt_seed_classification.txt"
+ exec sh -c "$FSLDIR/bin/find_the_biggest $probtrack(output)/seeds_to_* $probtrack(output)/biggest >> $probtrack(output)/fdt_seed_classification.txt"
}
}
}
if { !$FSLPARALLEL } {
- if { $probtrack(mode) == "simple" } {
- puts "rm ${filebase}_coordinates.txt"
- exec rm ${filebase}_coordinates.txt
- }
+ #if { $probtrack(mode) == "simple" } {
+ #puts "rm ${filebase}_coordinates.txt"
+ #exec rm ${filebase}_coordinates.txt
+ #}
if { $copylog != "" } {
puts "mv $logfile $copylog"
exec mv $logfile $copylog
--
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