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Commit 55005204 authored by Saad Jbabdi's avatar Saad Jbabdi
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Now uses probtrackx2 + many more options

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fdt.tcl
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...@@ -237,7 +237,7 @@ proc fdt:dialog { w tclstartupfile } { ...@@ -237,7 +237,7 @@ proc fdt:dialog { w tclstartupfile } {
$w.probtrack insert 1 options -text "Options" $w.probtrack insert 1 options -text "Options"
#-------- Mode specific option -------- #-------- Mode specific option --------
frame $w.data 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" TitleFrame $w.data.seed -text "Seed Space"
...@@ -272,7 +272,7 @@ proc fdt:dialog { w tclstartupfile } { ...@@ -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" 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.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.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.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 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 } { ...@@ -283,7 +283,7 @@ proc fdt:dialog { w tclstartupfile } {
listbox $w.data.seed.targets -height 6 -width 50 -yscrollcommand "$w.data.seed.sb set" 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 " scrollbar $w.data.seed.sb -command "$w.data.seed.targets yview "
frame $w.data.seed.tb 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.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.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} {}" 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 } { ...@@ -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" 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 " scrollbar $w.data.targets.wf.tf.sb -command "$w.data.targets.wf.tf.targets yview "
frame $w.data.targets.wf.tf.tb 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.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.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} {}" 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 } { ...@@ -350,12 +350,12 @@ proc fdt:dialog { w tclstartupfile } {
option add *targets*Checkbutton*anchor w option add *targets*Checkbutton*anchor w
frame $w.data.targets.ef 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" 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 pack $w.data.targets.ef.srt -side left
frame $w.data.targets.sf 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" 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 pack $w.data.targets.sf.sst -side left
frame $w.data.targets.cf frame $w.data.targets.cf
...@@ -364,7 +364,7 @@ proc fdt:dialog { w tclstartupfile } { ...@@ -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" 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 " scrollbar $w.data.targets.cf.tf.sb -command "$w.data.targets.cf.tf.targets yview "
frame $w.data.targets.cf.tf.tb 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.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.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} {}" 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 } { ...@@ -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 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 } { ...@@ -463,12 +463,12 @@ proc fdt:dialog { w tclstartupfile } {
set probtrack(omatrix2_yn) 0 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" 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 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" 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_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_mask2 -textvariable probtrack(mask32) -label "Column space mask" -title "Select column space mask" -filetypes "{*.nii,*.nii.gz,*.gii}"
pack \ pack \
$w.options.nparticles \ $w.options.nparticles \
...@@ -587,7 +587,7 @@ proc fdt:probtrack_mode { w } { ...@@ -587,7 +587,7 @@ proc fdt:probtrack_mode { w } {
seedmask { seedmask {
pack forget $w.data.seed.ssf.ssd pack forget $w.data.seed.ssf.ssd
pack $w.data.targets.cf -in $w.data.targets.f -anchor w 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 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 } 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 } { ...@@ -817,11 +817,11 @@ proc fdt:apply { w dialog } {
if { $probtrack(wayorder_yn) == 1 } { set flags "$flags --wayorder" } if { $probtrack(wayorder_yn) == 1 } { set flags "$flags --wayorder" }
if { $probtrack(omatrix1_yn) == 1 } { set flags "$flags --omatrix1" } 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 { $probtrack(omatrix2_yn) == 1 } { set flags "$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) && $probtrack(mask31) == "" } { set errorStr "$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) && $probtrack(mask32) == "" } { set errorStr "$errorStr You must specify a column space mask!" }
if { $probtrack(omatrix3_yn) == 1 } { set flags "$flags --omatrix3 --target3=$probtrack(mask31) --lrtarget3=$probtrackx(mask32)" } if { $probtrack(omatrix3_yn) == 1 } { set flags "$flags --omatrix3 --target3=$probtrack(mask31) --lrtarget3=$probtrack(mask32)" }
if { $probtrack(pd) } { set flags "$flags --pd" } if { $probtrack(pd) } { set flags "$flags --pd" }
set flags "$flags -c $probtrack(curvature) -S $probtrack(nsteps) --steplength=$probtrack(steplength) -P $probtrack(nparticles)" set flags "$flags -c $probtrack(curvature) -S $probtrack(nsteps) --steplength=$probtrack(steplength) -P $probtrack(nparticles)"
...@@ -870,7 +870,7 @@ proc fdt:apply { w dialog } { ...@@ -870,7 +870,7 @@ proc fdt:apply { w dialog } {
} }
if { $probtrack(useSurface) } { if { $probtrack(useSurface) } {
set flags "$flags --meshspace=$probtrack(meshspace) --seedref=$probtrack(surfref)" 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(meshspace) $probtrack(meshspace)"
puts $log "set probtrack(surfref) $probtrack(surfref)" puts $log "set probtrack(surfref) $probtrack(surfref)"
} }
...@@ -955,31 +955,30 @@ proc fdt:apply { w dialog } { ...@@ -955,31 +955,30 @@ proc fdt:apply { w dialog } {
exec chmod 777 ${filebase}_script.sh exec chmod 777 ${filebase}_script.sh
puts $script "#!/bin/sh" puts $script "#!/bin/sh"
puts $script "cd $probtrack(output)" puts $script "cd $probtrack(output)"
#puts $script "$FSLDIR/bin/probtrackx2 $flags" puts $script "$FSLDIR/bin/probtrackx2 $flags"
puts $script "~saad/fsl/src/ptx2/probtrackx2 $flags"
if { $probtrack(classify_yn) == 1 } { if { $probtrack(classify_yn) == 1 } {
puts $script "$FSLDIR/bin/find_the_biggest seeds_to_* biggest >> fdt_seed_classification.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"
} }
#if { $probtrack(mode) == "simple" } {
#puts $script "rm ${filebase}_coordinates.txt"
#}
puts $script "mv $logfile $copylog" puts $script "mv $logfile $copylog"
puts $script "rm ${filebase}_script.sh" puts $script "rm ${filebase}_script.sh"
close $script close $script
exec $FSLDIR/bin/fsl_sub -q long.q ${filebase}_script.sh exec $FSLDIR/bin/fsl_sub -q long.q ${filebase}_script.sh
} else { } else {
fdt_monitor_short $w "~saad/fsl/src/ptx2/probtrackx2 $flags" fdt_monitor_short $w "$FSLDIR/bin/probtrackx2 $flags"
if { $probtrack(classify_yn) == 1 } { 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 { !$FSLPARALLEL } {
if { $probtrack(mode) == "simple" } { #if { $probtrack(mode) == "simple" } {
puts "rm ${filebase}_coordinates.txt" #puts "rm ${filebase}_coordinates.txt"
exec rm ${filebase}_coordinates.txt #exec rm ${filebase}_coordinates.txt
} #}
if { $copylog != "" } { if { $copylog != "" } {
puts "mv $logfile $copylog" puts "mv $logfile $copylog"
exec mv $logfile $copylog exec mv $logfile $copylog
......
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