From 0764cc4d16b4333efd5c631f585e2e7876b14db9 Mon Sep 17 00:00:00 2001
From: Matthew Webster <mwebster@fmrib.ox.ac.uk>
Date: Thu, 8 Mar 2007 15:03:30 +0000
Subject: [PATCH] fdtx.tcl
---
fdtx.tcl | 872 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 872 insertions(+)
create mode 100644 fdtx.tcl
diff --git a/fdtx.tcl b/fdtx.tcl
new file mode 100644
index 0000000..248c16f
--- /dev/null
+++ b/fdtx.tcl
@@ -0,0 +1,872 @@
+
+# FSL interface for FDT (BEDPOST and ProbTrack)
+#
+# Timothy Behrens, Heidi Johansen-Berg, Dave Flitney and Matthew Webster FMRIB Image Analysis Group
+#
+# Copyright (C) 2006 University of Oxford
+#
+# TCLCOPYRIGHT
+
+#TO DO replace -filetypes * with -filetypes { } for directory selectors
+source [ file dirname [ info script ] ]/fslstart.tcl
+option add *FileEntry*Entry*width 35
+set TCLPATH [file dirname [ info script ] ]
+regsub tcl $TCLPATH bin BINPATH
+regsub tcl $TCLPATH doc/fdt HTMLPATH
+
+set VERSION "1.1x"
+
+proc mm_to_voxels { X Y Z mask } {
+
+ global FSLDIR
+
+ upvar $X cX
+ upvar $Y cY
+ upvar $Z cZ
+
+
+ set vcX [ exec sh -c "echo $cX $cY $cZ | $FSLDIR/bin/std2imgcoord -img $mask -vox - | awk '{print \$1}'" ]
+ set vcY [ exec sh -c "echo $cX $cY $cZ | $FSLDIR/bin/std2imgcoord -img $mask -vox - | awk '{print \$2}'" ]
+ set vcZ [ exec sh -c "echo $cX $cY $cZ | $FSLDIR/bin/std2imgcoord -img $mask -vox - | awk '{print \$3}'" ]
+ set cX $vcX
+ set cY $vcY
+ set cZ $vcZ
+}
+
+proc fdt:dialog { w tclstartupfile } {
+
+ global eddy bedpost registration dtifit probtrack HTMLPATH FSLDIR VERSION INMEDX VARS
+ set probtrack(tool) "probtrack"
+
+ if [winfo exists $w] {
+ wm deiconify $w
+ raise $w
+ return
+ }
+
+ toplevel $w
+ wm title $w "FDT - FMRIB's Diffusion Toolbox $VERSION"
+ wm iconname $w "FDT"
+ wm iconbitmap $w @$FSLDIR/tcl/fmrib.xbm
+
+ #-------- Stage and Mode Options --------
+
+ frame $w.tool
+ optionMenu2 $w.tool.menu probtrack(tool) -command "fdt:select_tool $w" eddy_current "Eddy current correction" bedpost "BEDPOSTX Estimation of diffusion parameters" registration "Registration" probtrack "ProbTrackX Probabilistic tracking" xutilssx "----------------------------------------------------" dtifit "DTIFit Reconstruct diffusion tensors"
+ $w.tool.menu.menu entryconfigure 4 -state disabled -background black
+ pack $w.tool.menu -side left -pady 3 -padx 6 -anchor nw
+
+ #-------- Tool Options... --------
+
+ frame $w.opts
+
+ #------- Registration --------
+
+ frame $w.registration
+
+ proc registration_set_directory { w dirname } {
+ global registration
+
+ set struct [ file join $dirname struct_brain ]
+
+ if { [ imtest $struct ] } {
+ set registration(struct_image) $struct
+ } else {
+ set registration(struct_image) ""
+ }
+ }
+
+ FileEntry $w.registration.directory -textvariable registration(directory) -label "BEDPOST directory:" -title "Choose directory" -filetypes * -command "registration_set_directory $w"
+
+ frame $w.registration.struct
+ checkbutton $w.registration.struct.yn -variable registration(struct_yn) -command "registration_packframe $w"
+ label $w.registration.struct.lb -text "Main structural image"
+ TitleFrame $w.registration.struct.tf -text "Main structural image"
+ optionMenu2 $w.registration.struct.tf.search registration(struct_search) 0 "No search" 90 "Normal search" 180 "Full search"
+ optionMenu2 $w.registration.struct.tf.dof registration(struct_dof) 6 "6 DOF" 7 "7 DOF" 9 "9 DOF" 12 "12 DOF"
+ optionMenu2 $w.registration.struct.tf.costfn registration(struct_costfn) corratio "Correlation ratio" mutualinfo "Mutual information"
+ FileEntry $w.registration.struct.tf.file -textvariable registration(struct_image) -filetypes IMAGE -width 45
+ pack $w.registration.struct.tf.file -side top -in [ $w.registration.struct.tf getframe ]
+ pack $w.registration.struct.tf.search $w.registration.struct.tf.dof $w.registration.struct.tf.costfn -side left -in [ $w.registration.struct.tf getframe ]
+ set registration(struct_costfn) mutualinfo
+ set registration(struct_dof) 12
+ set registration(struct_search) 90
+ set registration(struct_yn) 0
+
+ frame $w.registration.standard
+ checkbutton $w.registration.standard.yn -variable registration(standard_yn) -command "registration_packframe $w"
+ TitleFrame $w.registration.standard.tf -text "Standard space"
+ label $w.registration.standard.lb -text "Standard space"
+ optionMenu2 $w.registration.standard.tf.search registration(standard_search) 0 "No search" 90 "Normal search" 180 "Full search"
+ optionMenu2 $w.registration.standard.tf.dof registration(standard_dof) 6 "6 DOF" 7 "7 DOF" 9 "9 DOF" 12 "12 DOF"
+ optionMenu2 $w.registration.standard.tf.costfn registration(standard_costfn) corratio "Correlation ratio" mutualinfo "Mutual information"
+ FileEntry $w.registration.standard.tf.file -textvariable registration(standard_image) -filetypes IMAGE -width 45
+ pack $w.registration.standard.tf.file -side top -in [ $w.registration.standard.tf getframe ]
+ pack $w.registration.standard.tf.search $w.registration.standard.tf.dof $w.registration.standard.tf.costfn -side left -in [ $w.registration.standard.tf getframe ]
+ set registration(standard_yn) 1
+ set registration(standard_dof) 12
+ set registration(standard_search) 90
+ set registration(standard_image) [ file join ${FSLDIR} etc standard avg152T1_brain ]
+
+ pack $w.registration.directory $w.registration.struct $w.registration.standard -side top -padx 3 -pady 3 -anchor w
+
+ proc registration_packframe { w } {
+ global registration
+ pack forget $w.registration.struct.yn $w.registration.struct.tf $w.registration.struct.yn $w.registration.struct.lb
+ pack forget $w.registration.standard.yn $w.registration.standard.tf $w.registration.standard.yn $w.registration.standard.lb
+ if {$registration(struct_yn)} { pack $w.registration.struct.yn $w.registration.struct.tf -side left -anchor w } else { pack $w.registration.struct.yn $w.registration.struct.lb -side left -anchor w}
+ if {$registration(standard_yn)} { pack $w.registration.standard.yn $w.registration.standard.tf -side left -anchor w } else { pack $w.registration.standard.yn $w.registration.standard.lb -side left -anchor w}
+ }
+
+ registration_packframe $w
+ #------- ECC --------
+ frame $w.ecc
+
+ proc ecc_update_files { w filename } {
+ global eddy
+ set eddy(output) [ file join [file dirname $eddy(input)] data ]
+ }
+
+ FileEntry $w.ecc.input -textvariable eddy(input) -label "Diffusion weighted data:" -title "Choose diffusion weighted image" -filetypes IMAGE -command "ecc_update_files $w"
+
+ FileEntry $w.ecc.output -textvariable eddy(output) -label "Corrected output data:" -title "Choose output image name" -filetypes IMAGE -command "ecc_update_files $w"
+
+ set eddy(refnum) 0
+ LabelSpinBox $w.ecc.refnum -label "Reference volume" -textvariable eddy(refnum) -range {0 100 1 } -width 6
+
+ pack $w.ecc.input $w.ecc.output $w.ecc.refnum -side top -padx 3 -pady 3 -expand yes -anchor w
+
+ #------- DTIFit --------
+
+ frame $w.dtifit
+
+ FileEntry $w.dtifit.directory -textvariable dtifit(directory) -label "Input directory:" -title "Choose directory" -command "set_working_directory dtifit(cwd)"
+
+ proc dtifit_toggle_expert { w } {
+ global dtifit
+
+ if { $dtifit(expert_yn) } {
+ pack forget $w.dtifit.directory
+ pack $w.dtifit.expert -in $w.dtifit -after $w.dtifit.expert_yn
+ } else {
+ pack forget $w.dtifit.expert
+ pack $w.dtifit.directory -in $w.dtifit -before $w.dtifit.expert_yn
+ }
+ }
+
+ checkbutton $w.dtifit.expert_yn -text "Specify input files manually" \
+ -variable dtifit(expert_yn) -command "dtifit_toggle_expert $w"
+
+ frame $w.dtifit.expert
+
+ proc set_working_directory { cwd filename } {
+ global dtifit
+ set dirname [file dirname $filename]
+ puts "switching from $dtifit(cwd) to $dirname"
+ set dtifit(cwd) $dirname
+ }
+
+ proc dtifit_update_files { w filename } {
+ global dtifit
+
+ set dtifit(output) [ file join [file dirname $dtifit(input)] dti ]
+ set_working_directory dtifit(cwd) $dtifit(input)
+ }
+
+ set dtifit(cwd) [ pwd ]
+
+#All the below orignally had -directory $dtifit(cwd)
+ option add *dtifit.expert.FileEntry*labf*width 27
+ FileEntry $w.dtifit.expert.input -textvariable dtifit(input) -label "Diffusion weighted data:" -title "Choose diffusion weighted image" -filetypes IMAGE -command "dtifit_update_files $w"
+ FileEntry $w.dtifit.expert.mask -textvariable dtifit(mask) -label "BET binary brain mask:" -title "Choose BET brain mask file" -filetypes IMAGE -command "set_working_directory dtifit(cwd)"
+ FileEntry $w.dtifit.expert.output -textvariable dtifit(output) -label "Output basename:" -title "Choose output base name" -filetypes * -command "set_working_directory dtifit(cwd)"
+ FileEntry $w.dtifit.expert.bvecs -textvariable dtifit(bvecs) -label "Gradient directions:" -title "Choose bvecs file" -filetypes * -command "set_working_directory dtifit(cwd)"
+ FileEntry $w.dtifit.expert.bvals -textvariable dtifit(bvals) -label "b values:" -title "Choose bvals file" -command "set_working_directory dtifit(cwd)"
+
+ pack $w.dtifit.expert.input $w.dtifit.expert.mask $w.dtifit.expert.output \
+ $w.dtifit.expert.bvecs $w.dtifit.expert.bvals \
+ -side top -padx 3 -pady 3 -expand yes -anchor w
+
+ pack $w.dtifit.directory $w.dtifit.expert_yn -side top -padx 3 -pady 3 -expand yes -anchor w
+
+ #------- BEDPOST --------
+
+ frame $w.bedpost
+
+ FileEntry $w.bedpost.directory -textvariable bedpost(directory) -label "Input directory:" -title "Choose directory" -filetypes * -command "set_working_directory dtifit(cwd)"
+
+ collapsible frame $w.bedpost.advanced -title "Advanced Options"
+ set bedpost(nfibres) 2
+ set bedpost(weight) 1
+ set bedpost(burnin) 1000
+ LabelSpinBox $w.bedpost.advanced.nfibres -label "Fibres " -textvariable bedpost(nfibres) -range {1 1000000000 1 }
+ LabelSpinBox $w.bedpost.advanced.weight -label "Weight " -textvariable bedpost(weight) -range {0.0 100000000.0 1 }
+ LabelSpinBox $w.bedpost.advanced.burnin -label "Burn In" -textvariable bedpost(burnin) -range {1 1000000000 1 }
+
+ set bedpost(ecc_yn) 0
+ pack $w.bedpost.advanced.nfibres $w.bedpost.advanced.weight $w.bedpost.advanced.burnin -in $w.bedpost.advanced.b -anchor w
+ pack $w.bedpost.directory $w.bedpost.advanced -side top -padx 3 -pady 3 -expand yes -anchor w
+
+ #-------- ProbTrack --------
+ NoteBook $w.probtrack -bd 2 -tabpady {5 10} -arcradius 3
+ $w.probtrack insert 0 data -text "Data"
+ $w.probtrack insert 1 options -text "Options"
+ #-------- Mode specific option --------
+ frame $w.data
+ FileEntry $w.data.directory -textvariable probtrack(bedpost_dir) -label "BEDPOST directory" -title "Choose BEDPOST directory" -filetypes * -command "probtrack_update_files $w"
+
+ TitleFrame $w.data.seed -text "Seed Space"
+ optionMenu2 $w.data.seed.menu probtrack(mode) -command "fdt:probtrack_mode $w" simple "Single voxel" seedmask "Single mask" network "Multiple masks"
+ set probtrack(x) 0
+ set probtrack(y) 0
+ set probtrack(z) 0
+ set probtrack(units) vox
+ #Co-ordinate edit frame
+ frame $w.data.seed.voxel
+ LabelSpinBox $w.data.seed.voxel.x -label "X" -textvariable probtrack(x) -range {-1000000 1000000 1 }
+ LabelSpinBox $w.data.seed.voxel.y -label "Y" -textvariable probtrack(y) -range {-1000000 1000000 1 }
+ LabelSpinBox $w.data.seed.voxel.z -label "Z" -textvariable probtrack(z) -range {-1000000 1000000 1 }
+ radiobutton $w.data.seed.voxel.vox -text "vox" -value vox -variable probtrack(units)
+ radiobutton $w.data.seed.voxel.mm -text "mm" -value mm -variable probtrack(units)
+ FileEntry $w.data.seed.reference -textvariable probtrack(reference) -label "Seed reference image:" -title "Choose reference image" -filetypes IMAGE
+
+ option add *seed*FileEntry*labf*width 24
+
+ frame $w.data.seed.ssf
+ checkbutton $w.data.seed.ssf.ssd -text "Seed space is not diffusion" -variable probtrack(usereference_yn) -command " pack forget $w.data.seed.ssf.xfm ; if { \$probtrack(usereference_yn) } { pack $w.data.seed.ssf.xfm } ; $w.probtrack compute_size"
+ FileEntry $w.data.seed.ssf.xfm -textvariable probtrack(xfm) -label "Select Seed to diff transform" -title "Select seed-space to DTI-space transformation matrix" -filetypes *
+ pack $w.data.seed.ssf.ssd -side top -anchor nw
+
+
+
+
+ frame $w.data.seed.bcf
+ checkbutton $w.data.seed.bcf.bc -text "Blind Classification:" -variable probtrack(bcyn) -command " pack forget $w.data.seed.bcf.lrmask ; if { \$probtrack(bcyn) } { pack $w.data.seed.bcf.lrmask -side top } ; $w.probtrack compute_size"
+ FileEntry $w.data.seed.bcf.lrmask -textvariable probtrack(lrmask) -label "Set Low-res mask:" -title "Choose low resolution mask" -filetypes IMAGE
+ pack $w.data.seed.bcf.bc -side top -anchor w
+
+ 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 bottom -anchor w -pady 2
+ pack $w.data.seed.menu $w.data.seed.reference -in $w.data.seed.f -side left -anchor w -pady 2
+
+ TitleFrame $w.data.seed.target -text "Multiple Masks"
+ 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] IMAGE {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} {}"
+ pack $w.data.seed.tb.add $w.data.seed.tb.del $w.data.seed.tb.imp $w.data.seed.tb.exp -side left
+ pack $w.data.seed.tb -in [$w.data.seed.target getframe ] -side bottom -expand yes -fill x -anchor w -padx 3 -pady 3
+ pack $w.data.seed.targets $w.data.seed.sb -in [$w.data.seed.target getframe ] -side left -expand yes -fill y -anchor w -padx 3 -pady 3
+
+ TitleFrame $w.data.targets -text "Targets"
+
+ proc fdt_add { w listbox filename } {
+ set filename [ fix_cygwin_filename $filename ]
+ $listbox insert end $filename
+ }
+
+ proc fdt_sub { w listbox} {
+ set count 0
+ foreach file [ $listbox get 0 end ] {
+ if { [ $listbox selection includes $count ] == 1 } {
+ $listbox delete $count
+ incr count -1
+ }
+ incr count
+ }
+ }
+
+ proc fdt_imp { w listbox filename } {
+ if { ![ file exists $filename ] } {
+ MxPause "Warning: Bad or missing file!"
+ return
+ }
+ set fd [ open $filename ]
+ $listbox delete 0 end
+ while { [ gets $fd file ] >= 0 } {
+ $listbox insert end $file
+ }
+ close $fd
+ }
+
+ proc fdt_exp { w listbox filename } {
+ set fd [ open $filename w ]
+ foreach file [ $listbox get 0 end ] {
+ puts $fd $file
+ }
+ close $fd
+ }
+
+ frame $w.data.targets.wf
+ checkbutton $w.data.targets.wf.sct -text "Set Waypoints" -variable probtrack(waypoint_yn) -command " pack forget $w.data.targets.wf.tf ; if { \$probtrack(waypoint_yn) } { pack $w.data.targets.wf.tf } ; $w.probtrack compute_size"
+ TitleFrame $w.data.targets.wf.tf -text "Waypoints"
+ 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] IMAGE {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} {}"
+ pack $w.data.targets.wf.tf.tb.add $w.data.targets.wf.tf.tb.del $w.data.targets.wf.tf.tb.imp $w.data.targets.wf.tf.tb.exp -side left
+ pack $w.data.targets.wf.tf.tb -in [$w.data.targets.wf.tf getframe ] -side bottom -expand yes -fill x -anchor w -padx 3 -pady 3
+ pack $w.data.targets.wf.tf.targets $w.data.targets.wf.tf.sb -in [$w.data.targets.wf.tf getframe ] -side left -expand yes -fill y -anchor w -padx 3 -pady 3
+ pack $w.data.targets.wf.sct -side top -anchor nw
+ pack $w.data.targets.wf
+
+ option add *targets*Checkbutton*width 18
+ option add *targets*Checkbutton*anchor w
+ frame $w.data.targets.ef
+ checkbutton $w.data.targets.ef.srt -text "Set Exclusion targets" -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 IMAGE
+ pack $w.data.targets.ef.srt -side left
+
+ frame $w.data.targets.sf
+ checkbutton $w.data.targets.sf.sst -text "Set Termination targets" -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 IMAGE
+ pack $w.data.targets.sf.sst -side left
+
+ frame $w.data.targets.cf
+ checkbutton $w.data.targets.cf.sct -text "Set Classification targets" -variable probtrack(classify_yn) -command " pack forget $w.data.targets.cf.tf ; if { \$probtrack(classify_yn) } { pack $w.data.targets.cf.tf } ; $w.probtrack compute_size"
+ TitleFrame $w.data.targets.cf.tf -text "Classification"
+ 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] IMAGE {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} {}"
+ pack $w.data.targets.cf.tf.tb.add $w.data.targets.cf.tf.tb.del $w.data.targets.cf.tf.tb.imp $w.data.targets.cf.tf.tb.exp -side left
+ pack $w.data.targets.cf.tf.tb -in [$w.data.targets.cf.tf getframe ] -side bottom -expand yes -fill x -anchor w -padx 3 -pady 3
+ pack $w.data.targets.cf.tf.targets $w.data.targets.cf.tf.sb -in [$w.data.targets.cf.tf getframe ] -side left -expand yes -fill y -anchor w -padx 3 -pady 3
+ pack $w.data.targets.cf.sct -side top -anchor nw
+ pack $w.data.targets.cf
+
+
+ pack $w.data.targets.wf $w.data.targets.ef $w.data.targets.sf $w.data.targets.cf -in $w.data.targets.f -anchor w
+
+
+
+
+ set probtrack(xfm) ""
+ set probtrack(basename) "merged"
+ set probtrack(mask) "nodif_brain_mask"
+
+ proc probtrack_update_files { w filename } {
+ global probtrack
+ global FSLDIR
+
+ if { ($probtrack(bedpost_dir) != "") && ($probtrack(reference) != "") } {
+ set probtrack(output) \
+ [ file join $probtrack(bedpost_dir) [ file tail [ exec $FSLDIR/bin/remove_ext $probtrack(reference) ] ] ]
+ }
+ }
+
+ 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 $w.data -in [$w.probtrack getframe data] -padx 3 -pady 3 -anchor nw -expand yes -fill both
+
+ #-------- ...Options... --------
+ TitleFrame $w.options -text "Basic Options"
+
+ checkbutton $w.options.verbose -text "Verbose" -variable probtrack(verbose_yn)
+
+ set probtrack(nparticles) 5000
+ LabelSpinBox $w.options.nparticles -label "Number of samples" -textvariable probtrack(nparticles) -range {1 1e24 100 } -width 6
+
+ set probtrack(curvature) 0.2
+ LabelSpinBox $w.options.curvature -label "Curvature threshold" -textvariable probtrack(curvature) -range {0.0 1.0 0.01 }
+
+ set probtrack(loopcheck_yn) 1
+ checkbutton $w.options.loopcheck -text "Loopcheck" -variable probtrack(loopcheck_yn)
+
+ collapsible frame $w.advanced -title "Advanced Options"
+
+ set probtrack(nsteps) 2000
+ LabelSpinBox $w.advanced.nsteps -label "Maximum number of steps" -textvariable probtrack(nsteps) -range {2 1000000 10 } -width 6
+
+ set probtrack(steplength) 0.5
+ LabelSpinBox $w.advanced.steplength -label "Step length (mm)" -textvariable probtrack(steplength) -range {0 10000 0.1}
+
+ set probtrack(modeuler_yn) 0
+ checkbutton $w.advanced.modeuler -text "Use modified Euler streamlining" -variable probtrack(modeuler_yn)
+
+ set probtrack(pd) 0
+ checkbutton $w.advanced.pd -text "Use Distance correction" -variable probtrack(pd)
+
+ set probtrack(usef_yn) 0
+ checkbutton $w.advanced.usef -text "Use anisotropy to constrain tracking" -variable probtrack(usef_yn)
+
+ pack $w.advanced.modeuler $w.advanced.nsteps $w.advanced.steplength $w.advanced.usef $w.advanced.pd -in $w.advanced.b -side top -pady 3 -padx 6 -anchor nw
+
+ pack \
+ $w.options.nparticles \
+ $w.options.curvature \
+ $w.options.verbose \
+ $w.options.loopcheck \
+ -in [$w.options getframe ] -side top -pady 3 -padx 6 -anchor nw
+
+ pack $w.options $w.advanced -in [$w.probtrack getframe options] -side top -pady 3 -padx 6 -anchor nw -expand yes -fill both
+
+ #-------- Buttons --------
+
+ frame $w.btns
+ frame $w.btns.b -relief raised -borderwidth 1
+
+ button $w.apply -command "fdt:apply $w keep" \
+ -text "Go" -width 5
+ bind $w.apply <Return> {
+ [winfo toplevel %W].apply invoke}
+
+ button $w.cancel -command "fdt:destroy $w" \
+ -text "Exit" -width 5
+ bind $w.cancel <Return> {
+ [winfo toplevel %W].cancel invoke}
+
+ button $w.help -command "FmribWebHelp file: $HTMLPATH/index.html" \
+ -text "Help" -width 5
+ bind $w.help <Return> {
+ [winfo toplevel %W].help invoke}
+
+ pack $w.btns.b -side bottom -fill x -padx 3 -pady 5
+ pack $w.apply $w.cancel $w.help -in $w.btns.b \
+ -side left -expand yes -padx 3 -pady 10 -fill y
+
+ pack $w.tool $w.opts $w.btns -side top -expand yes -fill both
+
+
+
+ $w.probtrack raise data
+ fdt:select_tool $w
+ set probtrack(mode) simple
+ fdt:probtrack_mode $w
+
+ update idletasks
+ if { $tclstartupfile != "" } {
+ puts "Reading $tclstartupfile"
+ source $tclstartupfile
+ fdt:select_tool $w
+ fdt:probtrack_mode $w
+ }
+}
+
+proc fdt:probtrack_mode { w } {
+ global probtrack
+
+ pack forget $w.data.seed.voxel $w.data.seed.ssf $w.data.seed.menu $w.data.seed.reference $w.data.seed.bcf $w.data.seed.target $w.data.targets.cf
+ switch -- $probtrack(mode) {
+ simple {
+ pack $w.data.seed.ssf $w.data.seed.voxel -in $w.data.seed.f -side bottom -anchor w -pady 2
+ pack $w.data.seed.menu $w.data.seed.reference -in $w.data.seed.f -side left -anchor w -pady 2
+ $w.data.seed.reference configure -label "Seed reference image:" -title "Choose reference image"
+ }
+ seedmask {
+ pack $w.data.seed.ssf $w.data.seed.bcf -in $w.data.seed.f -side bottom -anchor w -pady 2
+ pack $w.data.seed.menu $w.data.seed.reference -in $w.data.seed.f -side left -anchor w -pady 2
+ pack $w.data.targets.cf -in $w.data.targets.f -anchor w
+
+ $w.data.seed.reference configure -label "Mask image:" -title "Choose mask image"
+ }
+ network {
+ pack $w.data.seed.target $w.data.seed.ssf -in $w.data.seed.f -side bottom -anchor w -pady 2
+ pack $w.data.seed.menu $w.data.seed.reference -in $w.data.seed.f -side left -anchor w -pady 2
+ pack $w.data.targets.cf -in $w.data.targets.f -anchor w
+ $w.data.seed.reference configure -label "First mask image:" -title "Choose mask image"
+
+ }
+ }
+ $w.probtrack compute_size
+}
+
+proc fdt:select_tool { w } {
+ global probtrack
+ pack forget $w.ecc
+ pack forget $w.probtrack
+ pack forget $w.bedpost
+ pack forget $w.registration
+ pack forget $w.dtifit
+ if {$probtrack(tool) == "bedpost"} {
+ pack $w.bedpost -in $w.opts -side top -padx 3 -pady 3 -anchor nw
+ } elseif {$probtrack(tool) == "probtrack"} {
+ pack $w.probtrack -in $w.opts -side top -padx 3 -pady 3 -anchor nw
+ } elseif {$probtrack(tool) == "dtifit"} {
+ pack $w.dtifit -in $w.opts -side top -padx 3 -pady 3 -anchor nw
+ } elseif {$probtrack(tool) == "eddy_current"} {
+ pack $w.ecc -in $w.opts -side top -padx 3 -pady 3 -anchor nw
+ } elseif {$probtrack(tool) == "registration"} {
+ pack $w.registration -in $w.opts -side top -padx 3 -pady 3 -anchor nw
+ }
+}
+proc fdt_monitor_short { w cmd } {
+ global debugging OSFLAVOUR
+
+ puts "$cmd"
+
+ if { $OSFLAVOUR != "cygwin" } {
+ set oldcursor [ $w configure -cursor { watch red white } ]
+
+ catch {
+ update idletasks
+ if { ! $debugging } {
+ set fd [ open "|$cmd" r ]
+# set fd [ open "|qrsh -V -now n -q short.q $cmd" r ]
+ while { ( [ gets $fd line ] >= 0 ) } {
+ update idletasks
+ puts $line
+ }
+ close $fd
+ }
+ } junk
+
+ $w configure -cursor $oldcursor
+
+ } else {
+ catch { exec sh -c $cmd } junk
+ }
+
+ if { $junk != "" } {
+ MxPause "Errors: $junk"
+ }
+
+ puts "Done!"
+}
+
+proc fdt_monitor { w cmd } {
+ global debugging OSFLAVOUR
+
+ puts "$cmd"
+
+ if { $OSFLAVOUR != "cygwin" } {
+ set oldcursor [ $w configure -cursor { watch red white } ]
+
+ catch {
+ update idletasks
+ if { ! $debugging } {
+ set fd [ open "|$cmd" r ]
+# set fd [ open "|qrsh -V -now n -q long.q $cmd" r ]
+ while { ( [ gets $fd line ] >= 0 ) } {
+ update idletasks
+ puts $line
+ }
+ close $fd
+ }
+ } junk
+
+ $w configure -cursor $oldcursor
+
+ } else {
+ catch { exec sh -c $cmd } junk
+ }
+
+ if { $junk != "" } {
+ MxPause "Errors: $junk"
+ }
+
+ puts "Done!"
+}
+
+proc fdt:apply { w dialog } {
+
+ global probtrack
+ global BINPATH
+ global FSLDIR
+
+ switch -- $probtrack(tool) {
+ eddy_current {
+ global eddy
+
+ set errorStr ""
+ if { $eddy(input) == "" } { set errorStr "You need to specify the input image! " }
+ if { $eddy(output) == "" } { set errorStr "$errorStr You need to specify an output image!" }
+ if { $errorStr != "" } {
+ MxPause $errorStr
+ return
+ }
+
+ # check output!=input
+ set canwrite 1
+ if { $eddy(input) == $eddy(output) } {
+ set canwrite [ YesNoWidget "Output and input images have the same name. Overwrite input?" Yes No ]
+ }
+ if { $canwrite } {
+ fdt_monitor $w "${FSLDIR}/bin/eddy_correct $eddy(input) $eddy(output) $eddy(refnum)"
+ }
+ }
+ dtifit {
+ global dtifit
+
+ if { ! $dtifit(expert_yn) } {
+ set dtifit(input) [ file join $dtifit(directory) data ]
+ set dtifit(output) [ file join $dtifit(directory) dti ]
+ set dtifit(mask) [ file join $dtifit(directory) nodif_brain_mask ]
+ set dtifit(bvecs) [ file join $dtifit(directory) bvecs ]
+ set dtifit(bvals) [ file join $dtifit(directory) bvals ]
+ }
+
+ set errorStr ""
+ if { $dtifit(directory) == "" && ! $dtifit(expert_yn) } { set errorStr "You must specify the input directory!" }
+ if { $dtifit(input) == "" } { set errorStr "You need to specify the diffusion weighted data image!" }
+ if { $dtifit(output) == "" } { set errorStr "$errorStr You need to specify the output basename!" }
+ if { $dtifit(mask) == "" } { set errorStr "$errorStr You need to specify a mask image!" }
+ if { $dtifit(bvecs) == "" } { set errorStr "$errorStr Please select a gradient directions file!" }
+ if { $dtifit(bvals) == "" } { set errorStr "$errorStr Please select a b values file!" }
+ if { $errorStr != "" } {
+ MxPause $errorStr
+ return
+ }
+
+ set canwrite 1
+ if { [file exists $dtifit(output) ] } {
+ set canwrite [ YesNoWidget "Overwrite $dtifit(output)?" Yes No ]
+ }
+ if { $canwrite } {
+ fdt_monitor_short $w "${FSLDIR}/bin/dtifit --data=$dtifit(input) --out=$dtifit(output) --mask=$dtifit(mask) --bvecs=$dtifit(bvecs) --bvals=$dtifit(bvals)"
+ }
+ }
+ bedpost {
+ global bedpost
+
+ set errorStr ""
+ if { $bedpost(directory) == "" } { set errorStr "You must specify the bedpost directory!" }
+ if { $errorStr != "" } {
+ MxPause $errorStr
+ return
+ }
+
+ set canwrite 1
+ if { [file exists ${bedpost(directory)}.bedpost ] } {
+ set canwrite [ YesNoWidget "Overwrite ${bedpost(directory)}.bedpost?" Yes No ]
+ if { $canwrite } {
+ puts "rm -rf ${bedpost(directory)}.bedpost"
+ catch { exec rm -rf ${bedpost(directory)}.bedpost } errmsg
+ }
+ }
+ if { $canwrite } {
+ puts "bedpostX $bedpost(directory) -n $bedpost(nfibres) -w $bedpost(weight) -b $bedpost(burnin)"
+ fdt_monitor $w "${FSLDIR}/bin/bedpostX $bedpost(directory) -n $bedpost(nfibres) -w $bedpost(weight) -b $bedpost(burnin)"
+ }
+ }
+ probtrack {
+ 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(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!" }
+ if { $probtrack(bcyn) && $probtrack(lrmask) == ""} { set errorStr "$errorStr You must specify a low res mask!" }
+ set flags ""
+ if { $probtrack(verbose_yn) == 1 } { set flags "$flags -V 1" }
+ if { $probtrack(loopcheck_yn) == 1 } { set flags "$flags -l" }
+ if { $probtrack(usef_yn) == 1 } { set flags "$flags -f" }
+ if { $probtrack(modeuler_yn) == 1 } { set flags "$flags --modeuler" }
+ set flags "$flags -c $probtrack(curvature) -S $probtrack(nsteps) --steplength=$probtrack(steplength) -P $probtrack(nparticles)"
+
+ if { $probtrack(pd) } { set flags "$flags --pd" }
+
+ set tn [open "| $BINPATH/tmpnam"]
+ gets $tn filebase
+ close $tn
+ set logfile "${filebase}_log.tcl"
+ set log [open "$logfile" w]
+ puts $log "set tool $probtrack(tool)"
+ set copylog ""
+
+ if { $probtrack(usereference_yn) } {
+ set flags "$flags --xfm==$probtrack(xfm)"
+ puts $log "set probtrack(xfm) $probtrack(xfm)"
+ }
+
+ if { $probtrack(exclude_yn) == 1 } {
+ set flags "$flags --avoid=$probtrack(exclude)"
+ puts $log "set probtrack(exclude) $probtrack(exclude)"
+ }
+
+ if { $probtrack(terminate_yn) == 1 } {
+ set flags "$flags --stop=$probtrack(stop)"
+ puts $log "set probtrack(stop) $probtrack(stop)"
+ }
+
+
+ set flags "$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} {
+ puts $log "set probtrack($entry) $probtrack($entry)"
+ }
+ switch $probtrack(mode) {
+ simple {
+ set fd [ open "${filebase}_coordinates.txt" w ]
+ set x $probtrack(x)
+ set y $probtrack(y)
+ set z $probtrack(z)
+ if { $probtrack(units) == "mm" } {
+ if { $probtrack(reference) != "" } {
+ mm_to_voxels x y z $probtrack(reference)
+ } else {
+ mm_to_voxels x y z [ file join $probtrack(bedpost_dir) nodif_brain_mask ]
+ }
+ puts $fd "$x $y $z"
+ puts "$probtrack(x) $probtrack(y) $probtrack(z) (mm) -> $x $y $z (voxels)"
+ } else {
+ puts $fd "$probtrack(x) $probtrack(y) $probtrack(z)"
+ }
+ close $fd
+ puts $log "set probtrack(x) $probtrack(x)"
+ 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
+ }
+ seedmask {
+ if { $probtrack(bcyn) } { set flags "$flags --lrmask=$probtrack(lrmask) --omatrix2" }
+ set probtrack(reference2) $probtrack(reference)
+ }
+ network {
+ set flags "$flags --network"
+ set probtrack(mode) seedmask
+ set probtrack(reference2) $probtrack(reference)
+ }
+ }
+
+ 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)
+ }
+ }
+ if { $canwrite } {
+ set copylog "fdt.log"
+
+ if { $probtrack(waypoint_yn) == 1 } {
+ fdt_exp w $w.data.targets.wf.tf.targets $probtrack(output)/waypoints.txt
+ set flags "$flags --waypoints==$probtrack(output)/waypoints.txt "
+ }
+ if { $probtrack(classify_yn) == 1 } {
+ fdt_exp w $w.data.targets.cf.tf.targets $probtrack(output)/targets.txt
+ set flags "$flags --targetmasks=$probtrack(output)/targets.txt --os2t "
+ }
+
+ fdt_monitor_short $w "$FSLDIR/bin/probtrackx --mode=$probtrack(mode) -x $probtrack(reference2) $flags"
+ }
+ if { $probtrack(mode) == "simple" } {
+ puts "rm ${filebase}_coordinates.txt"
+ exec rm ${filebase}_coordinates.txt
+ }
+ close $log
+ if { $copylog != "" } {
+ puts "mv $logfile $copylog"
+ exec mv $logfile $copylog
+ } else {
+ puts "rm $logfile"
+ exec rm $logfile
+ }
+ }
+ registration {
+ global registration
+
+ set errorStr ""
+ if { $registration(directory) == "" } { set errorStr "You must specify the bedpost directory!" }
+ if { $registration(struct_yn) && $registration(struct_image) == "" } { set errorStr "$errorStr You must specify the structural image!" }
+ if { $registration(standard_yn) && $registration(standard_image) == "" } { set errorStr "$errorStr You must specify the standard image!" }
+ if { $errorStr != "" } {
+ MxPause $errorStr
+ return
+ }
+
+ exec mkdir -p [ file join $registration(directory) xfms ]
+ set eyefd [ open [ file join $registration(directory) xfms eye.mat ] w ]
+ puts $eyefd "1 0 0 0"
+ puts $eyefd "0 1 0 0"
+ puts $eyefd "0 0 1 0"
+ puts $eyefd "0 0 0 1"
+ close $eyefd
+
+ set diff2str [ file join $registration(directory) xfms diff2str.mat ]
+ set str2diff [ file join $registration(directory) xfms str2diff.mat ]
+ set str2stand [ file join $registration(directory) xfms str2standard.mat ]
+ set stand2str [ file join $registration(directory) xfms standard2str.mat ]
+ set diff2stand [ file join $registration(directory) xfms diff2standard.mat ]
+ set stand2diff [ file join $registration(directory) xfms standard2diff.mat ]
+ set diff [ file join $registration(directory) nodif_brain ]
+ if { $registration(struct_yn) } {
+ set searchrx "-searchrx -$registration(struct_search) $registration(struct_search)"
+ set searchry "-searchry -$registration(struct_search) $registration(struct_search)"
+ set searchrz "-searchrz -$registration(struct_search) $registration(struct_search)"
+ set options "$searchrx $searchry $searchrz -dof $registration(struct_dof)"
+ fdt_monitor $w "${FSLDIR}/bin/flirt -in $diff -ref $registration(struct_image) -omat $diff2str $options -cost $registration(struct_costfn)"
+ fdt_monitor $w "${FSLDIR}/bin/convert_xfm -omat $str2diff -inverse $diff2str"
+ if { $registration(standard_yn) } {
+ set searchrx "-searchrx -$registration(standard_search) $registration(standard_search)"
+ set searchry "-searchry -$registration(standard_search) $registration(standard_search)"
+ set searchrz "-searchrz -$registration(standard_search) $registration(standard_search)"
+ set options "$searchrx $searchry $searchrz -dof $registration(standard_dof)"
+ fdt_monitor $w "${FSLDIR}/bin/flirt -in $registration(struct_image) -ref $registration(standard_image) -omat $str2stand $options -cost $registration(standard_costfn)"
+ fdt_monitor $w "${FSLDIR}/bin/convert_xfm -omat $stand2str -inverse $str2stand"
+ fdt_monitor $w "${FSLDIR}/bin/convert_xfm -omat $diff2stand -concat $str2stand $diff2str"
+ fdt_monitor $w "${FSLDIR}/bin/convert_xfm -omat $stand2diff -inverse $diff2stand"
+ }
+ } elseif { $registration(standard_yn) } {
+ set searchrx "-searchrx -$registration(standard_search) $registration(standard_search)"
+ set searchry "-searchry -$registration(standard_search) $registration(standard_search)"
+ set searchrz "-searchrz -$registration(standard_search) $registration(standard_search)"
+ set options "$searchrx $searchry $searchrz -dof $registration(standard_dof)"
+ fdt_monitor $w "${FSLDIR}/bin/flirt -in $diff -ref $registration(standard_image) -omat $diff2stand $options"
+ fdt_monitor $w "${FSLDIR}/bin/convert_xfm -omat $stand2diff -inverse $diff2stand"
+ }
+ puts "Done!"
+ # Fudge to make the logic work
+ set canwrite 1
+ }
+ }
+
+ if { $canwrite } {
+ MxPause " Done! "
+ update idletasks
+ }
+
+ if {$dialog == "destroy"} {
+ fdt:destroy $w
+ }
+}
+
+
+proc fdt:destroy { w } {
+ destroy $w
+}
+
+set debugging 0
+
+while {[llength $argv] > 0 } {
+ set flag [lindex $argv 0]
+ switch -- $flag {
+ "-debugging" {
+ set debugging 1
+ set argv [lrange $argv 1 end]
+ puts "Debug mode!"
+ }
+ default { break }
+ }
+}
+
+
+wm withdraw .
+if { [ info exists env(MRDATADIR) ] } {
+ set MRDATADIR $env(MRDATADIR)
+} else {
+ set MRDATADIR ~/MRdata
+}
+
+fdt:dialog .fdt $argv
+tkwait window .fdt
--
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