Skip to content
Snippets Groups Projects
Commit 0764cc4d authored by Matthew Webster's avatar Matthew Webster
Browse files

fdtx.tcl

parent 23145c7d
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
Showing
with 872 additions and 0 deletions
fdtx.tcl 0 → 100644
+ 872
− 0
View file @ 0764cc4d
# 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
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment