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|
# FSL interface for FDT (BEDPOSTX and PROBTRACKX)
#
# Timothy Behrens, Heidi Johansen-Berg, Dave Flitney, Matthew Webster, Saad Jbabdi and Stam Sotiropoulos, FMRIB Image Analysis Group
#
# Copyright (C) 2007 University of Oxford
#
# Part of FSL - FMRIB's Software Library
# http://www.fmrib.ox.ac.uk/fsl
# fsl@fmrib.ox.ac.uk
#
# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
# Imaging of the Brain), Department of Clinical Neurology, Oxford
# University, Oxford, UK
#
#
# LICENCE
#
# FMRIB Software Library, Release 5.0 (c) 2012, The University of
# Oxford (the "Software")
#
# The Software remains the property of the University of Oxford ("the
# University").
#
# The Software is distributed "AS IS" under this Licence solely for
# non-commercial use in the hope that it will be useful, but in order
# that the University as a charitable foundation protects its assets for
# the benefit of its educational and research purposes, the University
# makes clear that no condition is made or to be implied, nor is any
# warranty given or to be implied, as to the accuracy of the Software,
# or that it will be suitable for any particular purpose or for use
# under any specific conditions. Furthermore, the University disclaims
# all responsibility for the use which is made of the Software. It
# further disclaims any liability for the outcomes arising from using
# the Software.
#
# The Licensee agrees to indemnify the University and hold the
# University harmless from and against any and all claims, damages and
# liabilities asserted by third parties (including claims for
# negligence) which arise directly or indirectly from the use of the
# Software or the sale of any products based on the Software.
#
# No part of the Software may be reproduced, modified, transmitted or
# transferred in any form or by any means, electronic or mechanical,
# without the express permission of the University. The permission of
# the University is not required if the said reproduction, modification,
# transmission or transference is done without financial return, the
# conditions of this Licence are imposed upon the receiver of the
# product, and all original and amended source code is included in any
# transmitted product. You may be held legally responsible for any
# copyright infringement that is caused or encouraged by your failure to
# abide by these terms and conditions.
#
# You are not permitted under this Licence to use this Software
# commercially. Use for which any financial return is received shall be
# defined as commercial use, and includes (1) integration of all or part
# of the source code or the Software into a product for sale or license
# by or on behalf of Licensee to third parties or (2) use of the
# Software or any derivative of it for research with the final aim of
# developing software products for sale or license to a third party or
# (3) use of the Software or any derivative of it for research with the
# final aim of developing non-software products for sale or license to a
# third party, or (4) use of the Software to provide any service to an
# external organisation for which payment is received. If you are
# interested in using the Software commercially, please contact Isis
# Innovation Limited ("Isis"), the technology transfer company of the
# University, to negotiate a licence. Contact details are:
# innovation@isis.ox.ac.uk quoting reference DE/9564.
#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/redirects HTMLPATH
set VERSION "3.0"
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 -std $mask -vox - 2>/dev/null | awk '{print \$1}'" ]
set vcY [ exec sh -c "echo $cX $cY $cZ | $FSLDIR/bin/std2imgcoord -img $mask -std $mask -vox - 2>/dev/null | awk '{print \$2}'" ]
set vcZ [ exec sh -c "echo $cX $cY $cZ | $FSLDIR/bin/std2imgcoord -img $mask -std $mask -vox - 2>/dev/null | 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) "probtrackx"
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" bedpostx "BEDPOSTX Estimation of diffusion parameters" registration "Registration" probtrackx "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 "BEDPOSTX 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"
frame $w.registration.nonlin
checkbutton $w.registration.nonlin.yn -variable registration(nonlin_yn) -text "Non-betted structural (for nonlinear reg)" -command "registration_packframe $w"
FileEntry $w.registration.nonlin.file -textvariable registration(nonlin_image) -filetypes 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) corratio
set registration(struct_dof) 6
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} data standard MNI152_T1_2mm_brain ]
pack $w.registration.directory $w.registration.struct $w.registration.nonlin $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 $w.registration.nonlin.yn $w.registration.nonlin.file
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(struct_yn) } { pack $w.registration.nonlin.yn -side left }
if { $registration(struct_yn) && $registration(nonlin_yn) } { pack $w.registration.nonlin.file -side left }
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
FileEntry $w.ecc.bvecdata -textvariable eddy(bVecData) -label "bvecs file:" -title "Choose bvecs name" -filetypes IMAGE
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
collapsible frame $w.dtifit.advanced -title "Advanced Options"
checkbutton $w.dtifit.advanced.w -text "Weighted Least-Squares" -variable dtifit(doWLS)
checkbutton $w.dtifit.advanced.sse -text "Save Sum-squared Error" -variable dtifit(doSaveSSE)
checkbutton $w.dtifit.advanced.tensor -text "Save tensor" -variable dtifit(doSaveTensor)
pack $w.dtifit.advanced.w $w.dtifit.advanced.sse $w.dtifit.advanced.tensor -in $w.dtifit.advanced.b -anchor w
pack $w.dtifit.directory $w.dtifit.advanced -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 }
checkbutton $w.bedpost.advanced.multishell -text "Multi-Shell model" -variable bedpost(useMultiShell)
checkbutton $w.bedpost.advanced.noisefloor -text "Model Noise Floor" -variable bedpost(useNoiseFloor)
checkbutton $w.bedpost.advanced.rician -text "Rician Noise" -variable bedpost(useRician)
set bedpost(ecc_yn) 0
pack $w.bedpost.advanced.nfibres $w.bedpost.advanced.weight $w.bedpost.advanced.burnin $w.bedpost.advanced.multishell $w.bedpost.advanced.noisefloor $w.bedpost.advanced.rician -in $w.bedpost.advanced.b -anchor w
pack $w.bedpost.directory $w.bedpost.advanced -side top -padx 3 -pady 3 -expand yes -anchor w
#-------- ProbTrackX --------
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 "BEDPOSTX directory" -title "Choose BEDPOSTX 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"
pack $w.data.seed.menu -in $w.data.seed.f -side top -anchor w -pady 2
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)
option add *seed*FileEntry*labf*width 24
frame $w.data.seed.ssf
set probtrack(mode) simple
checkbutton $w.data.seed.ssf.ssd -text "Seed space is not diffusion" -variable probtrack(usereference_yn) -command " fdt:probtrack_mode $w "
checkbutton $w.data.seed.ssf.nonlinear -text "nonlinear" -variable probtrack(useNonlinear) -command " fdt:probtrack_mode $w "
checkbutton $w.data.seed.ssf.useSurface -text "surface" -variable probtrack(useSurface) -command " fdt:probtrack_mode $w "
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 *
FileEntry $w.data.seed.ssf.invxfm -textvariable probtrack(invxfm) -label "Select diff to Seed transform" -title "Select seed-space to DTI-space transformation matrix" -filetypes *
labelframe $w.data.seed.ssf.typelabel -text "Mesh convention" -labelanchor w -relief flat
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 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
TitleFrame $w.data.seed.target -text "Masks list"
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.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 "Optional 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 "Waypoints masks" -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 list"
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.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 "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}"
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}"
pack $w.data.targets.sf.sst -side left
frame $w.data.targets.cf
checkbutton $w.data.targets.cf.sct -text "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 "Targets list"
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.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 $w.advanced -title "Advanced Options" -command "$w.probtrack compute_size; set dummy"
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 {0.001 10000.0 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)
set probtrack(fibthresh) 0.01
LabelSpinBox $w.advanced.fibthresh -label "Subsidary fibre volume fraction threshold" -textvariable probtrack(fibthresh) -range {0.00 1.0 0.01}
set probtrack(distthresh) 0.0
LabelSpinBox $w.advanced.distthresh -label "Minimum length threshold (mm)" -textvariable probtrack(distthresh) -range {0.00 1000.0 1.0}
set probtrack(sampvox) 0.0
LabelSpinBox $w.advanced.sampvox -label "Seed sphere sampling (mm)" -textvariable probtrack(sampvox) -range {0.00 100.0 1.0}
collapsible frame $w.wayadvanced -title "Waypoint Options" -command "$w.probtrack compute_size; set dummy"
set probtrack(oneway_yn) 1
checkbutton $w.wayadvanced.oneway_yn -text "Apply waypoint independently to both directions" -variable probtrack(oneway_yn)
set probtrack(wayorder_yn) 0
checkbutton $w.wayadvanced.wayorder_yn -text "Force waypoint crossing in listed order" -variable probtrack(wayorder_yn)
set probtrack(waycond) AND
labelframe $w.wayadvanced.waylabel -text "Waypoint condition" -labelanchor w -relief flat
optionMenu2 $w.wayadvanced.waylabel.waycond probtrack(waycond) AND "AND" OR "OR"
pack $w.wayadvanced.waylabel $w.wayadvanced.waylabel.waycond -side top -anchor w -pady 2
collapsible frame $w.matadvanced -title "Matrix Options" -command "$w.probtrack compute_size; set dummy"
# Matrix Stuff
set probtrack(omatrix1_yn) 0
checkbutton $w.matadvanced.omatrix1_yn -text "Matrix1: Seed x Seed Matrix" -variable probtrack(omatrix1_yn)
set probtrack(omatrix2_yn) 0
checkbutton $w.matadvanced.omatrix2_yn -text "Matrix2: 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}"
set probtrack(omatrix3_yn) 0
checkbutton $w.matadvanced.omatrix3_yn -text "Matrix3: 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}"
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.advanced.modeuler \
$w.advanced.nsteps \
$w.advanced.steplength \
$w.advanced.usef \
$w.advanced.pd \
$w.advanced.fibthresh \
$w.advanced.distthresh \
$w.advanced.sampvox \
-in $w.advanced.b -side top -pady 3 -padx 6 -anchor nw
pack \
$w.wayadvanced.oneway_yn \
$w.wayadvanced.wayorder_yn \
$w.wayadvanced.waylabel \
-in $w.wayadvanced.b -side top -pady 3 -padx 6 -anchor nw
pack \
$w.matadvanced.omatrix1_yn \
$w.matadvanced.omatrix2_yn \
$w.matadvanced.omatrix3_yn \
-in $w.matadvanced.b -side top -pady 3 -padx 6 -anchor nw
pack \
$w.options \
$w.advanced \
$w.wayadvanced \
$w.matadvanced \
-in [$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/fdt.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
fdt:probtrack_mode $w
update idletasks
if { $tclstartupfile != "" } {
puts "Reading $tclstartupfile"
source $tclstartupfile
fdt:select_tool $w
fdt:probtrack_mode $w
}
}
proc fdt:eddycorrect_mode { w } {
global eddy
pack forget $w.ecc.bvecdata
}
proc fdt:matrix_mode { w } {
global probtrack
pack forget $w.matadvanced.omatrix2_mask $w.matadvanced.omatrix3_mask1 $w.matadvanced.omatrix3_mask2
if { $probtrack(omatrix2_yn) } { pack $w.matadvanced.omatrix2_yn $w.matadvanced.omatrix2_mask $w.matadvanced.omatrix3_yn -in $w.matadvanced.b -anchor w -pady 2 }
if { $probtrack(omatrix3_yn) } { pack $w.matadvanced.omatrix3_yn $w.matadvanced.omatrix3_mask1 $w.matadvanced.omatrix3_mask2 -in $w.matadvanced.b -anchor w -pady 2 }
$w.probtrack compute_size
}
proc fdt:probtrack_mode { w } {
global probtrack FSLDIR
pack forget $w.data.seed.voxel $w.data.seed.ssf $w.data.seed.ssf.xfm $w.data.seed.ssf.reference $w.data.seed.bcf $w.data.seed.target $w.data.targets.cf $w.data.seed.ssf.invxfm $w.data.seed.ssf.nonlinear $w.data.seed.ssf.meshspace $w.data.seed.ssf.typelabel $w.data.seed.ssf.useSurface $w.data.seed.ssf.surfref
$w.data.dir configure -label "Output directory:" -title "Name the output directory" -filetypes *
pack $w.data.seed.ssf -in $w.data.seed.f -side bottom -anchor w -pady 2
switch -- $probtrack(mode) {
simple {
pack $w.data.seed.voxel -in $w.data.seed.f -side bottom -anchor w -pady 2
if { $probtrack(usereference_yn) } { pack $w.data.seed.ssf.reference -side bottom -anchor w -pady 2 }
$w.data.seed.ssf.reference configure -label "Seed reference image:" -title "Choose reference image"
$w.data.dir configure -label "Output file:" -title "Name the output file" -filetypes IMAGE
if { $probtrack(usereference_yn) } { pack $w.data.seed.ssf.nonlinear $w.data.seed.ssf.xfm -side top -anchor w -pady 2 }
if { $probtrack(useNonlinear) && $probtrack(usereference_yn) } { pack $w.data.seed.ssf.xfm $w.data.seed.ssf.invxfm -side top -anchor w -pady 2 }
}
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 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 }
if { $probtrack(useNonlinear) && $probtrack(usereference_yn) } { pack $w.data.seed.ssf.xfm $w.data.seed.ssf.invxfm -side top -anchor w -pady 2 }
if { $probtrack(usereference_yn) } { pack $w.data.seed.ssf.useSurface -side top -anchor w -pady 2 }
if { $probtrack(useSurface) && $probtrack(usereference_yn) } { pack $w.data.seed.ssf.typelabel $w.data.seed.ssf.typelabel.type -side top -anchor w -pady 2 }
if { $probtrack(useSurface) && $probtrack(usereference_yn) } { pack $w.data.seed.ssf.surfref -side top -anchor w -pady 2 }
}
network {
if { $probtrack(usereference_yn) } { pack $w.data.seed.ssf.nonlinear $w.data.seed.ssf.xfm -side top -anchor w -pady 2 }
if { $probtrack(useNonlinear) && $probtrack(usereference_yn) } { pack $w.data.seed.ssf.xfm $w.data.seed.ssf.invxfm -side top -anchor w -pady 2 }
if { $probtrack(usereference_yn) } { pack $w.data.seed.ssf.useSurface -side top -anchor w -pady 2 }
if { $probtrack(useSurface) && $probtrack(usereference_yn) } { pack $w.data.seed.ssf.typelabel $w.data.seed.ssf.typelabel.type -side top -anchor w -pady 2 }
if { $probtrack(useSurface) && $probtrack(usereference_yn) } { pack $w.data.seed.ssf.surfref -side top -anchor w -pady 2 }
pack $w.data.seed.target -in $w.data.seed.f -side bottom -anchor w -pady 2
}
}
if { $probtrack(waypoint_yn) } { pack $w.data.targets.wf.tf }
if { $probtrack(classify_yn) } { pack $w.data.targets.cf.tf }
$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) == "bedpostx"} {
pack $w.bedpost -in $w.opts -side top -padx 3 -pady 3 -anchor nw
} elseif {$probtrack(tool) == "probtrackx"} {
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 $w.opts -side top -padx 3 -pady 3 -anchor nw
}
}
proc fdt_monitor_short { w cmd } {
global debugging OSFLAVOUR FSLPARALLEL
puts "$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 BINPATH FSLDIR FSLPARALLEL
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 { $canwrite } {
set flags "--data=$dtifit(input) --out=$dtifit(output) --mask=$dtifit(mask) --bvecs=$dtifit(bvecs) --bvals=$dtifit(bvals)"
if { $dtifit(doWLS) } { set flags "$flags --wls" }
if { $dtifit(doSaveSSE) } { set flags "$flags --sse" }
if { $dtifit(doSaveTensor) } { set flags "$flags --save_tensor" }
fdt_monitor_short $w "${FSLDIR}/bin/dtifit $flags"
}
}
bedpostx {
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)}.bedpostX?" Yes No ]
if { $canwrite } {
puts "rm -rf ${bedpost(directory)}.bedpostX"
catch { exec rm -rf ${bedpost(directory)}.bedpost } errmsg
}
}
if { $canwrite } {
set flags "$bedpost(directory) --nf=$bedpost(nfibres) --fudge=$bedpost(weight) --bi=$bedpost(burnin)"
if { $bedpost(useMultiShell) } { set flags "$flags --model=2" }
if { $bedpost(useNoiseFloor) } { set flags "$flags --f0 --ardf0" }
if { $bedpost(useRician) } { set flags "$flags --rician" }
puts "bedpostx $flags"
set filebase $bedpost(directory)/bedpostcom
set logfile "${filebase}_log.tcl"
set log [open "$logfile" w]
puts $log "bedpostx $flags"
close $log
fdt_monitor $w "${FSLDIR}/bin/bedpostx $flags"
}
}
probtrackx {
global probtrack env
set errorStr ""
# there seems to be no need to reset FSLPARALLEL since the desired
# configuration is already determined in fslstart.tcl (sourced at the
#top of this file) in a way that is not SGE-specific.
#set FSLPARALLEL 0
#if { [ info exists env(SGE_ROOT) ] && $env(SGE_ROOT) != "" } { set FSLPARALLEL 1 }
if { $probtrack(bedpost_dir) == "" } { set errorStr "You must specify the bedpostX directory!" }
if { $probtrack(mode) == "simple" && $probtrack(usereference_yn) && $probtrack(reference) == "" } { set errorStr "$errorStr You must specify a reference image" }
if { $probtrack(mode) == "seedmask" && $probtrack(reference) == "" } { set errorStr "$errorStr You must specify a mask image" }
if { $probtrack(exclude_yn) && $probtrack(exclude) == "" } { set errorStr "$errorStr You must specify the exclusion mask!" }
if { $probtrack(useNonlinear) && $probtrack(usereference_yn) && $probtrack(invxfm) == "" } { set errorStr "$errorStr You must specify the inverse transform!" }
if { $probtrack(useSurface) && $probtrack(usereference_yn) && $probtrack(surfref) == "" } { set errorStr "$errorStr You must specify the surface reference!" }
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!" }
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" }
if { $probtrack(oneway_yn) == 1 } { set flags "$flags --onewaycondition" }
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 { $probtrack(omatrix2_yn) == 1 } { set flags "$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=$probtrack(mask31) --lrtarget3=$probtrack(mask32)" }
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 --fibthresh=$probtrack(fibthresh)"
set flags "$flags --distthresh=$probtrack(distthresh)"
set flags "$flags --sampvox=$probtrack(sampvox)"
if { $errorStr != "" } {
MxPause $errorStr
return
}
set canwrite 1
if { [ file exists $probtrack(output) ] } {
set canwrite [ YesNoWidget "Overwrite $probtrack(output)?" Yes No ]
}
set deslashedFileName [ rmSlash $probtrack(output) ]
if {[string index $deslashedFileName 0] != "/"} {
#remove ./ if name only typed in by tailing value
set deslashedFileName [file tail $deslashedFileName ]
set deslashedFileName [pwd]/$deslashedFileName
set probtrack(output) [rmSlash $deslashedFileName]
}
if { $canwrite } {
puts "rm -rf $probtrack(output)"
exec rm -rf $probtrack(output)
puts "mkdir -p $probtrack(output)"
exec mkdir -p $probtrack(output)
}
set filebase $probtrack(output)/fdt
set logfile "${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(usereference_yn) $probtrack(usereference_yn)"
puts $log "set probtrack(xfm) $probtrack(xfm)"
if { $probtrack(useNonlinear) } {
set flags "$flags --invxfm=$probtrack(invxfm)"
puts $log "set $probtrack(useNonlinear) $probtrack(useNonlinear)"
puts $log "set probtrack(invxfm) $probtrack(invxfm)"
}
if { $probtrack(useSurface) } {
set flags "$flags --meshspace=$probtrack(meshspace) --seedref=$probtrack(surfref)"
puts $log "set probtrack(useSurface) $probtrack(useSurface)"
puts $log "set probtrack(meshspace) $probtrack(meshspace)"
puts $log "set probtrack(surfref) $probtrack(surfref)"
}
}
if { $probtrack(exclude_yn) == 1 } {
set flags "$flags --avoid=$probtrack(exclude)"
puts $log "set probtrack(exclude_yn) $probtrack(exclude_yn)"
puts $log "set probtrack(exclude) $probtrack(exclude)"
}
if { $probtrack(terminate_yn) == 1 } {
set flags "$flags --stop=$probtrack(stop)"
puts $log "set probtrack(terminate_yn) $probtrack(terminate_yn)"
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 fibthresh distthresh sampvox oneway_yn wayorder_yn waycond} {
puts $log "set probtrack($entry) $probtrack($entry)"
}
set singleFileName $probtrack(output)
switch $probtrack(mode) {
simple {
set singleFileName [ file tail $probtrack(output) ]
set fd [ open "${filebase}_coordinates.txt" w ]
set x $probtrack(x)
set y $probtrack(y)
set z $probtrack(z)
if { ! $probtrack(usereference_yn) } {
set probtrack(reference) [ file join $probtrack(bedpost_dir) nodif_brain_mask ]
}
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) $probtrack(units)"
set flags "--simple --seedref=$probtrack(reference) -o ${singleFileName} -x ${filebase}_coordinates.txt $flags"
}
seedmask {
set flags " -x $probtrack(reference) $flags"
}
network {
fdt_exp w $w.data.seed.targets $probtrack(output)/masks.txt
set flags "--network -x $probtrack(output)/masks.txt $flags"
puts $log " $w.data.seed.targets insert end [ $w.data.seed.targets get 0 end ]"
}
}
puts $log "set probtrack(reference) $probtrack(reference)"
puts $log "set probtrack(output) $probtrack(output)"
if { $canwrite } {
set copylog "$probtrack(output)/fdt.log"
if { $probtrack(waypoint_yn) == 1 } {
fdt_exp w $w.data.targets.wf.tf.targets $probtrack(output)/waypoints.txt
puts $log "set probtrack(waypoint_yn) $probtrack(waypoint_yn)"
puts $log " $w.data.targets.wf.tf.targets insert end [ $w.data.targets.wf.tf.targets get 0 end ]"
set flags "$flags --waypoints=$probtrack(output)/waypoints.txt "
set flags "$flags --waycond=$probtrack(waycond)"
}
if { $probtrack(classify_yn) == 1 } {
fdt_exp w $w.data.targets.cf.tf.targets $probtrack(output)/targets.txt
puts $log "set probtrack(classify_yn) $probtrack(classify_yn)"
puts $log " $w.data.targets.cf.tf.targets insert end [ $w.data.targets.cf.tf.targets get 0 end ]"
set flags "$flags --targetmasks=$probtrack(output)/targets.txt --os2t "
}
close $log
if { $FSLPARALLEL } {
set script [open "${filebase}_script.sh" w]
puts "${filebase}_script.sh"
exec chmod 777 ${filebase}_script.sh
puts $script "#!/bin/sh"
puts $script "cd $probtrack(output)"
puts $script "$FSLDIR/bin/probtrackx2 $flags"
if { $probtrack(classify_yn) == 1 } {
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
# Don't specify specific queue name (to leave the logic within
# fsl_sub, but specify a long time (20 hours) to achieve the same
# goal)
#exec $FSLDIR/bin/fsl_sub -q long.q ${filebase}_script.sh
exec $FSLDIR/bin/fsl_sub -T 1200 ${filebase}_script.sh
} else {
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_* $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 { $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 bedpostX directory!" }
if { $registration(struct_yn) && $registration(struct_image) == "" } { set errorStr "$errorStr You must specify the structural image!" }
if { $registration(struct_yn) && $registration(nonlin_yn) && $registration(nonlin_image) == "" } { set errorStr "$errorStr You must specify the non-betted 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 str2stand_warp [ file join $registration(directory) xfms str2standard_warp ]
set stand2str [ file join $registration(directory) xfms standard2str.mat ]
set stand2str_warp [ file join $registration(directory) xfms standard2str_warp ]
set diff2stand [ file join $registration(directory) xfms diff2standard.mat ]
set diff2stand_warp [ file join $registration(directory) xfms diff2standard_warp ]
set stand2diff [ file join $registration(directory) xfms standard2diff.mat ]
set stand2diff_warp [ file join $registration(directory) xfms standard2diff_warp ]
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"
if { $registration(nonlin_yn) } {
fdt_monitor $w "${FSLDIR}/bin/fnirt --in=$registration(nonlin_image) --aff=$str2stand --cout=$str2stand_warp --config=T1_2_MNI152_2mm"
fdt_monitor $w "${FSLDIR}/bin/invwarp -w $str2stand_warp -o $stand2str_warp -r $registration(struct_image)"
fdt_monitor $w "${FSLDIR}/bin/convertwarp -o $diff2stand_warp -r ${FSLDIR}/data/standard/MNI152_T1_2mm -m $diff2str -w $str2stand_warp"
fdt_monitor $w "${FSLDIR}/bin/convertwarp -o $stand2diff_warp -r ${diff}_mask -w $stand2str_warp --postmat=$str2diff"
}
}
} 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 } {
if { $FSLPARALLEL == 1 && [ string match *x* $probtrack(tool) ]} { MxPause " Job submitted to queue" } else { MxPause " Done! " }
update idletasks
}
if {$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
|
