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Commit c989e0f5 authored by Matthew Webster's avatar Matthew Webster
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less tix, more fix

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# FSL interface for FDT (BEDPOST and ProbTrack)
#
# Timothy Behrens, Heidi Johansen-Berg and Dave Flitney, FMRIB Image Analysis Group
# Timothy Behrens, Heidi Johansen-Berg, Dave Flitney and Matthew Webster FMRIB Image Analysis Group
#
# Copyright (C) 2004 University of Oxford
# Copyright (C) 2006 University of Oxford
#
# TCLCOPYRIGHT
#TO DO replace -filetypes * with -filetypes { } for directory selectors
source [ file dirname [ info script ] ]/fslstart.tcl
set TCLPATH [file dirname [ info script ] ]
regsub tcl $TCLPATH bin BINPATH
......@@ -13,275 +14,6 @@ regsub tcl $TCLPATH doc/fdt HTMLPATH
set VERSION "1.0a"
tixWidgetClass registrationImageSelect {
-superclass tixPrimitive
-classname RegistrationImageSelect
-flag {
-variable -filename -labelwidth -label -search -dof -pattern -filterhist -costfn
}
-configspec {
{-variable variable Variable N}
{-labelwidth labelwidth Labelwidth {}}
{-label label Label ""}
{-directory directory Directory {}}
{-filterhist filterhist Filterhist {}}
{-filename filename Filename {}}
{-search search Search N}
{-dof dof DOF N}
{-costfn costfn Costfn N}
{-pattern pattern Pattern "*.{hdr,hdr.gz,nii,nii.gz}"}
}
}
proc registrationImageSelect:ConstructWidget { w } {
upvar \#0 $w data
tixChainMethod $w ConstructWidget
set data(w:fsd) [ tixFileSelectDialog $w.fsd ]
frame $w.frame
set data(w:chkbutton) [ checkbutton $w.frame.visible_yn -variable $data(-variable) \
-command "registrationImageSelect:toggle_visible $w" ]
label $w.frame.label -text $data(-label)
set data(w:options) [ tixLabelFrame $w.frame.options -label $data(-label) ]
set data(w:file) [ FSLFileEntry $w.frame.options.f \
-variable $data(-filename) \
-directory $data(-directory) \
-label "" \
-title "Select file" \
-width 40 \
-pattern $data(-pattern) \
-filterhist VARS(history) ]
tixOptionMenu $w.frame.options.search -variable $data(-search)
$w.frame.options.search add command 0 -label "No search"
$w.frame.options.search add command 90 -label "Normal search"
$w.frame.options.search add command 180 -label "Full search"
tixOptionMenu $w.frame.options.dof -variable $data(-dof)
$w.frame.options.dof add command 6 -label "6 DOF"
$w.frame.options.dof add command 7 -label "7 DOF"
$w.frame.options.dof add command 9 -label "9 DOF"
$w.frame.options.dof add command 12 -label "12 DOF"
tixOptionMenu $w.frame.options.costfn -variable $data(-costfn)
$w.frame.options.costfn add command corratio -label "Correlation ratio"
$w.frame.options.costfn add command mutualinfo -label "Mutual information"
pack $w.frame.options.f -in [$w.frame.options subwidget frame] -side top -expand yes -fill x
pack $w.frame.options.costfn $w.frame.options.dof $w.frame.options.search -in [$w.frame.options subwidget frame] -side right
pack $w.frame.visible_yn $w.frame.label -in $w.frame -side left -expand yes -padx 3
pack $w.frame -in $w
registrationImageSelect:toggle_visible $w
}
proc registrationImageSelect:toggle_visible { w } {
upvar \#0 $w data
upvar \#0 $data(-variable) visible_yn
if { $visible_yn } {
pack forget $w.frame.label
pack [$w subwidget options] -side left -after [$w subwidget chkbutton] -padx 3 -pady 3
} else {
pack $w.frame.label -side left -after [$w subwidget chkbutton] -padx 3 -pady 3
pack forget [$w subwidget options]
}
}
tixWidgetClass multiFileSelect {
-superclass tixPrimitive
-classname MultiFileSelect
-method {
save load
}
-flag {
-variable -labelwidth -label -directory -pattern -title -filterhist
}
-configspec {
{-variable variable Variable N}
{-labelwidth labelwidth Labelwidth {}}
{-label label Label "File"}
{-directory directory Directory {}}
{-filterhist filterhist Filterhist {}}
{-pattern pattern Pattern "*.{hdr,hdr.gz,nii,nii.gz}"}
{-title title Title "Select a file"}
}
}
proc multiFileSelect:InitWidgetRec { w } {
upvar #0 $w data
tixChainMethod $w InitWidgetRec
set data(filename) filename$w
}
proc multiFileSelect:ConstructWidget { w } {
upvar #0 $w data
tixChainMethod $w ConstructWidget
set data(w:fsd) [ tixFileSelectDialog $w.fsd ]
frame $w.frame -borderwidth 2 -relief sunken
frame $w.frame.l
set data(w:files) [ listbox $w.frame.l.files -height 4 -yscrollcommand "$w.frame.l.scroller set" ]
scrollbar $w.frame.l.scroller -command "$w.frame.l.files yview"
pack $w.frame.l.files -in $w.frame.l -side left -expand yes -fill x
pack $w.frame.l.scroller -in $w.frame.l -side right -fill y
set data(w:file) [FSLFileDirSelectDialog $w.browser \
-title $data(-title) \
-command "multiFileSelect:Invoke $w" \
-filterhist $data(-filterhist) \
-directory $data(-directory) \
-pattern $data(-pattern)
]
frame $w.frame.b
button $w.frame.b.add -text "Add..." -command "$w.browser popup"
button $w.frame.b.del -text "Remove" -command "multiFileSelect:remove $w"
button $w.frame.b.imp -text "Load list..." -command "multiFileSelect:import $w"
button $w.frame.b.exp -text "Save list..." -command "multiFileSelect:export $w"
pack $w.frame.b.add $w.frame.b.del $w.frame.b.imp $w.frame.b.exp -in $w.frame.b -side left -expand yes -fill x
pack $w.frame.l $w.frame.b -in $w.frame -side top -padx 2 -pady 2 -expand yes -fill x
pack $w.frame -in $w -expand yes -fill x
}
proc multiFileSelect:Invoke { w filename } {
upvar #0 $w data
upvar $data(-variable) Variable
set filename [ fix_cygwin_filename $filename ]
set Variable $filename
[$w subwidget files] insert end $filename
}
proc multiFileSelect:remove { w } {
upvar #0 $w data
set count 0
foreach file [ [$w subwidget files] get 0 end ] {
if { [ [$w subwidget files] selection includes $count ] == 1 } {
[$w subwidget files] delete $count
incr count -1
}
incr count
}
}
proc multiFileSelect:load { w filename } {
upvar #0 $w data
if { ![ file exists $filename ] } {
MxPause "Warning: Bad or missing file!"
return
}
set fd [ open $filename ]
[$w subwidget files] delete 0 end
while { [ gets $fd file ] >= 0 } {
[$w subwidget files] insert end $file
}
close $fd
}
proc multiFileSelect:save { w filename } {
upvar #0 $w data
set fd [ open $filename w ]
foreach file [ [$w subwidget files] get 0 end ] {
puts $fd $file
}
close $fd
}
proc multiFileSelect:import { w } {
upvar #0 $w data
set fsd $data(w:fsd)
$fsd configure -title "Import list from..." -command "multiFileSelect:load $w"
$fsd popup
}
proc multiFileSelect:export { w } {
upvar #0 $w data
set fsd $data(w:fsd)
$fsd configure -title "Export list to..." -command "multiFileSelect:save $w"
$fsd popup
}
tixWidgetClass coordinateEdit {
-superclass tixPrimitive
-classname CoordinateEdit
-method {
update
}
-flag {
-variablex -variabley -variablez -variablemm -labelwidth -label
}
-configspec {
{-variablex variablex VariableX N}
{-variabley variabley VariableY N}
{-variablez variablez VariableZ N}
{-variableunits variableunits VariableUnits N}
{-label label Label "File"}
{-labelwidth labelwidth Labelwidth {}}
}
}
proc coordinateEdit:ConstructWidget { w } {
upvar #0 $w data
tixChainMethod $w ConstructWidget
frame $w.frame
set data($w:label) [ label $w.frame.label -text $data(-label) ]
if {$data(-labelwidth) != ""} {
$w.frame.label configure -width $data(-labelwidth)
}
label $w.frame.padlbl -width 1
frame $w.frame.f -borderwidth 2
set data(w:x) [ tixControl $w.frame.f.x -label "X" -step 1 -variable $data(-variablex)\
-selectmode normal -options { entry.width 6 } ]
set data(w:y) [ tixControl $w.frame.f.y -label "Y" -step 1 -variable $data(-variabley)\
-selectmode normal -options { entry.width 6 } ]
set data(w:z) [ tixControl $w.frame.f.z -label "Z" -step 1 -variable $data(-variablez)\
-selectmode normal -options { entry.width 6 } ]
radiobutton $w.frame.vox -text "vox" -value vox -variable $data(-variableunits)
radiobutton $w.frame.mm -text "mm" -value mm -variable $data(-variableunits)
pack $w.frame.f.x $w.frame.f.y $w.frame.f.z -in $w.frame.f -side left -padx 2 -pady 0
pack $w.frame.label $w.frame.padlbl $w.frame.f $w.frame.vox $w.frame.mm -in $w.frame -side left -padx 0 -pady 0
pack $w.frame -in $w
}
proc coordinateEdit:update { w } {
......@@ -307,44 +39,15 @@ proc mm_to_voxels { X Y Z mask } {
set cX $vcX
set cY $vcY
set cZ $vcZ
#set o1 [ exec sh -c "$FSLDIR/bin/avwval $mask origin1" ]
#set o2 [ exec sh -c "$FSLDIR/bin/avwval $mask origin2" ]
#set o3 [ exec sh -c "$FSLDIR/bin/avwval $mask origin3" ]
#if { $o1 != 0 && $o2 != 0 && $o3 != 0 } {
# set o1 [ expr $o1 - 0.5 ]
# set o2 [ expr $o2 - 1.5 ]
# set o3 [ expr $o3 - 0.5 ]
#}
# puts "Using origin $o1 $o2 $o3"
#set cX [ expr int( ( double($cX) / [ exec sh -c "$FSLDIR/bin/avwval $mask pixdim1" ] ) + $o1 ) ]
#set cY [ expr int( ( double($cY) / [ exec sh -c "$FSLDIR/bin/avwval $mask pixdim2" ] ) + $o2 ) ]
#set cZ [ expr int( ( double($cZ) / [ exec sh -c "$FSLDIR/bin/avwval $mask pixdim3" ] ) + $o3 ) ]
# puts "Setting co-ordinates $cX $cY $cZ"
}
proc fdt:dialog { w tclstartupfile } {
global tool
global eddy
global bedpost
global registration
global dtifit
global probtrack
global HTMLPATH
global FSLDIR
global VERSION
global INMEDX
global VARS
set VARS(history) ""
global eddy bedpost registration dtifit probtrack HTMLPATH FSLDIR VERSION INMEDX VARS
set LWIDTH 27
set PWD [ pwd ]
set probtrack(tool) "probtrack"
if [winfo exists $w] {
wm deiconify $w
......@@ -360,16 +63,9 @@ proc fdt:dialog { w tclstartupfile } {
#-------- Stage and Mode Options --------
frame $w.tool
tixOptionMenu $w.tool.menu -variable tool
$w.tool.menu add command eddy_current -label "Eddy current correction"
$w.tool.menu add command bedpost -label "BEDPOST Estimation of diffusion parameters"
$w.tool.menu add command registration -label "Registration"
$w.tool.menu add command probtrack -label "ProbTrack Probabilistic tracking"
$w.tool.menu add separator xutilsx
$w.tool.menu add command dtifit -label "DTIFit Reconstruct diffusion tensors"
pack $w.tool.menu -in $w.tool -side left -pady 3 -padx 6 -anchor nw
optionMenu2 $w.tool.menu probtrack(tool) -command "fdt:select_tool $w" eddy_current "Eddy current correction" bedpost "BEDPOST Estimation of diffusion parameters" registration "Registration" probtrack "ProbTrack 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... --------
......@@ -391,94 +87,71 @@ proc fdt:dialog { w tclstartupfile } {
}
}
FSLFileEntry $w.registration.directory \
-variable registration(directory) \
-directory $PWD \
-label "BEDPOST directory:" \
-labelwidth $LWIDTH \
-title "Choose directory" \
-width 35 \
-command "registration_set_directory $w" \
-filterhist VARS(history)
registrationImageSelect $w.registration.struct \
-variable registration(struct_yn) \
-filename registration(struct_image) \
-dof registration(struct_dof) \
-search registration(struct_search) \
-costfn registration(struct_costfn) \
-directory $PWD \
-label "Main structural image" \
-labelwidth $LWIDTH \
-filterhist VARS(history)
FileEntry $w.registration.directory -textvariable registration(directory) -label "BEDPOST directory:" -title "Choose directory" -width 35 -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
registrationImageSelect $w.registration.standard \
-variable registration(standard_yn) \
-filename registration(standard_image) \
-dof registration(standard_dof) \
-search registration(standard_search) \
-costfn registration(standard_costfn) \
-directory $PWD \
-label "Standard space" \
-labelwidth $LWIDTH \
-filterhist VARS(history)
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 -in $w.registration -side top -padx 3 -pady 3 -anchor nw
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 ]
}
FSLFileEntry $w.ecc.input \
-variable eddy(input) \
-directory $PWD \
-label "Diffusion weighted data:" \
-labelwidth $LWIDTH \
-title "Choose diffusion weighted image" \
-pattern "IMAGE" \
-width 35 \
-command "ecc_update_files $w" \
-filterhist VARS(history)
FSLFileEntry $w.ecc.output \
-variable eddy(output) \
-directory $PWD \
-label "Corrected output data:" \
-labelwidth $LWIDTH \
-title "Choose output image name" \
-pattern "IMAGE" \
-width 35 \
-filterhist VARS(history)
tixControl $w.ecc.refnum -label "Reference volume" \
-variable eddy(refnum) -step 1 -min 0 \
-selectmode immediate -options { entry.width 6 }
pack $w.ecc.input $w.ecc.output $w.ecc.refnum -in $w.ecc -side top -padx 3 -pady 3 -expand yes -anchor w
}
FileEntry $w.ecc.input -textvariable eddy(input) -label "Diffusion weighted data:" -title "Choose diffusion weighted image" -width 35 -filetypes IMAGE -command "ecc_update_files $w"
FileEntry $w.ecc.output -textvariable eddy(output) -label "Corrected output data:" -title "Choose output image name" -width 35 -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
FSLFileEntry $w.dtifit.directory \
-variable dtifit(directory) \
-directory $PWD \
-label "Input directory:" \
-labelwidth $LWIDTH \
-title "Choose directory" \
-command "set_working_directory dtifit(cwd)" \
-width 35 \
-filterhist VARS(history)
FileEntry $w.dtifit.directory -textvariable dtifit(directory) -label "Input directory:" -title "Choose directory" -width 35 -command "set_working_directory dtifit(cwd)"
proc dtifit_toggle_expert { w } {
global dtifit
......@@ -513,60 +186,20 @@ proc fdt:dialog { w tclstartupfile } {
}
set dtifit(cwd) $PWD
FSLFileEntry $w.dtifit.expert.input \
-variable dtifit(input) \
-directory $dtifit(cwd) \
-label "Diffusion weighted data:" \
-labelwidth $LWIDTH \
-title "Choose diffusion weighted image" \
-pattern "IMAGE" \
-width 35 \
-command "dtifit_update_files $w" \
-filterhist VARS(history)
FSLFileEntry $w.dtifit.expert.mask \
-variable dtifit(mask) \
-directory $dtifit(cwd) \
-label "BET binary brain mask:" \
-labelwidth $LWIDTH \
-title "Choose BET brain mask file" \
-pattern "IMAGE" \
-command "set_working_directory dtifit(cwd)" \
-width 35 \
-filterhist VARS(history)
FSLFileEntry $w.dtifit.expert.output \
-variable dtifit(output) \
-directory $dtifit(cwd) \
-label "Output basename:" \
-labelwidth $LWIDTH \
-title "Choose output base name" \
-command "set_working_directory dtifit(cwd)" \
-width 35 \
-filterhist VARS(history)
FSLFileEntry $w.dtifit.expert.bvecs \
-variable dtifit(bvecs) \
-directory $dtifit(cwd) \
-label "Gradient directions:" \
-labelwidth $LWIDTH \
-title "Choose bvecs file" \
-command "set_working_directory dtifit(cwd)" \
-pattern "*" \
-width 35 \
-filterhist VARS(history)
FSLFileEntry $w.dtifit.expert.bvals \
-variable dtifit(bvals) \
-directory $dtifit(cwd) \
-label "b values:" \
-labelwidth $LWIDTH \
-title "Choose bvals file" \
-command "set_working_directory dtifit(cwd)" \
-pattern "*" \
-width 35 \
-filterhist VARS(history)
#All the below orignally had -directory $dtifit(cwd)
FileEntry $w.dtifit.expert.input -textvariable dtifit(input) -label "Diffusion weighted data:" -title "Choose diffusion weighted image" -width 35 -filetypes IMAGE -command "dtifit_update_files $w"
$w.dtifit.expert.input.labf configure -width $LWIDTH
FileEntry $w.dtifit.expert.mask -textvariable dtifit(mask) -label "BET binary brain mask:" -title "Choose BET brain mask file" -width 35 -filetypes IMAGE -command "set_working_directory dtifit(cwd)"
$w.dtifit.expert.mask.labf configure -width $LWIDTH
FileEntry $w.dtifit.expert.output -textvariable dtifit(output) -label "Output basename:" -title "Choose output base name" -width 35 -filetypes * -command "set_working_directory dtifit(cwd)"
$w.dtifit.expert.output.labf configure -width $LWIDTH
FileEntry $w.dtifit.expert.bvecs -textvariable dtifit(bvecs) -label "Gradient directions:" -title "Choose bvecs file" -width 35 -filetypes * -command "set_working_directory dtifit(cwd)"
$w.dtifit.expert.bvecs.labf configure -width $LWIDTH
FileEntry $w.dtifit.expert.bvals -textvariable dtifit(bvals) -label "b values:" -title "Choose bvals file" -width 35 -filetypes * -command "set_working_directory dtifit(cwd)"
$w.dtifit.expert.bvals.labf configure -width $LWIDTH
pack $w.dtifit.expert.input $w.dtifit.expert.mask $w.dtifit.expert.output \
$w.dtifit.expert.bvecs $w.dtifit.expert.bvals \
-in $w.dtifit.expert -side top -padx 3 -pady 3 -expand yes -anchor w
......@@ -578,14 +211,7 @@ proc fdt:dialog { w tclstartupfile } {
frame $w.bedpost
FSLFileEntry $w.bedpost.directory \
-variable bedpost(directory) \
-directory $PWD \
-label "Input directory:" \
-labelwidth $LWIDTH \
-title "Choose directory" \
-width 35 \
-filterhist VARS(history)
FileEntry $w.bedpost.directory -textvariable bedpost(directory) -label "Input directory:" -title "Choose directory" -width 35 -filetypes * -command "set_working_directory dtifit(cwd)"
set bedpost(ecc_yn) 0
......@@ -594,32 +220,30 @@ proc fdt:dialog { w tclstartupfile } {
#-------- ...ProbTrack... --------
tixNoteBook $w.probtrack -ipadx 5 -ipady 5
$w.probtrack add data -label "Data"
$w.probtrack add options -label "Options"
NoteBook $w.probtrack -bd 2 -tabpady {5 10} -arcradius 3
$w.probtrack insert 0 data -text "Data"
$w.probtrack insert 1 options -text "Options"
#-------- ...Mode specific options... --------
set dataf [$w.probtrack subwidget data]
set dataf [$w.probtrack getframe data]
frame $w.data
tixOptionMenu $w.data.mode -label "Mode: " -variable probtrack(mode)
[ $w.data.mode subwidget menu ] configure -disabledforeground darkred
$w.data.mode add command xtitlex -label "Path distribution estimation" -state disabled
$w.data.mode add command simple -label " Single seed voxel"
$w.data.mode add command all -label " Seed mask"
$w.data.mode add command maska -label " Seed mask and waypoint masks"
$w.data.mode add command masks -label " Two masks - symmetric"
$w.data.mode add separator xseedsx
$w.data.mode add command seeds -label "Connectivity-based seed classification"
LabelFrame $w.data.mode -text "Mode: "
if { [ file exists [ file join $FSLDIR bin reord_OM ] ] } {
$w.data.mode add separator xmatrixx
$w.data.mode add command mat1 -label "Matrix 1"
$w.data.mode add command mat2 -label "Matrix 2"
$w.data.mode add command mskmat -label "Mask matrix"
optionMenu2 $w.data.mode.menu probtrack(mode) -command "fdt:probtrack_mode $w" xtitlex "Path distribution estimation" simple " Single seed voxel" all " Seed mask" maska " Seed mask and waypoint masks" masks " Two masks - symmetric" xutilssx "--------------------------------------------" seeds "Connectivity-based seed classification" xmatrixx "--------------------------------------------" mat1 "Matrix 1" mat2 "Matrix 2" mskmat "Mask matrix"
$w.data.mode.menu.menu entryconfigure 0 -state disabled -background black
$w.data.mode.menu.menu entryconfigure 5 -state disabled -background black
$w.data.mode.menu.menu entryconfigure 7 -state disabled -background black
} else {
optionMenu2 $w.data.mode.menu probtrack(mode) -command "fdt:probtrack_mode $w" xtitlex "Path distribution estimation" simple " Single seed voxel" all " Seed mask" maska " Seed mask and waypoint masks" masks " Two masks - symmetric" xutilssx "--------------------------------------------" seeds "Connectivity-based seed classification"
$w.data.mode.menu.menu entryconfigure 0 -state disabled -background black
$w.data.mode.menu.menu entryconfigure 5 -state disabled -background black
}
pack $w.data.mode.menu
set probtrack(xfm) ""
set probtrack(basename) "merged"
......@@ -635,70 +259,96 @@ proc fdt:dialog { w tclstartupfile } {
}
}
FSLFileEntry $w.data.directory \
-variable probtrack(bedpost_dir) \
-directory $PWD \
-label "BEDPOST directory" \
-labelwidth $LWIDTH \
-title "Choose BEDPOST directory" \
-width 35 \
-command "probtrack_update_files $w" \
-filterhist VARS(history)
tixLabelFrame $w.data.target -label "Target list"
multiFileSelect $w.data.targets -label "Target file: " -labelwidth $LWIDTH -directory $PWD
pack $w.data.targets -in [$w.data.target subwidget frame] \
-side top -anchor w -padx 3 -pady 3
tixLabelFrame $w.data.seedspace -label "Seed space"
FSLFileEntry $w.data.seed \
-variable probtrack(seed) \
-directory $PWD \
-label "Seed image:" \
-labelwidth $LWIDTH \
-title "Choose seed image" \
-pattern "IMAGE" \
-width 35 \
-command "probtrack_update_files $w" \
-filterhist VARS(history)
FSLFileEntry $w.data.seed2 \
-variable probtrack(seed2) \
-directory $PWD \
-label "Target image:" \
-labelwidth $LWIDTH \
-title "Choose target image" \
-pattern "IMAGE" \
-width 35 \
-command "probtrack_update_files $w" \
-filterhist VARS(history)
tixLabelFrame $w.data.waypoint -label "Waypoint masks"
multiFileSelect $w.data.waypoints -label "Waypoint mask file: " -labelwidth $LWIDTH -directory $PWD
pack $w.data.waypoints -in [$w.data.waypoint subwidget frame] \
-side top -anchor w -padx 3 -pady 3
FileEntry $w.data.directory -textvariable probtrack(bedpost_dir) -label "BEDPOST directory" -title "Choose BEDPOST directory" -width 35 -filetypes * -command "probtrack_update_files $w"
TitleFrame $w.data.target -text "Target list"
listbox $w.data.targets -height 6 -width 40 -yscrollcommand "$w.data.sb set"
scrollbar $w.data.sb -command "$w.data.targets yview "
frame $w.data.tb
button $w.data.tb.add -text "Add..." -command "feat_file:setup_dialog $w a a a [namespace current] IMAGE {Select File} {fdt_add $w $w.data.targets} {}"
button $w.data.tb.del -text "Remove" -command "fdt_sub $w $w.data.targets"
button $w.data.tb.imp -text "Load list..." -command "feat_file:setup_dialog $w a a a [namespace current] * {Select File} {fdt_imp $w $w.data.targets} {}"
button $w.data.tb.exp -text "Save list..." -command "feat_file:setup_dialog $w a a a [namespace current] * {Select File} {fdt_exp $w $w.data.targets} {}"
pack $w.data.tb.add $w.data.tb.del $w.data.tb.imp $w.data.tb.exp -side left
pack $w.data.tb -in [$w.data.target getframe ] -side bottom -expand yes -fill x -anchor w -padx 3 -pady 3
pack $w.data.targets $w.data.sb -in [$w.data.target getframe ] -side left -expand yes -fill y -anchor w -padx 3 -pady 3
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
}
TitleFrame $w.data.seedspace -text "Seed space"
FileEntry $w.data.seed -textvariable probtrack(seed) -label "Seed image:" -title "Choose seed image" -width 35 -filetypes IMAGE -command "probtrack_update_files $w"
FileEntry $w.data.seed2 -textvariable probtrack(seed2) -label "Target image:" -title "Choose target image" -width 35 -filetypes IMAGE -command "probtrack_update_files $w"
TitleFrame $w.data.waypoint -text "Waypoint masks"
listbox $w.data.waypoints -height 6 -width 40 -yscrollcommand "$w.data.waypoint.sb set"
scrollbar $w.data.waypoint.sb -command "$w.data.waypoints yview "
frame $w.data.waybut
button $w.data.waybut.add -text "Add..." -command "feat_file:setup_dialog $w a a a [namespace current] IMAGE {Select File} {fdt_add $w $w.data.waypoints} {}"
button $w.data.waybut.del -text "Remove" -command "fdt_sub $w $w.data.waypoints"
button $w.data.waybut.imp -text "Load list..." -command "feat_file:setup_dialog $w a a a [namespace current] * {Select File} {fdt_imp $w $w.data.waypoints} {}"
button $w.data.waybut.exp -text "Save list..." -command "feat_file:setup_dialog $w a a a [namespace current] * {Select File} {fdt_exp $w $w.data.waypoints} {}"
pack $w.data.waybut.add $w.data.waybut.del $w.data.waybut.imp $w.data.waybut.exp -in $w.data.waybut -side left
pack $w.data.waybut -in [$w.data.waypoint getframe ] -side bottom -expand yes -fill x -anchor w -padx 3 -pady 3
pack $w.data.waypoints $w.data.waypoint.sb -in [$w.data.waypoint getframe ] -side left -expand yes -fill y -anchor w -padx 3 -pady 3
set probtrack(x) 0
set probtrack(y) 0
set probtrack(z) 0
set probtrack(units) vox
coordinateEdit $w.data.seedxyz -label "Seed:" -labelwidth $LWIDTH \
-variablex probtrack(x) \
-variabley probtrack(y) \
-variablez probtrack(z) \
-variableunits probtrack(units)
#Co-ordinate edit frame
LabelFrame $w.data.seedxyz -text "Seed:"
LabelSpinBox $w.data.seedxyz.x -label "X" -textvariable probtrack(x) -range {-1000000 1000000 1 } -width 6
LabelSpinBox $w.data.seedxyz.y -label "Y" -textvariable probtrack(x) -range {-1000000 1000000 1 } -width 6
LabelSpinBox $w.data.seedxyz.z -label "Z" -textvariable probtrack(x) -range {-1000000 1000000 1 } -width 6
radiobutton $w.data.seedxyz.vox -text "vox" -value vox -variable probtrack(units)
radiobutton $w.data.seedxyz.mm -text "mm" -value mm -variable probtrack(units)
pack $w.data.seedxyz.x $w.data.seedxyz.y $w.data.seedxyz.z $w.data.seedxyz.vox $w.data.seedxyz.mm -side left -padx 2 -pady 0
proc probtrack_toggle_reference { w } {
global probtrack
if { $probtrack(usereference_yn) } {
if { $probtrack(mode) == "simple" } {
pack $w.data.reference $w.data.xfm -in [$w.data.seedspace subwidget frame] \
pack $w.data.reference $w.data.xfm -in [$w.data.seedspace getframe ] \
-side top -after $w.data.usereference_yn -padx 3 -pady 3
} else {
pack $w.data.xfm -in [$w.data.seedspace subwidget frame] \
pack $w.data.xfm -in [$w.data.seedspace getframe ] \
-side top -after $w.data.usereference_yn -padx 3 -pady 3
}
} else {
......@@ -711,31 +361,15 @@ proc fdt:dialog { w tclstartupfile } {
-variable probtrack(usereference_yn) \
-command "probtrack_toggle_reference $w"
FSLFileEntry $w.data.reference \
-variable probtrack(reference) \
-directory $PWD \
-label "Seed space reference image:" \
-labelwidth $LWIDTH \
-title "Choose reference image" \
-pattern "IMAGE" \
-width 35 \
-filterhist VARS(history)
FSLFileEntry $w.data.xfm \
-variable probtrack(xfm) \
-directory $PWD \
-label "Seed to diff-space transform:" \
-labelwidth $LWIDTH \
-title "Select seed-space to DTI-space transformation matrix" \
-pattern "*.mat" \
-width 35 \
-filterhist VARS(history)
FileEntry $w.data.reference -textvariable probtrack(reference) -label "Seed space reference image:" -title "Choose reference image" -width 35 -filetypes IMAGE
FileEntry $w.data.xfm -textvariable probtrack(xfm) -label "Seed to diff-space transform:" -title "Select seed-space to DTI-space transformation matrix" -width 35 -filetypes *.mat
proc probtrack_toggle_exclude { w } {
global probtrack
if { $probtrack(exclude_yn) } {
pack $w.data.exclude -in [$w.data.seedspace subwidget frame] \
pack $w.data.exclude -in [$w.data.seedspace getframe ] \
-side top -after $w.data.exclude_yn -padx 3 -pady 3
} else {
pack forget $w.data.exclude
......@@ -745,59 +379,27 @@ proc fdt:dialog { w tclstartupfile } {
checkbutton $w.data.exclude_yn -text "Use exclusion mask" -variable probtrack(exclude_yn) \
-command "probtrack_toggle_exclude $w"
FSLFileEntry $w.data.exclude \
-variable probtrack(exclude) \
-directory $PWD \
-label "Exclusion mask:" \
-labelwidth $LWIDTH \
-title "Select exclusion mask image" \
-pattern "IMAGE" \
-width 35 \
-filterhist VARS(history)
FileEntry $w.data.exclude -textvariable probtrack(exclude) -label "Exclusion mask:" -title "Select exclusion mask image" -width 35 -filetypes IMAGE
pack $w.data.seed $w.data.usereference_yn $w.data.exclude_yn -in\
[$w.data.seedspace subwidget frame] -padx 3 -pady 3 -side top -anchor w
[$w.data.seedspace getframe ] -padx 3 -pady 3 -side top -anchor w
probtrack_toggle_reference $w
probtrack_toggle_exclude $w
FSLFileEntry $w.data.lrmask \
-variable probtrack(lrmask) \
-directory $PWD \
-label "Low resolution mask:" \
-labelwidth $LWIDTH \
-title "Choose low resolution mask" \
-pattern "IMAGE" \
-width 35 \
-filterhist VARS(history)
FileEntry $w.data.lrmask -textvariable probtrack(lrmask) -label "Low resolution mask:" -title "Choose low resolution mask" -width 35 -filetypes IMAGE
pack $w.data.lrmask \
-in [$w.data.seedspace subwidget frame] \
-in [$w.data.seedspace getframe ] \
-side top -padx 3 -pady 3 -anchor w
tixLabelFrame $w.data.output -label "Ouput"
FSLFileEntry $w.data.dir \
-variable probtrack(dir) \
-directory $PWD \
-label "Output directory:" \
-labelwidth $LWIDTH \
-title "Name the output directory" \
-width 35 \
-filterhist VARS(history)
FSLFileEntry $w.data.out \
-variable probtrack(output) \
-directory $PWD \
-label "Output:" \
-labelwidth $LWIDTH \
-title "Choose output file name" \
-pattern "IMAGE" \
-width 35 \
-filterhist VARS(history)
pack $w.data.out $w.data.dir -in [$w.data.output subwidget frame] \
-side top -padx 3 -pady 3 -anchor w
TitleFrame $w.data.output -text "Ouput"
FileEntry $w.data.dir -textvariable probtrack(dir) -label "Output directory:" -title "Name the output directory" -width 35 -filetypes *
FileEntry $w.data.out -textvariable probtrack(output) -label "Output:" -title "Choose output file name" -width 35 -filetypes IMAGE
pack $w.data.out $w.data.dir -in [$w.data.output getframe ] -side top -expand yes -fill x -padx 3 -pady 3 -anchor w
pack $w.data.mode $w.data.directory $w.data.target $w.data.seedspace $w.data.output \
-in $w.data -side top -padx 3 -pady 3 -anchor nw
......@@ -806,25 +408,19 @@ proc fdt:dialog { w tclstartupfile } {
#-------- ...Options... --------
set optionsf [$w.probtrack subwidget options]
set optionsf [$w.probtrack getframe options]
tixLabelFrame $w.options -label "Basic Options"
TitleFrame $w.options -text "Basic Options"
checkbutton $w.options.verbose \
-text "Verbose" \
-variable probtrack(verbose_yn)
set probtrack(nparticles) 5000
tixControl $w.options.nparticles -label "Number of samples" \
-variable probtrack(nparticles) -step 100 -min 1 \
-selectmode immediate -options { entry.width 6 }
$w.options.nparticles subwidget label config -width $LWIDTH
LabelSpinBox $w.options.nparticles -label "Number of samples" -textvariable probtrack(nparticles) -range {1 1e24 100 } -width 6
set probtrack(curvature) 0.2
tixControl $w.options.curvature -label "Curvature threshold" \
-variable probtrack(curvature) -step 0.01 -min 0.0 -max 1.0 \
-selectmode immediate -options { entry.width 4 }
$w.options.curvature subwidget label config -width $LWIDTH
LabelSpinBox $w.options.curvature -label "Curvature threshold" -textvariable probtrack(curvature) -range {0.0 1.0 0.01 } -width 4
set probtrack(loopcheck_yn) 1
checkbutton $w.options.loopcheck \
......@@ -834,22 +430,10 @@ proc fdt:dialog { w tclstartupfile } {
collapsible frame $w.advanced -title "Advanced Options"
set probtrack(nsteps) 2000
tixControl $w.advanced.nsteps -label "Maximum number of steps" \
-variable probtrack(nsteps) -step 10 -min 2 \
-selectmode immediate -options { entry.width 6 }
$w.advanced.nsteps subwidget label config -width $LWIDTH
LabelSpinBox $w.advanced.nsteps -label "Maximum number of steps" -textvariable probtrack(nsteps) -range {2 1000000 10 } -width 6
set probtrack(steplength) 0.5
tixControl $w.advanced.steplength -label "Step length (mm)" \
-variable probtrack(steplength) -step 0.1 -min 0 \
-selectmode immediate -options { entry.width 4 }
$w.advanced.steplength subwidget label config -width $LWIDTH
# set probtrack(usef_yn) 0
# checkbutton $w.advanced.usef \
# -text "Use anisotropy constraints" \
# -variable probtrack(usef_yn) \
# -command "if { \$probtrack(usef_yn) } { set probtrack(nsteps) 20000 } else { set probtrack(nsteps) 1000 }"
LabelSpinBox $w.advanced.steplength -label "Step length (mm)" -textvariable probtrack(steplength) -range {0 10000 0.1} -width 4
set probtrack(modeuler_yn) 0
checkbutton $w.advanced.modeuler \
......@@ -867,7 +451,7 @@ proc fdt:dialog { w tclstartupfile } {
$w.options.curvature \
$w.options.verbose \
$w.options.loopcheck \
-in [$w.options subwidget frame] -side top -pady 3 -padx 6 -anchor nw
-in [$w.options getframe ] -side top -pady 3 -padx 6 -anchor nw
pack $w.options $w.advanced -in $optionsf -side top -pady 3 -padx 6 -anchor nw -expand yes -fill both
......@@ -897,27 +481,26 @@ proc fdt:dialog { w tclstartupfile } {
pack $w.tool $w.opts $w.btns -side top -expand yes -fill both
$w.data.mode configure -command "fdt:probtrack_mode $w"
$w.tool.menu configure -command "fdt:select_tool $w"
set tool probtrack
fdt:select_tool $w $tool
$w.probtrack raise data
fdt:select_tool $w
set probtrack(mode) simple
fdt:probtrack_mode $w $probtrack(mode)
fdt:probtrack_mode $w
update idletasks
if { $tclstartupfile != "" } {
puts "Reading $tclstartupfile"
source $tclstartupfile
fdt:select_tool $w $tool
fdt:probtrack_mode $w $probtrack(mode)
fdt:select_tool $w
fdt:probtrack_mode $w
}
}
proc fdt:probtrack_mode { w mode } {
proc fdt:probtrack_mode { w } {
global probtrack
set seedspacef [$w.data.seedspace subwidget frame]
set seedspacef [$w.data.seedspace getframe ]
pack forget $w.data.target
pack forget $w.data.lrmask
......@@ -929,13 +512,13 @@ proc fdt:probtrack_mode { w mode } {
pack forget $w.data.out
pack $w.data.seed $w.data.usereference_yn $w.data.xfm -in $seedspacef -side top \
-before $w.data.exclude_yn -padx 3 -pady 3 -anchor nw
[$w.data.seed subwidget label] configure -text "Seed image:"
pack $w.data.dir -in [$w.data.output subwidget frame] -side top -padx 3 -pady 3 -anchor nw
switch -- $mode {
$w.data.seed configure -label "Seed image:"
pack $w.data.dir -in [$w.data.output getframe ] -side top -padx 3 -pady 3 -anchor nw
switch -- $probtrack(mode) {
simple {
pack $w.data.seedxyz -in $seedspacef -side top -padx 3 -pady 3 -before $w.data.usereference_yn
pack $w.data.reference -in $seedspacef -side top -padx 3 -pady 3 -before $w.data.xfm -anchor nw
pack $w.data.out -in [$w.data.output subwidget frame] -side top -padx 3 -pady 3 -anchor nw
pack $w.data.out -in [$w.data.output getframe] -side top -padx 3 -pady 3 -anchor nw
pack forget $w.data.dir
pack forget $w.data.seed
}
......@@ -944,8 +527,8 @@ proc fdt:probtrack_mode { w mode } {
}
masks {
pack $w.data.seed2 -in $seedspacef -side top -after $w.data.seed
[$w.data.seed subwidget label] configure -text "Mask image 1:"
[$w.data.seed2 subwidget label] configure -text "Mask image 2:"
$w.data.seed configure -label "Mask image 1:"
$w.data.seed2 configure -label "Mask image 2:"
}
seeds {
pack $w.data.target -in $w.data -side top -padx 3 -pady 3 -after $w.data.seedspace -anchor nw
......@@ -957,23 +540,25 @@ proc fdt:probtrack_mode { w mode } {
}
probtrack_toggle_reference $w
probtrack_toggle_exclude $w
$w.probtrack compute_size
}
proc fdt:select_tool { w tool } {
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 $w.dtifit
if {$tool == "bedpost"} {
if {$probtrack(tool) == "bedpost"} {
pack $w.bedpost -in $w.opts -side top -padx 3 -pady 3 -anchor nw
} elseif {$tool == "probtrack"} {
} elseif {$probtrack(tool) == "probtrack"} {
pack $w.probtrack -in $w.opts -side top -padx 3 -pady 3 -anchor nw
} elseif {$tool == "dtifit"} {
} elseif {$probtrack(tool) == "dtifit"} {
pack $w.dtifit -in $w.opts -side top -padx 3 -pady 3 -anchor nw
} elseif {$tool == "eddy_current"} {
} elseif {$probtrack(tool) == "eddy_current"} {
pack $w.ecc -in $w.opts -side top -padx 3 -pady 3 -anchor nw
} elseif {$tool == "registration"} {
} elseif {$probtrack(tool) == "registration"} {
pack $w.registration -in $w.opts -side top -padx 3 -pady 3 -anchor nw
}
}
......@@ -1047,11 +632,11 @@ proc fdt_monitor { w cmd } {
proc fdt:apply { w dialog } {
global tool
global probtrack(tool)
global BINPATH
global FSLDIR
switch -- $tool {
switch -- $probtrack(tool) {
eddy_current {
global eddy
......@@ -1146,7 +731,7 @@ proc fdt:apply { w dialog } {
close $tn
set logfile "${filebase}_log.tcl"
set log [open "$logfile" w]
puts $log "set tool $tool"
puts $log "set tool $probtrack(tool)"
set copylog ""
set ssopts ""
if { $probtrack(usereference_yn) } {
......
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