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David Flitney authoredDavid Flitney authored
fdt.tcl 45.88 KiB
# FSL interface for FDT (BEDPOST and ProbTrack)
# Copyright (c) Timothy Behrens and Heidi Johansen-Berg and Dave Flitney (GUIs), FMRIB Centre, University of Oxford.
#
# This program should be considered a beta test version
# and must not be used for any clinical purposes.
#
# Uses fdt_proc.tcl for processing
source [ file dirname [ info script ] ]/fslstart.tcl
set TCLPATH [file dirname [ info script ] ]
regsub tcl $TCLPATH bin BINPATH
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
}
-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}
{-pattern pattern Pattern "*.{hdr,hdr.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 3 -label "3 DOF (translation-only)"
$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"
pack $w.frame.options.f -in [$w.frame.options subwidget frame] -side top -expand yes -fill x
pack $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}"}
{-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 targets 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 } {
upvar #0 $w data
[$w subwidget x] update
[$w subwidget y] update
[$w subwidget z] update
}
proc mm_to_voxels { X Y Z mask } {
global FSLDIR
upvar $X cX
upvar $Y cY
upvar $Z cZ
set o1 [ exec sh -c "$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) ""
set LWIDTH 27
set PWD [ pwd ]
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
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 Probabalistic 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
#-------- 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 { [ file exists ${struct}.gz] } {
set registration(struct_image) ${struct}.hdr.gz
} elseif { [ file exists $struct] } {
set registration(struct_image) ${struct}.hdr
} else {
set registration(struct_image) ""
}
}
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) \
-directory $PWD \
-label "Main structural image" \
-labelwidth $LWIDTH \
-filterhist VARS(history)
set registration(struct_dof) 12
set registration(struct_search) 90
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) \
-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
#------- 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 "*.{hdr,hdr.gz}" \
-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 "*.{hdr,hdr.gz}" \
-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
#------- 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)
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 } {
upvar $cwd myCWD
set dirname [file dirname $filename]
puts "switching from $myCWD to $dirname" set myCWD $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
FSLFileEntry $w.dtifit.expert.input \
-variable dtifit(input) \
-directory $dtifit(cwd) \
-label "Diffusion weighted data:" \
-labelwidth $LWIDTH \
-title "Choose diffusion weighted image" \
-pattern "*.{hdr,hdr.gz}" \
-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 "*.{hdr,hdr.gz}" \
-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)
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
pack $w.dtifit.directory $w.dtifit.expert_yn -in $w.dtifit \ -side top -padx 3 -pady 3 -expand yes -anchor w
#------- BEDPOST --------
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)
set bedpost(ecc_yn) 0
pack $w.bedpost.directory \
-in $w.bedpost -side top -padx 3 -pady 3 -expand yes -anchor w
#-------- ...ProbTrack... --------
tixNoteBook $w.probtrack -ipadx 5 -ipady 5
$w.probtrack add data -label "Data"
$w.probtrack add options -label "Options"
#-------- ...Mode specific options... --------
set dataf [$w.probtrack subwidget 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 target mask"
$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"
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"
$w.data.mode add command mskmat -label "Mask matrix"
}
set probtrack(xfm) ""
set probtrack(basename) "merged"
set probtrack(mask) "nodif_brain_mask"
proc probtrack_update_files { w filename } {
global probtrack
global FSLDIR
if { ($probtrack(bedpost_dir) != "") && ($probtrack(seed) != "") } {
set probtrack(dir) \
[ file join $probtrack(bedpost_dir) [ file tail [ exec $FSLDIR/bin/remove_ext $probtrack(seed) ] ] ]
}
}
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 "*.{hdr,hdr.gz}" \
-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 "*.{hdr,hdr.gz}" \
-width 35 \
-command "probtrack_update_files $w" \
-filterhist VARS(history)
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)
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] \
-side top -after $w.data.usereference_yn -padx 3 -pady 3
} else {
pack $w.data.xfm -in [$w.data.seedspace subwidget frame] \
-side top -after $w.data.usereference_yn -padx 3 -pady 3
}
} else {
pack forget $w.data.reference
pack forget $w.data.xfm
}
}
checkbutton $w.data.usereference_yn -text "Seed space is not diffusion" \
-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 "*.{hdr,hdr.gz}" \
-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)
proc probtrack_toggle_exclude { w } {
global probtrack
if { $probtrack(exclude_yn) } {
pack $w.data.exclude -in [$w.data.seedspace subwidget frame] \
-side top -after $w.data.exclude_yn -padx 3 -pady 3
} else {
pack forget $w.data.exclude
}
}
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 "*.{hdr,hdr.gz}" \
-width 35 \
-filterhist VARS(history)
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
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 "*.{hdr,hdr.gz}" \
-width 35 \
-filterhist VARS(history)
pack $w.data.lrmask \
-in [$w.data.seedspace subwidget frame] \
-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 "*.{hdr,hdr.gz}" \
-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
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
pack $w.data -in $dataf -side top -padx 3 -pady 3 -anchor nw -expand yes -fill both
#-------- ...Options... --------
set optionsf [$w.probtrack subwidget options]
tixLabelFrame $w.options -label "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
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
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
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
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) } { puts yes; set probtrack(nsteps) 20000 } else { puts no; set probtrack(nsteps) 1000 }"
set probtrack(modeuler_yn) 0
checkbutton $w.advanced.modeuler \
-text "Use modified Euler streamlining" \
-variable probtrack(modeuler_yn)
pack \
$w.advanced.usef \
$w.advanced.modeuler \
$w.advanced.nsteps \
$w.advanced.steplength \
-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 subwidget frame] -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
#-------- 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.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
set probtrack(mode) simple
fdt:probtrack_mode $w $probtrack(mode)
update idletasks
if { $tclstartupfile != "" } {
puts "Reading $tclstartupfile"
source $tclstartupfile
fdt:select_tool $w $tool
fdt:probtrack_mode $w $probtrack(mode)
}
}
proc fdt:probtrack_mode { w mode } {
global probtrack
set seedspacef [$w.data.seedspace subwidget frame]
pack forget $w.data.target
pack forget $w.data.lrmask
pack forget $w.data.usereference_yn
pack forget $w.data.reference
pack forget $w.data.seed2 pack forget $w.data.seedxyz
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 {
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 forget $w.data.dir
pack forget $w.data.seed
}
maska {
pack $w.data.seed2 -in $seedspacef -side top -after $w.data.seed
[$w.data.seed2 subwidget label] configure -text "Target image:"
}
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:"
}
seeds {
pack $w.data.target -in $w.data -side top -padx 3 -pady 3 -after $w.data.seedspace -anchor nw
}
mat2 {
pack $w.data.lrmask -in $seedspacef \
-side top -padx 3 -pady 3 -after $w.data.xfm -anchor nw
}
}
probtrack_toggle_reference $w
probtrack_toggle_exclude $w
}
proc fdt:select_tool { w tool } {
pack forget $w.ecc
pack forget $w.probtrack
pack forget $w.bedpost
pack forget $w.registration
pack forget $w.dtifit
if {$tool == "bedpost"} {
pack $w.bedpost -in $w.opts -side top -padx 3 -pady 3 -anchor nw
} elseif {$tool == "probtrack"} {
pack $w.probtrack -in $w.opts -side top -padx 3 -pady 3 -anchor nw
} elseif {$tool == "dtifit"} {
pack $w.dtifit -in $w.opts -side top -padx 3 -pady 3 -anchor nw
} elseif {$tool == "eddy_current"} {
pack $w.ecc -in $w.opts -side top -padx 3 -pady 3 -anchor nw
} elseif {$tool == "registration"} {
pack $w.registration -in $w.opts -side top -padx 3 -pady 3 -anchor nw
}
}
proc fdt_monitor { w cmd } {
global debugging
puts "$cmd"
set oldcursor [ $w configure -cursor { watch red white } ]
catch {
update idletasks
if { ! $debugging } {
set fd [ open "|$cmd" r ]
while { ( [ gets $fd line ] >= 0 ) } {
update idletasks
puts $line
}
close $fd
}
} junk $w configure -cursor $oldcursor
if { $junk != "" } {
MxPause "Errors: $junk"
}
puts "Done!"
}
proc fdt:apply { w dialog } {
global tool
global BINPATH
global FSLDIR
switch -- $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 canwite 1
if { $eddy(input) == $eddy(ouput) } {
set canwrite [ YesNoWidget "Output and input images have the same name. Overwrite input?" Yes No ]
}
if { $canwrite } {
puts "eddy_correct $eddy(input) $eddy(output) $eddy(refnum)"
catch { exec sh -c "eddy_correct $eddy(input) $eddy(output) $eddy(refnum)" } junk
}
}
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 $w "dtifit --data=$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)"
exec rm -rf $bedpost(directory)
}
}
if { $canwrite } {
puts "bedpost $bedpost(directory)"
fdt_monitor $w "bedpost $bedpost(directory)"
}
}
probtrack {
global probtrack
set errorStr ""
if { $probtrack(bedpost_dir) == "" } { set errorStr "You must specify the bedpost directory!" }
if { $probtrack(usereference_yn) && $probtrack(xfm) == "" } { set errorStr "$errorStr You must specify the seed-diff transform!" }
if { $probtrack(exclude_yn) && $probtrack(exclude) == "" } { set errorStr "$errorStr You must specify the exclusion 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)"
set tn [open "| $BINPATH/tmpnam"]
gets $tn filebase
close $tn
set logfile "${filebase}_log.tcl"
set log [open "$logfile" w]
puts $log "set tool $tool"
set copylog ""
set ssopts ""
if { $probtrack(usereference_yn) } {
set ssopts "--xfm=$probtrack(xfm)"
}
if { $probtrack(exclude_yn) == 1 } {
set ssopts "$ssopts --rubbish=$probtrack(exclude)"
puts $log "set probtrack(exclude) $probtrack(exclude)"
}
set basics "--forcedir -s $probtrack(bedpost_dir)/merged -m $probtrack(bedpost_dir)/nodif_brain_mask"
foreach entry {bedpost_dir xfm mode exclude_yn usereference_yn verbose_yn loopcheck_yn usef_yn modeuler_yn \
curvature nsteps steplength nparticles} {
puts $log "set probtrack($entry) $probtrack($entry)"
}
switch -- $probtrack(mode) {
simple {
if { $probtrack(output) == "" } { set errorStr "$errorStr You must specify the output basename!" }
if { $probtrack(usereference_yn) && $probtrack(reference) == "" } {
set errorStr "$errorStr You must specify a seed space reference image!"
}
if { $probtrack(usereference_yn) == 1 } {
set ssopts "--xfm=$probtrack(xfm) --seedref=$probtrack(reference)"
puts $log "set probtrack(reference) $probtrack(reference)"
puts $log "set probtrack(xfm) $probtrack(xfm)"
} else {
set ssopts ""
}
if { $probtrack(exclude_yn) == 1 } { set ssopts "$ssopts --rubbish=$probtrack(exclude)"
}
set fd [ open "${filebase}_coordinates.txt" w ]
$w.data.seedxyz update
if { $probtrack(units) == "mm" } {
set x $probtrack(x)
set y $probtrack(y)
set z $probtrack(z)
if { $probtrack(usereference_yn) && $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)"
puts $log "set probtrack(output) $probtrack(output)"
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)
}
}
if { $canwrite } {
set copylog "fdt.log"
fdt_monitor $w "$FSLDIR/bin/probtrack --mode=simple -x ${filebase}_coordinates.txt $basics $ssopts $flags -o $probtrack(output)"
}
puts "rm ${filebase}_coordinates.txt"
exec rm ${filebase}_coordinates.txt
}
all {
if { $probtrack(seed) == "" } { set errorStr "$errorStr You must specify a seed image!" }
if { $probtrack(dir) == "" } { set errorStr "$errorStr You must specify the output directory!" }
if { $errorStr != "" } {
MxPause $errorStr
return
}
puts $log "set probtrack(seed) $probtrack(seed)"
puts $log "set probtrack(dir) $probtrack(dir)"
set canwrite 1
if { [ file exists $probtrack(dir) ] } {
set canwrite [ YesNoWidget "Overwrite $probtrack(dir)?" Yes No ]
if { $canwrite } {
puts "rm -rf $probtrack(dir)"
exec rm -rf $probtrack(dir)
}
}
if { $canwrite } {
puts "mkdir -p $probtrack(dir)"
exec mkdir -p $probtrack(dir)
set copylog "$probtrack(dir)/fdt.log"
fdt_monitor $w "$FSLDIR/bin/probtrack --mode=seedmask -x $probtrack(seed) $basics $ssopts $flags -o fdt_paths --dir=$probtrack(dir)"
}
} masks {
if { $probtrack(seed2) == "" } { set errorStr "$errorStr You must select a target image!" }
if { $probtrack(dir) == "" } { set errorStr "$errorStr You must specify the output directory!" }
if { $errorStr != "" } {
MxPause $errorStr
return
}
puts $log "set probtrack(seed) $probtrack(seed)"
puts $log "set probtrack(seed2) $probtrack(seed2)"
puts $log "set probtrack(dir) $probtrack(dir)"
set canwrite 1
if { [ file exists $probtrack(dir) ] } {
set canwrite [ YesNoWidget "Overwrite $probtrack(dir)?" Yes No ]
if { $canwrite } {
puts "rm -rf $probtrack(dir)"
exec rm -rf $probtrack(dir)
}
}
if { $canwrite } {
puts "mkdir -p $probtrack(dir)"
exec mkdir -p $probtrack(dir)
set copylog "$probtrack(dir)/fdt.log"
fdt_monitor $w "$FSLDIR/bin/probtrack --mode=twomasks_symm --seed=$probtrack(seed) --mask2=$probtrack(seed2) $basics $ssopts $flags -o fdt_paths --dir=$probtrack(dir)"
}
}
maska {
if { $probtrack(seed) == "" } { set errorStr "$errorStr You must specify a seed image!" }
if { $probtrack(seed2) == "" } { set errorStr "$errorStr You must select a target image!" }
if { $probtrack(dir) == "" } { set errorStr "$errorStr You must specify the output directory!" }
if { $errorStr != "" } {
MxPause $errorStr
return
}
puts $log "set probtrack(seed) $probtrack(seed)"
puts $log "set probtrack(seed2) $probtrack(seed2)"
puts $log "set probtrack(dir) $probtrack(dir)"
set canwrite 1
if { [ file exists $probtrack(dir) ] } {
set canwrite [ YesNoWidget "Overwrite $probtrack(dir)?" Yes No ]
if { $canwrite } {
puts "rm -rf $probtrack(dir)"
exec rm -rf $probtrack(dir)
}
}
if { $canwrite } {
puts "mkdir -p $probtrack(dir)"
exec mkdir -p $probtrack(dir)
set copylog "$probtrack(dir)/fdt.log"
fdt_monitor $w "$FSLDIR/bin/probtrack --mode=twomasks_asymm --seed=$probtrack(seed) --mask2=$probtrack(seed2) $basics $ssopts $flags -o fdt_paths --dir=$probtrack(dir)"
}
}
seeds {
if { $probtrack(seed) == "" } { set errorStr "$errorStr You must specify a seed image!" }
if { $probtrack(dir) == "" } { set errorStr "$errorStr You must specify the output directory!" }
if { $errorStr != "" } {
MxPause $errorStr
return
}
puts $log "set probtrack(seed) $probtrack(seed)"
puts $log "set probtrack(dir) $probtrack(dir)"
set canwrite 1
if { [ file exists $probtrack(dir) ] } {
set canwrite [ YesNoWidget "Overwrite $probtrack(dir)?" Yes No ]
if { $canwrite } {
puts "rm -rf $probtrack(dir)"
exec rm -rf $probtrack(dir) }
}
if { $canwrite } {
puts "mkdir -p $probtrack(dir)"
exec mkdir -p $probtrack(dir)
puts $log "$w.data.targets load \"$probtrack(dir)/targets.txt\""
$w.data.targets save "$probtrack(dir)/targets.txt"
set copylog "$probtrack(dir)/fdt.log"
fdt_monitor $w "$FSLDIR/bin/probtrack --mode=seeds_to_targets -x $probtrack(seed) $basics $ssopts $flags --targetmasks=${probtrack(dir)}/targets.txt --dir=$probtrack(dir)"
}
}
mat1 {
if { $probtrack(seed) == "" } { set errorStr "$errorStr You must specify a seed image!" }
if { $probtrack(dir) == "" } { set errorStr "$errorStr You must specify the output directory!" }
if { $errorStr != "" } {
MxPause $errorStr
return
}
puts $log "set probtrack(seed) $probtrack(seed)"
puts $log "set probtrack(dir) $probtrack(dir)"
set canwrite 1
if { [ file exists $probtrack(dir) ] } {
set canwrite [ YesNoWidget "Overwrite $probtrack(dir)?" Yes No ]
if { $canwrite } {
puts "rm -rf $probtrack(dir)"
exec rm -rf $probtrack(dir)
}
}
if { $canwrite } {
puts "mkdir -p $probtrack(dir)"
exec mkdir -p $probtrack(dir)
set copylog "$probtrack(dir)/fdt.log"
fdt_monitor $w "$FSLDIR/bin/probtrack --mode=matrix1 -x $probtrack(seed) $basics $ssopts $flags -o fdt_matrix --dir=$probtrack(dir)"
}
}
mat2 {
if { $probtrack(seed) == "" } { set errorStr "$errorStr You must specify a seed image!" }
if { $probtrack(dir) == "" } { set errorStr "$errorStr You must specify the output directory!" }
if { $probtrack(lrmask) == "" } { set errorStr "$errorStr You must specify the low resolution mask!" }
if { $errorStr != "" } {
MxPause $errorStr
return
}
puts $log "set probtrack(seed) $probtrack(seed)"
puts $log "set probtrack(dir) $probtrack(dir)"
puts $log "set probtrack(lrmask) $probtrack(lrmask)"
set canwrite 1
if { [ file exists $probtrack(dir) ] } {
set canwrite [ YesNoWidget "Overwrite $probtrack(dir)?" Yes No ]
if { $canwrite } {
puts "rm -rf $probtrack(dir)"
exec rm -rf $probtrack(dir)
}
}
if { $canwrite } {
puts "mkdir -p $probtrack(dir)"
exec mkdir -p $probtrack(dir)
set copylog "$probtrack(dir)/fdt.log"
fdt_monitor $w "$FSLDIR/bin/probtrack --mode=matrix2 -x $probtrack(seed) $basics $ssopts --lrmask=$probtrack(lrmask) $flags -o fdt_matrix --dir=$probtrack(dir)"
}
}
mskmat {
if { $probtrack(seed) == "" } { set errorStr "$errorStr You must specify a seed image!" }
if { $probtrack(dir) == "" } { set errorStr "$errorStr You must specify the output directory!" }
if { $errorStr != "" } {
MxPause $errorStr
return
} puts $log "set probtrack(seed) $probtrack(seed)"
puts $log "set probtrack(dir) $probtrack(dir)"
set canwrite 1
if { [ file exists $probtrack(dir) ] } {
set canwrite [ YesNoWidget "Overwrite $probtrack(dir)?" Yes No ]
if { $canwrite } {
puts "rm -rf $probtrack(dir)"
exec rm -rf $probtrack(dir)
}
}
if { $canwrite } {
puts "mkdir -p $probtrack(dir)"
exec mkdir -p $probtrack(dir)
set copylog "$probtrack(dir)/fdt.log"
fdt_monitor $w "$FSLDIR/bin/probtrack --mode=maskmatrix -x $probtrack(seed) $basics $ssopts $flags -o fdt_matrix --dir=$probtrack(dir)"
}
}
}
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 "flirt -in $diff -ref $registration(struct_image) -omat $diff2str $options"
fdt_monitor $w "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 "flirt -in $registration(struct_image) -ref $registration(standard_image) -omat $str2stand $options"
fdt_monitor $w "convert_xfm -omat $stand2str -inverse $str2stand"
fdt_monitor $w "convert_xfm -omat $diff2stand -concat $str2stand $diff2str" fdt_monitor $w "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 "flirt -in $diff -ref $registration(standard_image) -omat $diff2stand $options"
fdt_monitor $w "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