bet.tcl

#

#   bet.tcl - GUI for BET - Brain Extraction Tool
#
#   Stephen Smith and Matthew Webster, FMRIB Image Analysis Group
#
#   Copyright (C) 1999-2006 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.

#{{{ setups

source [ file dirname [ info script ] ]/fslstart.tcl

set VARS(history) {}

#}}}
#{{{ bet:updatevariations

proc bet:updatevariations { w } {

    global bet

    pack forget $w.f.variations.input

    if { $bet($w,variations) == "-A2" } { 
	pack $w.f.variations.input -in $w.f.variations -side bottom -padx 5 -pady 2 -anchor s
    }
}

#}}}
#{{{ bet:select

proc bet:select { w { dummy "" } } {

    global bet

    set bet($w,input)  [ remove_ext $bet($w,input) ]
    set bet($w,output) [ remove_ext $bet($w,input) ]_brain

#    if { [ string length $bet($w,output) ] == 0 } {
#	set bet($w,output) [ file rootname $bet($w,input) ]_brain
#    }
}

#}}}
#{{{ bet:apply

proc bet:apply { w dialog } {
    global bet

    bet_proc $bet($w,input) $bet($w,output) $bet($w,segment_yn) $bet($w,overlay_yn) $bet($w,mask_yn) $bet($w,threshold_yn) $bet($w,xtopol_yn) $bet($w,cost_yn) $bet($w,skull_yn) $bet($w,fraction) $bet($w,gradient) $bet($w,c_x) $bet($w,c_y) $bet($w,c_z) $bet($w,variations) $bet($w,input2)

    update idletasks

    if {$dialog == "destroy"} {
        bet:destroy $w
    }
}

#}}}
#{{{ bet:destroy

# Summary:      Destroys bet dialog box
proc bet:destroy { w } {
    destroy $w
}

#}}}
#{{{ bet

proc bet { w } {

    #{{{ vars and setup

global bet FSLDIR argc argv PWD

toplevel $w
wm title $w "BET - Brain Extraction Tool - v2.1"
wm iconname $w "BET"
wm iconbitmap $w @${FSLDIR}/tcl/fmrib.xbm

frame $w.f

#}}}
    #{{{ input image

if { $argc > 0 && [ string length [ lindex $argv 0 ] ] > 0 } {
    set inputname [ imglob [ lindex $argv 0 ] ]
    if { [ imtest $inputname ] } {
	if { [ string first / $inputname ] == 0 || [ string first ~ $inputname ] == 0 } {
	    set bet($w,input) $inputname
	} else {
	    set bet($w,input) ${PWD}/$inputname
	}
	set bet($w,output) $bet($w,input)_brain
    }
}


FileEntry $w.f.input -textvariable bet($w,input) -label "Input image   " -title "Select the input image"  -width 50 -filedialog directory  -filetypes IMAGE -command "bet:select $w"
FileEntry $w.f.output -textvariable bet($w,output) -label "Output image" -title "Select the output image"  -width 50 -filedialog directory  -filetypes IMAGE 

#}}}
    #{{{ fractional brain threshold

set bet($w,fraction) 0.5

LabelSpinBox  $w.f.fraction -label "Fractional intensity threshold; smaller values give larger brain outline estimates" -textvariable bet($w,fraction) -range " 0.0 1.0 0.05 " 

#}}}
    #{{{ variations

frame $w.f.variations

set bet($w,variations) -default

optionMenu2 $w.f.variations.menu bet($w,variations) -command "bet:updatevariations $w" -default "Run standard brain extraction using bet2" -R "Robust brain centre estimation (iterates bet2 several times)" -S "Eye & optic nerve cleanup (can be useful in SIENA)" -B "Bias field & neck cleanup (can be useful in SIENA)" -Z "Improve BET if FOV is very small in Z" -F "Apply to 4D FMRI data" -A "Run bet2 and then betsurf to get additional skull and scalp surfaces" -A2 "As above, when also feeding in non-brain-extracted T2"

FileEntry $w.f.variations.input -textvariable bet($w,input2) -label "Input T2 image   " -title "Select T2 input image"  -width 50 -filedialog directory  -filetypes IMAGE

pack $w.f.variations.menu -in $w.f.variations -side top -anchor w

#}}}
    #{{{ Advanced Options

collapsible frame $w.f.opts -title "Advanced options"
set bet($w,xtopol_yn) 0
set bet($w,cost_yn) 0

#{{{ generate segmented image

frame $w.f.opts.segment

label $w.f.opts.segment.label -text "Output brain-extracted image"

set bet($w,segment_yn) 1
checkbutton $w.f.opts.segment.yn -variable bet($w,segment_yn)

pack $w.f.opts.segment.label $w.f.opts.segment.yn -in $w.f.opts.segment -side left

#}}}
#{{{ generate binary brain image

frame $w.f.opts.mask

label $w.f.opts.mask.label -text "Output binary brain mask image"

set bet($w,mask_yn) 0
checkbutton $w.f.opts.mask.yn -variable bet($w,mask_yn)

pack $w.f.opts.mask.label $w.f.opts.mask.yn -in $w.f.opts.mask -side left

#}}}
#{{{ apply thresholding

frame $w.f.opts.threshold

label $w.f.opts.threshold.label -text "Apply thresholding to brain and mask image"

set bet($w,threshold_yn) 0
checkbutton $w.f.opts.threshold.yn -variable bet($w,threshold_yn)

pack $w.f.opts.threshold.label $w.f.opts.threshold.yn -in $w.f.opts.threshold -side left

#}}}
#{{{ generate skull image

frame $w.f.opts.skull

label $w.f.opts.skull.label -text "Output exterior skull surface image"
set bet($w,skull_yn) 0
checkbutton $w.f.opts.skull.yn -variable bet($w,skull_yn)

pack $w.f.opts.skull.label $w.f.opts.skull.yn -in $w.f.opts.skull -side left

#}}}
#{{{ generate overlay image

frame $w.f.opts.overlay

label $w.f.opts.overlay.label -text "Output brain surface overlaid onto original image"

set bet($w,overlay_yn) 0
checkbutton $w.f.opts.overlay.yn -variable bet($w,overlay_yn)

pack $w.f.opts.overlay.label $w.f.opts.overlay.yn -in $w.f.opts.overlay -side left

#}}}
#{{{ gradient brain threshold

set bet($w,gradient) 0

LabelSpinBox $w.f.opts.gradient -label "Threshold gradient; positive values give larger brain outline at bottom, smaller at top" -textvariable bet($w,gradient) -range " -1.0 1.0 0.05 " 

#}}}
#{{{ co-ordinates for centre of initial brain surface sphere

frame $w.f.opts.c

set bet($w,c_x) 0
LabelSpinBox  $w.f.opts.c_x -label "Coordinates (voxels) for centre of initial brain surface sphere " -textvariable bet($w,c_x) -range " 0.0 10000 0.05 " -width 3
set bet($w,c_y) 0
LabelSpinBox  $w.f.opts.c_y -label " Y " -textvariable bet($w,c_y) -range " 0.0 10000 0.05 " -width 3
set bet($w,c_z) 0
LabelSpinBox  $w.f.opts.c_z -label " Z " -textvariable bet($w,c_z) -range " 0.0 10000 0.05 " -width 3

pack $w.f.opts.c_x $w.f.opts.c_y $w.f.opts.c_z  -in $w.f.opts.c  -side left

#}}}

pack $w.f.opts.segment $w.f.opts.mask $w.f.opts.threshold $w.f.opts.skull $w.f.opts.overlay -in $w.f.opts.b -side top -anchor w -pady 0
pack $w.f.opts.gradient $w.f.opts.c -in $w.f.opts.b -side top -anchor w -pady 5

#}}}

    pack $w.f.input $w.f.output $w.f.fraction $w.f.variations $w.f.opts -in $w.f -side top -padx 5 -pady 2 -anchor w

    #{{{ Button Frame

    frame $w.btns
    frame $w.btns.b -relief raised -borderwidth 1
 
    button $w.apply     -command "bet:apply $w keep" \
        -text "Go" -width 5
    bind $w.apply <Return> {
        [winfo toplevel %W].apply invoke}
 
    button $w.cancel    -command "bet:destroy $w" \
        -text "Exit" -width 5
    bind $w.cancel <Return> {
        [winfo toplevel %W].cancel invoke}
 
    button $w.help -command "FmribWebHelp file: ${FSLDIR}/doc/redirects/bet.html" \
            -text "Help" -width 5
    bind $w.help <Return> {
        [winfo toplevel %W].help invoke}

    pack $w.btns.b -side bottom -fill x
    pack $w.apply $w.cancel $w.help -in $w.btns.b \
        -side left -expand yes -padx 3 -pady 10 -fill y
 
    pack $w.f $w.btns -expand yes -fill both

#}}}
}

#}}}

wm withdraw .
bet .rename
tkwait window .rename