diff --git a/Makefile b/Makefile
index 990faa5da2220f920a23f87fbcff896d2760fc6c..c13823298dd7cab7716a99d2d3bc6388c57ff093 100644
--- a/Makefile
+++ b/Makefile
@@ -5,7 +5,6 @@ PROJNAME = fdt
USRINCFLAGS = -I${INC_NEWMAT} -I${INC_NEWRAN} -I${INC_CPROB} -I${INC_PROB} -I${INC_ZLIB}
USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_NEWRAN} -L${LIB_CPROB} -L${LIB_PROB} -L${LIB_ZLIB}
-
DLIBS = -lmeshclass -lbint -lnewimage -lutils -lmiscmaths -lnewmat -lnewran -lfslio -lniftiio -lznz -lcprob -lprob -lm -lz
#DLIBS = -lbint -lnewimage -lutils -lmiscmaths -lnewmat -lfslio -lniftiio -lznz -lcprob -lprob -lm -lz
@@ -48,7 +47,7 @@ TESTOBJS=testfile.o
VECREGOBJS=vecreg.o
SGEBEDPOST = bedpost bedpost_datacheck
-SGEBEDPOSTX = bedpostX bedpostX_postproc.sh bedpostX_preproc.sh bedpostX_single_slice.sh
+SGEBEDPOSTX = bedpostx bedpostx_postproc.sh bedpostx_preproc.sh bedpostx_single_slice.sh
SCRIPTS = eddy_correct zeropad maskdyads ${SGEBEDPOST} ${SGEBEDPOSTX}
FSCRIPTS = correct_and_average ocmr_preproc
@@ -58,7 +57,7 @@ XFILES = dtifit ccops probtrack find_the_biggest medianfilter diff_pvm make_dyad
FXFILES = reord_OM sausages replacevols fdt_matrix_ops probtrackx indexer
-RUNTCLS = Fdt Fdtx
+RUNTCLS = Fdt
all: ${XFILES} ${FXFILES}
@@ -113,14 +112,3 @@ ${TEST}: ${TESTOBJS}
${VECREG}: ${VECREGOBJS}
${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${VECREGOBJS} ${DLIBS}
-
-
-
-
-
-
-
-
-
-
-
diff --git a/bedpost b/bedpost
index c2565a63b61303ba0e515a97bb3f6ca42c5daa1f..11f15ca8e030487aa988e66b1ba70843c27ed702 100755
--- a/bedpost
+++ b/bedpost
@@ -1,13 +1,11 @@
#!/bin/sh
-# Copyright (C) 2004 University of Oxford
+# Copyright (C) 2007 University of Oxford
#
# SHCOPYRIGHT
-
echo
-echo "Warning - bedpost has been deprecated! Please use bedpostX instead."
-[ -z "$@" ] && ${FSLDIR}/bin/bedpostX
-echo "Executing \"bedpostX $@ -n 1\" instead."
+echo "Error - bedpost has been superceded by bedpostx! Please instead run:"
+echo bedpostx $@ -n 1
echo
-${FSLDIR}/bin/bedpostX $@ -n 1
+
diff --git a/bedpostx b/bedpostx
index ed404f182da3e71dfdf6653085171ca73dd63853..ebf7df1cb5a7ebacc09bc9ce26f2cb918648589e 100755
--- a/bedpostx
+++ b/bedpostx
@@ -14,7 +14,7 @@ fi
Usage() {
echo ""
- echo "Usage: bedpostX <subject directory> [options]"
+ echo "Usage: bedpostx <subject directory> [options]"
echo ""
echo "expects to find bvals and bvecs in subject directory"
echo "expects to find data nodif_brain_mask nodif in subject directory"
@@ -93,7 +93,7 @@ if [ `${FSLDIR}/bin/imtest ${subjdir}/nodif_brain_mask` -eq 0 ]; then
exit 1
fi
-echo Making bedpostX directory structure
+echo Making bedpostx directory structure
mkdir -p ${subjdir}.bedpostX/
mkdir -p ${subjdir}.bedpostX/diff_slices
@@ -103,19 +103,19 @@ mkdir -p ${subjdir}.bedpostX/xfms
mailto=`whoami`@fmrib.ox.ac.uk
echo Queuing preprocessing stages
-preprocid=`${FSLDIR}/bin/fsl_sub -F -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostX_preproc.sh ${subjdir}`
+preprocid=`${FSLDIR}/bin/fsl_sub -F -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_preproc.sh ${subjdir}`
echo Queuing parallel processing stage
nslices=`${FSLDIR}/bin/fslval ${subjdir}/data dim3`
[ -f ${subjdir}.bedpostX/commands.txt ] && rm ${subjdir}.bedpostX/commands.txt
for ((slice=0; slice < $nslices; slice++)) ; do
- echo "${FSLDIR}/bin/bedpostX_single_slice.sh $subjdir $nfibres $fudge $burnin $slice" \
+ echo "${FSLDIR}/bin/bedpostx_single_slice.sh $subjdir $nfibres $fudge $burnin $slice" \
>> ${subjdir}.bedpostX/commands.txt
done
bedpostid=`${FSLDIR}/bin/fsl_sub -j $preprocid -l ${subjdir}.bedpostX/logs -M $mailto -N bedpostx -t ${subjdir}.bedpostX/commands.txt`
echo Queuing post processing stage
-mergeid=`${FSLDIR}/bin/fsl_sub -j $bedpostid -F -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostX_postproc.sh $subjdir`
+mergeid=`${FSLDIR}/bin/fsl_sub -j $bedpostid -F -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_postproc.sh $subjdir`
if [ "x$SGE_ROOT" != "x" ]; then
echo
diff --git a/fdt.tcl b/fdt.tcl
index 2a813915720f190ba1d9f1c91b65d50acea94e1f..5560cdfea977ff57333c70fc9d12e5cc13a150fd 100644
--- a/fdt.tcl
+++ b/fdt.tcl
@@ -1,3 +1,4 @@
+
# FSL interface for FDT (BEDPOST and ProbTrack)
#
# Timothy Behrens, Heidi Johansen-Berg, Dave Flitney and Matthew Webster FMRIB Image Analysis Group
@@ -8,11 +9,12 @@
#TO DO replace -filetypes * with -filetypes { } for directory selectors
source [ file dirname [ info script ] ]/fslstart.tcl
+option add *FileEntry*Entry*width 35
set TCLPATH [file dirname [ info script ] ]
regsub tcl $TCLPATH bin BINPATH
regsub tcl $TCLPATH doc/fdt HTMLPATH
-set VERSION "1.0a"
+set VERSION "2.0"
proc mm_to_voxels { X Y Z mask } {
@@ -34,9 +36,6 @@ proc mm_to_voxels { X Y Z mask } {
proc fdt:dialog { w tclstartupfile } {
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] {
@@ -53,7 +52,7 @@ proc fdt:dialog { w tclstartupfile } {
#-------- Stage and Mode Options --------
frame $w.tool
- 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"
+ optionMenu2 $w.tool.menu probtrack(tool) -command "fdt:select_tool $w" eddy_current "Eddy current correction" bedpost "BEDPOSTX Estimation of diffusion parameters" registration "Registration" probtrack "ProbTrackX Probabilistic tracking" xutilssx "----------------------------------------------------" dtifit "DTIFit Reconstruct diffusion tensors"
$w.tool.menu.menu entryconfigure 4 -state disabled -background black
pack $w.tool.menu -side left -pady 3 -padx 6 -anchor nw
@@ -77,7 +76,7 @@ proc fdt:dialog { w tclstartupfile } {
}
}
- FileEntry $w.registration.directory -textvariable registration(directory) -label "BEDPOST directory:" -title "Choose directory" -width 35 -filetypes * -command "registration_set_directory $w"
+ FileEntry $w.registration.directory -textvariable registration(directory) -label "BEDPOST directory:" -title "Choose directory" -filetypes * -command "registration_set_directory $w"
frame $w.registration.struct
checkbutton $w.registration.struct.yn -variable registration(struct_yn) -command "registration_packframe $w"
@@ -128,20 +127,20 @@ proc fdt:dialog { w tclstartupfile } {
set eddy(output) [ file join [file dirname $eddy(input)] data ]
}
- FileEntry $w.ecc.input -textvariable eddy(input) -label "Diffusion weighted data:" -title "Choose diffusion weighted image" -width 35 -filetypes IMAGE -command "ecc_update_files $w"
+ FileEntry $w.ecc.input -textvariable eddy(input) -label "Diffusion weighted data:" -title "Choose diffusion weighted image" -filetypes IMAGE -command "ecc_update_files $w"
- FileEntry $w.ecc.output -textvariable eddy(output) -label "Corrected output data:" -title "Choose output image name" -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" -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 --------
+ #------- DTIFit --------
frame $w.dtifit
- FileEntry $w.dtifit.directory -textvariable dtifit(directory) -label "Input directory:" -title "Choose directory" -width 35 -command "set_working_directory dtifit(cwd)"
+ FileEntry $w.dtifit.directory -textvariable dtifit(directory) -label "Input directory:" -title "Choose directory" -command "set_working_directory dtifit(cwd)"
proc dtifit_toggle_expert { w } {
global dtifit
@@ -174,93 +173,96 @@ proc fdt:dialog { w tclstartupfile } {
set_working_directory dtifit(cwd) $dtifit(input)
}
- set dtifit(cwd) $PWD
+ set dtifit(cwd) [ pwd ]
#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
+ option add *dtifit.expert.FileEntry*labf*width 27
+ FileEntry $w.dtifit.expert.input -textvariable dtifit(input) -label "Diffusion weighted data:" -title "Choose diffusion weighted image" -filetypes IMAGE -command "dtifit_update_files $w"
+ FileEntry $w.dtifit.expert.mask -textvariable dtifit(mask) -label "BET binary brain mask:" -title "Choose BET brain mask file" -filetypes IMAGE -command "set_working_directory dtifit(cwd)"
+ FileEntry $w.dtifit.expert.output -textvariable dtifit(output) -label "Output basename:" -title "Choose output base name" -filetypes * -command "set_working_directory dtifit(cwd)"
+ FileEntry $w.dtifit.expert.bvecs -textvariable dtifit(bvecs) -label "Gradient directions:" -title "Choose bvecs file" -filetypes * -command "set_working_directory dtifit(cwd)"
+ FileEntry $w.dtifit.expert.bvals -textvariable dtifit(bvals) -label "b values:" -title "Choose bvals file" -command "set_working_directory dtifit(cwd)"
pack $w.dtifit.expert.input $w.dtifit.expert.mask $w.dtifit.expert.output \
$w.dtifit.expert.bvecs $w.dtifit.expert.bvals \
- -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
+ pack $w.dtifit.directory $w.dtifit.expert_yn -side top -padx 3 -pady 3 -expand yes -anchor w
+
#------- BEDPOST --------
frame $w.bedpost
- FileEntry $w.bedpost.directory -textvariable bedpost(directory) -label "Input directory:" -title "Choose directory" -width 35 -filetypes * -command "set_working_directory dtifit(cwd)"
+ FileEntry $w.bedpost.directory -textvariable bedpost(directory) -label "Input directory:" -title "Choose directory" -filetypes * -command "set_working_directory dtifit(cwd)"
- set bedpost(ecc_yn) 0
-
- pack $w.bedpost.directory \
- -in $w.bedpost -side top -padx 3 -pady 3 -expand yes -anchor w
+ collapsible frame $w.bedpost.advanced -title "Advanced Options"
+ set bedpost(nfibres) 2
+ set bedpost(weight) 1
+ set bedpost(burnin) 1000
+ LabelSpinBox $w.bedpost.advanced.nfibres -label "Fibres " -textvariable bedpost(nfibres) -range {1 1000000000 1 }
+ LabelSpinBox $w.bedpost.advanced.weight -label "Weight " -textvariable bedpost(weight) -range {0.0 100000000.0 1 }
+ LabelSpinBox $w.bedpost.advanced.burnin -label "Burn In" -textvariable bedpost(burnin) -range {1 1000000000 1 }
- #-------- ...ProbTrack... --------
+ set bedpost(ecc_yn) 0
+ pack $w.bedpost.advanced.nfibres $w.bedpost.advanced.weight $w.bedpost.advanced.burnin -in $w.bedpost.advanced.b -anchor w
+ pack $w.bedpost.directory $w.bedpost.advanced -side top -padx 3 -pady 3 -expand yes -anchor w
+ #-------- ProbTrack --------
NoteBook $w.probtrack -bd 2 -tabpady {5 10} -arcradius 3
$w.probtrack insert 0 data -text "Data"
$w.probtrack insert 1 options -text "Options"
-
- #-------- ...Mode specific options... --------
-
- set dataf [$w.probtrack getframe data]
+ #-------- Mode specific option --------
frame $w.data
+ FileEntry $w.data.directory -textvariable probtrack(bedpost_dir) -label "BEDPOST directory" -title "Choose BEDPOST directory" -filetypes * -command "probtrack_update_files $w"
- LabelFrame $w.data.mode -text "Mode: "
-
- if { [ file exists [ file join $FSLDIR bin reord_OM ] ] } {
- 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
+ TitleFrame $w.data.seed -text "Seed Space"
+ optionMenu2 $w.data.seed.menu probtrack(mode) -command "fdt:probtrack_mode $w" simple "Single voxel" seedmask "Single mask" network "Multiple masks"
+ set probtrack(x) 0
+ set probtrack(y) 0
+ set probtrack(z) 0
+ set probtrack(units) vox
+ #Co-ordinate edit frame
+ frame $w.data.seed.voxel
+ LabelSpinBox $w.data.seed.voxel.x -label "X" -textvariable probtrack(x) -range {-1000000 1000000 1 }
+ LabelSpinBox $w.data.seed.voxel.y -label "Y" -textvariable probtrack(y) -range {-1000000 1000000 1 }
+ LabelSpinBox $w.data.seed.voxel.z -label "Z" -textvariable probtrack(z) -range {-1000000 1000000 1 }
+ radiobutton $w.data.seed.voxel.vox -text "vox" -value vox -variable probtrack(units)
+ radiobutton $w.data.seed.voxel.mm -text "mm" -value mm -variable probtrack(units)
+ FileEntry $w.data.seed.reference -textvariable probtrack(reference) -label "Seed reference image:" -title "Choose reference image" -filetypes IMAGE
- set probtrack(xfm) ""
- set probtrack(basename) "merged"
- set probtrack(mask) "nodif_brain_mask"
+ option add *seed*FileEntry*labf*width 24
- proc probtrack_update_files { w filename } {
- global probtrack
- global FSLDIR
+ frame $w.data.seed.ssf
+ checkbutton $w.data.seed.ssf.ssd -text "Seed space is not diffusion" -variable probtrack(usereference_yn) -command " pack forget $w.data.seed.ssf.xfm ; if { \$probtrack(usereference_yn) } { pack $w.data.seed.ssf.xfm } ; $w.probtrack compute_size"
+ FileEntry $w.data.seed.ssf.xfm -textvariable probtrack(xfm) -label "Select Seed to diff transform" -title "Select seed-space to DTI-space transformation matrix" -filetypes *
+ pack $w.data.seed.ssf.ssd -side top -anchor nw
- if { ($probtrack(bedpost_dir) != "") && ($probtrack(seed) != "") } {
- set probtrack(dir) \
- [ file join $probtrack(bedpost_dir) [ file tail [ exec $FSLDIR/bin/remove_ext $probtrack(seed) ] ] ]
- }
- }
+
- 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
+ frame $w.data.seed.bcf
+ checkbutton $w.data.seed.bcf.bc -text "Blind Classification:" -variable probtrack(bcyn) -command " pack forget $w.data.seed.bcf.w ; if { \$probtrack(bcyn) } { pack $w.data.seed.bcf.w -side left} ; $w.probtrack compute_size"
+ set probtrack(scale) 5
+ LabelSpinBox $w.data.seed.bcf.w -label "Low resolution rescaling factor" -textvariable probtrack(scale) -range {1 1000000 1 }
+ pack $w.data.seed.bcf.bc -side left -anchor w
+
+ pack $w.data.seed.voxel.x $w.data.seed.voxel.y $w.data.seed.voxel.z $w.data.seed.voxel.vox $w.data.seed.voxel.mm -side left -padx 2
+ pack $w.data.seed.voxel $w.data.seed.ssf -in $w.data.seed.f -side bottom -anchor w -pady 2
+ pack $w.data.seed.menu $w.data.seed.reference -in $w.data.seed.f -side left -anchor w -pady 2
+
+ TitleFrame $w.data.seed.target -text "Multiple Masks"
+ listbox $w.data.seed.targets -height 6 -width 50 -yscrollcommand "$w.data.seed.sb set"
+ scrollbar $w.data.seed.sb -command "$w.data.seed.targets yview "
+ frame $w.data.seed.tb
+ button $w.data.seed.tb.add -text "Add Image" -command "feat_file:setup_dialog $w a a a [namespace current] IMAGE {Select File} {fdt_add $w $w.data.seed.targets} {}"
+ button $w.data.seed.tb.del -text "Remove Image" -command "fdt_sub $w $w.data.seed.targets"
+ button $w.data.seed.tb.imp -text "Load List" -command "feat_file:setup_dialog $w a a a [namespace current] * {Select File} {fdt_imp $w $w.data.seed.targets} {}"
+ button $w.data.seed.tb.exp -text "Save List" -command "feat_file:setup_dialog $w a a a [namespace current] * {Select File} {fdt_exp $w $w.data.seed.targets} {}"
+ pack $w.data.seed.tb.add $w.data.seed.tb.del $w.data.seed.tb.imp $w.data.seed.tb.exp -side left
+ pack $w.data.seed.tb -in [$w.data.seed.target getframe ] -side bottom -expand yes -fill x -anchor w -padx 3 -pady 3
+ pack $w.data.seed.targets $w.data.seed.sb -in [$w.data.seed.target getframe ] -side left -expand yes -fill y -anchor w -padx 3 -pady 3
+
+ TitleFrame $w.data.targets -text "Optional Targets"
proc fdt_add { w listbox filename } {
set filename [ fix_cygwin_filename $filename ]
@@ -299,143 +301,108 @@ proc fdt:dialog { w tclstartupfile } {
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
+ frame $w.data.targets.wf
+ checkbutton $w.data.targets.wf.sct -text "Waypoints masks" -variable probtrack(waypoint_yn) -command " pack forget $w.data.targets.wf.tf ; if { \$probtrack(waypoint_yn) } { pack $w.data.targets.wf.tf } ; $w.probtrack compute_size"
+ TitleFrame $w.data.targets.wf.tf -text "Waypoints"
+ listbox $w.data.targets.wf.tf.targets -height 6 -width 50 -yscrollcommand "$w.data.targets.wf.tf.sb set"
+ scrollbar $w.data.targets.wf.tf.sb -command "$w.data.targets.wf.tf.targets yview "
+ frame $w.data.targets.wf.tf.tb
+ button $w.data.targets.wf.tf.tb.add -text "Add Image" -command "feat_file:setup_dialog $w a a a [namespace current] IMAGE {Select File} {fdt_add $w $w.data.targets.wf.tf.targets} {}"
+ button $w.data.targets.wf.tf.tb.del -text "Remove Image" -command "fdt_sub $w $w.data.targets.wf.tf.targets"
+ button $w.data.targets.wf.tf.tb.imp -text "Load List" -command "feat_file:setup_dialog $w a a a [namespace current] * {Select File} {fdt_imp $w $w.data.targets.wf.tf.targets} {}"
+ button $w.data.targets.wf.tf.tb.exp -text "Save List" -command "feat_file:setup_dialog $w a a a [namespace current] * {Select File} {fdt_exp $w $w.data.targets.wf.tf.targets} {}"
+ pack $w.data.targets.wf.tf.tb.add $w.data.targets.wf.tf.tb.del $w.data.targets.wf.tf.tb.imp $w.data.targets.wf.tf.tb.exp -side left
+ pack $w.data.targets.wf.tf.tb -in [$w.data.targets.wf.tf getframe ] -side bottom -expand yes -fill x -anchor w -padx 3 -pady 3
+ pack $w.data.targets.wf.tf.targets $w.data.targets.wf.tf.sb -in [$w.data.targets.wf.tf getframe ] -side left -expand yes -fill y -anchor w -padx 3 -pady 3
+ pack $w.data.targets.wf.sct -side top -anchor nw
+ pack $w.data.targets.wf
+
+ option add *targets*Checkbutton*width 18
+ option add *targets*Checkbutton*anchor w
+ frame $w.data.targets.ef
+ checkbutton $w.data.targets.ef.srt -text "Exclusion mask" -variable probtrack(exclude_yn) -command " pack forget $w.data.targets.ef.rubbish ; if { \$probtrack(exclude_yn) } { pack $w.data.targets.ef.rubbish } ; $w.probtrack compute_size"
+ FileEntry $w.data.targets.ef.rubbish -textvariable probtrack(exclude) -title "Select exclusion image" -filetypes IMAGE
+ pack $w.data.targets.ef.srt -side left
+
+ frame $w.data.targets.sf
+ checkbutton $w.data.targets.sf.sst -text "Termination mask" -variable probtrack(terminate_yn) -command " pack forget $w.data.targets.sf.stop ; if { \$probtrack(terminate_yn) } { pack $w.data.targets.sf.stop } ; $w.probtrack compute_size"
+ FileEntry $w.data.targets.sf.stop -textvariable probtrack(stop) -title "Select termination image" -filetypes IMAGE
+ pack $w.data.targets.sf.sst -side left
+
+ frame $w.data.targets.cf
+ checkbutton $w.data.targets.cf.sct -text "Classification targets" -variable probtrack(classify_yn) -command " pack forget $w.data.targets.cf.tf ; if { \$probtrack(classify_yn) } { pack $w.data.targets.cf.tf } ; $w.probtrack compute_size"
+ TitleFrame $w.data.targets.cf.tf -text "Classification"
+ listbox $w.data.targets.cf.tf.targets -height 6 -width 50 -yscrollcommand "$w.data.targets.cf.tf.sb set"
+ scrollbar $w.data.targets.cf.tf.sb -command "$w.data.targets.cf.tf.targets yview "
+ frame $w.data.targets.cf.tf.tb
+ button $w.data.targets.cf.tf.tb.add -text "Add Image" -command "feat_file:setup_dialog $w a a a [namespace current] IMAGE {Select File} {fdt_add $w $w.data.targets.cf.tf.targets} {}"
+ button $w.data.targets.cf.tf.tb.del -text "Remove Image" -command "fdt_sub $w $w.data.targets.cf.tf.targets"
+ button $w.data.targets.cf.tf.tb.imp -text "Load List" -command "feat_file:setup_dialog $w a a a [namespace current] * {Select File} {fdt_imp $w $w.data.targets.cf.tf.targets} {}"
+ button $w.data.targets.cf.tf.tb.exp -text "Save List" -command "feat_file:setup_dialog $w a a a [namespace current] * {Select File} {fdt_exp $w $w.data.targets.cf.tf.targets} {}"
+ pack $w.data.targets.cf.tf.tb.add $w.data.targets.cf.tf.tb.del $w.data.targets.cf.tf.tb.imp $w.data.targets.cf.tf.tb.exp -side left
+ pack $w.data.targets.cf.tf.tb -in [$w.data.targets.cf.tf getframe ] -side bottom -expand yes -fill x -anchor w -padx 3 -pady 3
+ pack $w.data.targets.cf.tf.targets $w.data.targets.cf.tf.sb -in [$w.data.targets.cf.tf getframe ] -side left -expand yes -fill y -anchor w -padx 3 -pady 3
+ pack $w.data.targets.cf.sct -side top -anchor nw
+ pack $w.data.targets.cf
+
+
+ pack $w.data.targets.wf $w.data.targets.ef $w.data.targets.sf $w.data.targets.cf -in $w.data.targets.f -anchor w
- set probtrack(x) 0
- set probtrack(y) 0
- set probtrack(z) 0
- set probtrack(units) vox
-
- #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(y) -range {-1000000 1000000 1 } -width 6
- LabelSpinBox $w.data.seedxyz.z -label "Z" -textvariable probtrack(z) -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 getframe ] \
- -side top -after $w.data.usereference_yn -padx 3 -pady 3
- } else {
- pack $w.data.xfm -in [$w.data.seedspace getframe ] \
- -side top -after $w.data.usereference_yn -padx 3 -pady 3
- }
- } else {
- pack forget $w.data.reference
- pack forget $w.data.xfm
- }
- $w.probtrack compute_size
- }
- checkbutton $w.data.usereference_yn -text "Seed space is not diffusion" \
- -variable probtrack(usereference_yn) \
- -command "probtrack_toggle_reference $w"
- 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
+ set probtrack(xfm) ""
+ set probtrack(basename) "merged"
+ set probtrack(mask) "nodif_brain_mask"
- proc probtrack_toggle_exclude { w } {
+ proc probtrack_update_files { w filename } {
global probtrack
+ global FSLDIR
- if { $probtrack(exclude_yn) } {
- pack $w.data.exclude -in [$w.data.seedspace getframe ] \
- -side top -after $w.data.exclude_yn -padx 3 -pady 3
- } else {
- pack forget $w.data.exclude
+ if { ($probtrack(bedpost_dir) != "") && ($probtrack(reference) != "") } {
+ set probtrack(output) \
+ [ file join $probtrack(bedpost_dir) [ file tail [ exec $FSLDIR/bin/remove_ext $probtrack(reference) ] ] ]
}
- $w.probtrack compute_size
}
- checkbutton $w.data.exclude_yn -text "Use exclusion mask" -variable probtrack(exclude_yn) \
- -command "probtrack_toggle_exclude $w"
-
- 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 getframe ] -padx 3 -pady 3 -side top -anchor w
-
- probtrack_toggle_reference $w
- probtrack_toggle_exclude $w
-
- 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 getframe ] \
- -side top -padx 3 -pady 3 -anchor w
-
- TitleFrame $w.data.output -text "Ouput"
+ FileEntry $w.data.dir -textvariable probtrack(output) -label "Output directory:" -title "Name the output directory" -filetypes *
- FileEntry $w.data.dir -textvariable probtrack(dir) -label "Output directory:" -title "Name the output directory" -width 35 -filetypes *
+ pack $w.data.directory $w.data.seed $w.data.targets $w.data.dir -padx 3 -pady 3 -anchor nw
- 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
-
- pack $w.data -in $dataf -side top -padx 3 -pady 3 -anchor nw -expand yes -fill both
+ pack $w.data -in [$w.probtrack getframe data] -padx 3 -pady 3 -anchor nw -expand yes -fill both
#-------- ...Options... --------
-
- set optionsf [$w.probtrack getframe options]
-
TitleFrame $w.options -text "Basic Options"
- checkbutton $w.options.verbose \
- -text "Verbose" \
- -variable probtrack(verbose_yn)
+ checkbutton $w.options.verbose -text "Verbose" -variable probtrack(verbose_yn)
set probtrack(nparticles) 5000
LabelSpinBox $w.options.nparticles -label "Number of samples" -textvariable probtrack(nparticles) -range {1 1e24 100 } -width 6
set probtrack(curvature) 0.2
- LabelSpinBox $w.options.curvature -label "Curvature threshold" -textvariable probtrack(curvature) -range {0.0 1.0 0.01 } -width 4
+ LabelSpinBox $w.options.curvature -label "Curvature threshold" -textvariable probtrack(curvature) -range {0.0 1.0 0.01 }
set probtrack(loopcheck_yn) 1
- checkbutton $w.options.loopcheck \
- -text "Loopcheck" \
- -variable probtrack(loopcheck_yn)
+ checkbutton $w.options.loopcheck -text "Loopcheck" -variable probtrack(loopcheck_yn)
- collapsible frame $w.advanced -title "Advanced Options"
+ collapsible frame $w.advanced -title "Advanced Options" -command "$w.probtrack compute_size; set dummy"
set probtrack(nsteps) 2000
LabelSpinBox $w.advanced.nsteps -label "Maximum number of steps" -textvariable probtrack(nsteps) -range {2 1000000 10 } -width 6
set probtrack(steplength) 0.5
- LabelSpinBox $w.advanced.steplength -label "Step length (mm)" -textvariable probtrack(steplength) -range {0 10000 0.1} -width 4
+ LabelSpinBox $w.advanced.steplength -label "Step length (mm)" -textvariable probtrack(steplength) -range {0.001 10000.0 0.1}
set probtrack(modeuler_yn) 0
- checkbutton $w.advanced.modeuler \
- -text "Use modified Euler streamlining" \
- -variable probtrack(modeuler_yn)
+ checkbutton $w.advanced.modeuler -text "Use modified Euler streamlining" -variable probtrack(modeuler_yn)
- pack \
- $w.advanced.modeuler \
- $w.advanced.nsteps \
- $w.advanced.steplength \
- -in $w.advanced.b -side top -pady 3 -padx 6 -anchor nw
+ set probtrack(pd) 0
+ checkbutton $w.advanced.pd -text "Use Distance correction" -variable probtrack(pd)
+
+ set probtrack(usef_yn) 0
+ checkbutton $w.advanced.usef -text "Use anisotropy to constrain tracking" -variable probtrack(usef_yn)
+
+ pack $w.advanced.modeuler $w.advanced.nsteps $w.advanced.steplength $w.advanced.usef $w.advanced.pd -in $w.advanced.b -side top -pady 3 -padx 6 -anchor nw
pack \
$w.options.nparticles \
@@ -444,7 +411,7 @@ proc fdt:dialog { w tclstartupfile } {
$w.options.loopcheck \
-in [$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
+ pack $w.options $w.advanced -in [$w.probtrack getframe options] -side top -pady 3 -padx 6 -anchor nw -expand yes -fill both
#-------- Buttons --------
@@ -491,46 +458,25 @@ proc fdt:dialog { w tclstartupfile } {
proc fdt:probtrack_mode { w } {
global probtrack
- set seedspacef [$w.data.seedspace getframe ]
-
- 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.waypoint
- 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 configure -label "Seed image:"
- pack $w.data.dir -in [$w.data.output getframe ] -side top -padx 3 -pady 3 -anchor nw
+ pack forget $w.data.seed.voxel $w.data.seed.ssf $w.data.seed.menu $w.data.seed.reference $w.data.seed.bcf $w.data.seed.target $w.data.targets.cf
+ $w.data.dir configure -label "Output directory:" -title "Name the output directory" -filetypes *
switch -- $probtrack(mode) {
simple {
- pack $w.data.seedxyz -in $seedspacef -side top -padx 3 -pady 3 -before $w.data.usereference_yn -anchor nw
- 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 getframe] -side top -padx 3 -pady 3 -anchor nw
- pack forget $w.data.dir
- pack forget $w.data.seed
+ pack $w.data.seed.ssf $w.data.seed.voxel -in $w.data.seed.f -side bottom -anchor w -pady 2
+ pack $w.data.seed.menu $w.data.seed.reference -in $w.data.seed.f -side left -anchor w -pady 2
+ $w.data.seed.reference configure -label "Seed reference image:" -title "Choose reference image"
+ $w.data.dir configure -label "Output file:" -title "Name the output file" -filetypes IMAGE
+ }
+ seedmask {
+ pack $w.data.seed.ssf $w.data.seed.bcf -in $w.data.seed.f -side bottom -anchor w -pady 2
+ pack $w.data.seed.menu $w.data.seed.reference -in $w.data.seed.f -side left -anchor w -pady 2
+ pack $w.data.targets.cf -in $w.data.targets.f -anchor w
+ $w.data.seed.reference configure -label "Mask image:" -title "Choose mask image"
}
- maska {
- pack $w.data.waypoint -in $w.data -side top -padx 3 -pady 3 -after $w.data.seedspace -anchor nw
- }
- masks {
- pack $w.data.seed2 -in $seedspacef -side top -after $w.data.seed
- $w.data.seed configure -label "Mask image 1:"
- $w.data.seed2 configure -label "Mask image 2:"
+ network {
+ pack $w.data.seed.target $w.data.seed.ssf $w.data.seed.menu -in $w.data.seed.f -side bottom -anchor w -pady 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
$w.probtrack compute_size
}
@@ -554,7 +500,7 @@ proc fdt:select_tool { w } {
}
}
proc fdt_monitor_short { w cmd } {
- global debugging OSFLAVOUR
+ global debugging OSFLAVOUR FSLPARALLEL
puts "$cmd"
@@ -623,9 +569,7 @@ proc fdt_monitor { w cmd } {
proc fdt:apply { w dialog } {
- global probtrack
- global BINPATH
- global FSLDIR
+ global probtrack BINPATH FSLDIR FSLPARALLEL
switch -- $probtrack(tool) {
eddy_current {
@@ -698,69 +642,76 @@ proc fdt:apply { w dialog } {
}
}
if { $canwrite } {
- puts "bedpost $bedpost(directory)"
- fdt_monitor $w "${FSLDIR}/bin/bedpost $bedpost(directory)"
+ puts "bedpostx $bedpost(directory) -n $bedpost(nfibres) -w $bedpost(weight) -b $bedpost(burnin)"
+ fdt_monitor $w "${FSLDIR}/bin/bedpostx $bedpost(directory) -n $bedpost(nfibres) -w $bedpost(weight) -b $bedpost(burnin)"
}
}
probtrack {
- global probtrack
-
+ global probtrack env
set errorStr ""
+ set FSLPARALLEL 0
+ if { [ info exists env(SGE_ROOT) ] && $env(SGE_ROOT) != "" } { set FSLPARALLEL 1 }
if { $probtrack(bedpost_dir) == "" } { set errorStr "You must specify the bedpost directory!" }
- if { $probtrack(usereference_yn) && $probtrack(xfm) == "" } { set errorStr "$errorStr You must specify the seed-diff transform!" }
+ if { $probtrack(mode) != "network" && $probtrack(reference) == "" } { set errorStr "$errorStr You must specify a reference image" }
if { $probtrack(exclude_yn) && $probtrack(exclude) == "" } { set errorStr "$errorStr You must specify the exclusion mask!" }
-
+ if { $probtrack(terminate_yn) && $probtrack(stop) == ""} { set errorStr "$errorStr You must specify the termination mask!" }
+ if { $probtrack(output) == "" } { set errorStr "$errorStr You must specify the output basename!" }
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 { $probtrack(usef_yn) == 1 } { set flags "$flags -f" }
if { $probtrack(modeuler_yn) == 1 } { set flags "$flags --modeuler" }
+ if { $probtrack(pd) } { set flags "$flags --pd" }
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
+
+ if { $errorStr != "" } {
+ MxPause $errorStr
+ return
+ }
+ set canwrite 1
+ if { [ file exists $probtrack(output) ] } {
+ set canwrite [ YesNoWidget "Overwrite $probtrack(output)?" Yes No ]
+ }
+ if { $canwrite } {
+ puts "rm -rf $probtrack(output)"
+ exec rm -rf $probtrack(output)
+ puts "mkdir -p $probtrack(output)"
+ exec mkdir -p $probtrack(output)
+ }
+
+ set filebase $probtrack(output)/fdtx
set logfile "${filebase}_log.tcl"
set log [open "$logfile" w]
puts $log "set tool $probtrack(tool)"
set copylog ""
- set ssopts ""
+
if { $probtrack(usereference_yn) } {
- set ssopts "--xfm=$probtrack(xfm)"
+ set flags "$flags --xfm=$probtrack(xfm)"
+ puts $log "set probtrack(xfm) $probtrack(xfm)"
}
+
if { $probtrack(exclude_yn) == 1 } {
- set ssopts "$ssopts --rubbish=$probtrack(exclude)"
+ set flags "$flags --avoid=$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 modeuler_yn \
- curvature nsteps steplength nparticles} {
- puts $log "set probtrack($entry) $probtrack($entry)"
+ if { $probtrack(terminate_yn) == 1 } {
+ set flags "$flags --stop=$probtrack(stop)"
+ puts $log "set probtrack(stop) $probtrack(stop)"
}
- 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=$probtrack(exclude)"
- }
+ set flags "$flags --forcedir --opd -s $probtrack(bedpost_dir)/merged -m $probtrack(bedpost_dir)/nodif_brain_mask --dir=$probtrack(output)"
+ foreach entry {bedpost_dir xfm mode exclude_yn usereference_yn verbose_yn loopcheck_yn modeuler_yn curvature nsteps steplength nparticles} {
+ puts $log "set probtrack($entry) $probtrack($entry)"
+ }
+ switch $probtrack(mode) {
+ simple {
set fd [ open "${filebase}_coordinates.txt" w ]
+ set x $probtrack(x)
+ set y $probtrack(y)
+ set z $probtrack(z)
if { $probtrack(units) == "mm" } {
- set x $probtrack(x)
- set y $probtrack(y)
- set z $probtrack(z)
- if { $probtrack(usereference_yn) && $probtrack(reference) != "" } {
+ if { $probtrack(reference) != "" } {
mm_to_voxels x y z $probtrack(reference)
} else {
mm_to_voxels x y z [ file join $probtrack(bedpost_dir) nodif_brain_mask ]
@@ -775,220 +726,92 @@ proc fdt:apply { w dialog } {
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_short $w "$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 { $probtrack(dir) == "" } { set errorStr "$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.watpoints load \"$probtrack(dir)/waypoints.txt\""
- $w.data.waypoints save "$probtrack(dir)/waypoints.txt"
- set copylog "$probtrack(dir)/fdt.log"
- fdt_monitor $w "$FSLDIR/bin/probtrack --mode=waypoints --seed=$probtrack(seed) --mask2=${probtrack(dir)}/waypoints.txt $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) $probtrack(dir)"
-
+ set flags "--mode=simple --seedref=$probtrack(reference) -o $probtrack(output) -x ${filebase}_coordinates.txt $flags"
+ }
+ seedmask {
+ if { $probtrack(bcyn) } {
+ fdt_monitor_short $w "${FSLDIR}/bin/convert_xfm -omat $probtrack(output)/tmp_xfm_mat -inverse $probtrack(xfm)"
+ fdt_monitor_short $w "${FSLDIR}/bin/flirt -in $probtrack(bedpost_dir)/nodif_brain_mask -ref $probtrack(reference) -applyxfm -init $probtrack(output)/tmp_xfm_mat -out $probtrack(output)/tmp_brain_mask"
+ fdt_monitor_short $w "${FSLDIR}/bin/flirt -in $probtrack(output)/tmp_brain_mask -ref $probtrack(output)/tmp_brain_mask -applyisoxfm $probtrack(scale) -out $probtrack(output)/lowresmask"
+ fdt_monitor_short $w "${FSLDIR}/bin/fslmaths $probtrack(output)/lowresmask -thr 0.5 -bin $probtrack(output)/lowresmask"
+ set flags "$flags --lrmask=$probtrack(output)/lowresmask --omatrix2"
+ fdt_monitor_short $w "${FSLDIR}/bin/imrm $probtrack(output)/tmp_brain_mask"
+ fdt_monitor_short $w "/bin/rm $probtrack(output)/tmp_xfm_mat"
+ }
+ set flags "--mode=seedmask -x $probtrack(reference) $flags"
+ }
+ network {
+ fdt_exp w $w.data.seed.targets $probtrack(output)/masks.txt
+ set flags "--network --mode=seedmask -x $probtrack(output)/masks.txt $flags"
+ }
+ }
- 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 } {
+ set copylog "fdt.log"
+
+ if { $probtrack(waypoint_yn) == 1 } {
+ fdt_exp w $w.data.targets.wf.tf.targets $probtrack(output)/waypoints.txt
+ set flags "$flags --waypoints=$probtrack(output)/waypoints.txt "
+ }
+ if { $probtrack(classify_yn) == 1 } {
+ fdt_exp w $w.data.targets.cf.tf.targets $probtrack(output)/targets.txt
+ set flags "$flags --targetmasks=$probtrack(output)/targets.txt --os2t "
+ }
+
+ #TODO
+
+
+ if { $FSLPARALLEL } {
+ set script [open "${filebase}_script.sh" w]
+ puts "${filebase}_script.sh"
+ exec chmod 777 ${filebase}_script.sh
+ puts $script "#!/bin/sh"
+ puts $script "cd $probtrack(output)"
+ puts $script "$FSLDIR/bin/probtrackx $flags"
+ if { $probtrack(classify_yn) == 1 } {
+ puts $script "$FSLDIR/bin/find_the_biggest seeds_to_* biggest >> fdt_seed_classification.txt"
}
- 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)"
+ if { $probtrack(mode) == "simple" } {
+ puts $script "rm ${filebase}_coordinates.txt"
}
- }
- 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 $script "mv $logfile $copylog"
+ puts $script "rm ${filebase}_script.sh"
+ close $script
+ exec batch -q long.q ${filebase}_script.sh
+ } else {
+
+ fdt_monitor_short $w "$FSLDIR/bin/probtrackx $flags"
+ if { $probtrack(classify_yn) == 1 } {
+ fdt_monitor_short $w "$FSLDIR/bin/find_the_biggest ${logdir}/seeds_to_* biggest >> ${logdir}/fdt_seed_classification.txt"
}
- 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 $probtrack(dir)
- }
+ set script [open "${filebase}_script.sh" w]
+ puts "${filebase}_script.sh"
+ exec chmod 777 ${filebase}_script.sh
+ puts $script "#!/bin/sh"
+ puts $script "$FSLDIR/bin/probtrackx $flags"
+ if { $probtrack(classify_yn) == 1 } {
+ puts $script "$FSLDIR/bin/find_the_biggest ${logdir}/seeds_to_* biggest >> ${logdir}/fdt_seed_classification.txt"
}
- 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)"
+ puts $script "rm ${filebase}_coordinates.txt"
+ puts $script "mv $logfile $copylog"
+ puts $script "rm ${filebase}_script.sh"
+ close $script
}
+ }
+ if { !$FSLPARALLEL } {
+ if { $probtrack(mode) == "simple" } {
+ puts "rm ${filebase}_coordinates.txt"
+ exec rm ${filebase}_coordinates.txt
}
- 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
}
}
- close $log
- if { $copylog != "" } {
- puts "mv $logfile $copylog"
- exec mv $logfile $copylog
- } else {
- puts "rm $logfile"
- exec rm $logfile
- }
}
registration {
global registration
@@ -1049,7 +872,7 @@ proc fdt:apply { w dialog } {
}
if { $canwrite } {
- MxPause " Done! "
+ if { $FSLPARALLEL } { MxPause " Job submitted to queue" } else { MxPause " Done! " }
update idletasks
}
diff --git a/fdtx.tcl b/fdtx.tcl
deleted file mode 100644
index 36a09c86e7a88a693461d0e12ec3f985fd89f37b..0000000000000000000000000000000000000000
--- a/fdtx.tcl
+++ /dev/null
@@ -1,912 +0,0 @@
-
-# FSL interface for FDT (BEDPOST and ProbTrack)
-#
-# Timothy Behrens, Heidi Johansen-Berg, Dave Flitney and Matthew Webster FMRIB Image Analysis Group
-#
-# Copyright (C) 2006 University of Oxford
-#
-# TCLCOPYRIGHT
-
-#TO DO replace -filetypes * with -filetypes { } for directory selectors
-source [ file dirname [ info script ] ]/fslstart.tcl
-option add *FileEntry*Entry*width 35
-set TCLPATH [file dirname [ info script ] ]
-regsub tcl $TCLPATH bin BINPATH
-regsub tcl $TCLPATH doc/fdt HTMLPATH
-
-set VERSION "1.1x"
-
-proc mm_to_voxels { X Y Z mask } {
-
- global FSLDIR
-
- upvar $X cX
- upvar $Y cY
- upvar $Z cZ
-
-
- set vcX [ exec sh -c "echo $cX $cY $cZ | $FSLDIR/bin/std2imgcoord -img $mask -vox - | awk '{print \$1}'" ]
- set vcY [ exec sh -c "echo $cX $cY $cZ | $FSLDIR/bin/std2imgcoord -img $mask -vox - | awk '{print \$2}'" ]
- set vcZ [ exec sh -c "echo $cX $cY $cZ | $FSLDIR/bin/std2imgcoord -img $mask -vox - | awk '{print \$3}'" ]
- set cX $vcX
- set cY $vcY
- set cZ $vcZ
-}
-
-proc fdt:dialog { w tclstartupfile } {
-
- global eddy bedpost registration dtifit probtrack HTMLPATH FSLDIR VERSION INMEDX VARS
- set probtrack(tool) "probtrack"
-
- if [winfo exists $w] {
- wm deiconify $w
- raise $w
- return
- }
-
- toplevel $w
- wm title $w "FDT - FMRIB's Diffusion Toolbox $VERSION"
- wm iconname $w "FDT"
- wm iconbitmap $w @$FSLDIR/tcl/fmrib.xbm
-
- #-------- Stage and Mode Options --------
-
- frame $w.tool
- optionMenu2 $w.tool.menu probtrack(tool) -command "fdt:select_tool $w" eddy_current "Eddy current correction" bedpost "BEDPOSTX Estimation of diffusion parameters" registration "Registration" probtrack "ProbTrackX Probabilistic tracking" xutilssx "----------------------------------------------------" dtifit "DTIFit Reconstruct diffusion tensors"
- $w.tool.menu.menu entryconfigure 4 -state disabled -background black
- pack $w.tool.menu -side left -pady 3 -padx 6 -anchor nw
-
- #-------- Tool Options... --------
-
- frame $w.opts
-
- #------- Registration --------
-
- frame $w.registration
-
- proc registration_set_directory { w dirname } {
- global registration
-
- set struct [ file join $dirname struct_brain ]
-
- if { [ imtest $struct ] } {
- set registration(struct_image) $struct
- } else {
- set registration(struct_image) ""
- }
- }
-
- FileEntry $w.registration.directory -textvariable registration(directory) -label "BEDPOST directory:" -title "Choose directory" -filetypes * -command "registration_set_directory $w"
-
- frame $w.registration.struct
- checkbutton $w.registration.struct.yn -variable registration(struct_yn) -command "registration_packframe $w"
- label $w.registration.struct.lb -text "Main structural image"
- TitleFrame $w.registration.struct.tf -text "Main structural image"
- optionMenu2 $w.registration.struct.tf.search registration(struct_search) 0 "No search" 90 "Normal search" 180 "Full search"
- optionMenu2 $w.registration.struct.tf.dof registration(struct_dof) 6 "6 DOF" 7 "7 DOF" 9 "9 DOF" 12 "12 DOF"
- optionMenu2 $w.registration.struct.tf.costfn registration(struct_costfn) corratio "Correlation ratio" mutualinfo "Mutual information"
- FileEntry $w.registration.struct.tf.file -textvariable registration(struct_image) -filetypes IMAGE -width 45
- pack $w.registration.struct.tf.file -side top -in [ $w.registration.struct.tf getframe ]
- pack $w.registration.struct.tf.search $w.registration.struct.tf.dof $w.registration.struct.tf.costfn -side left -in [ $w.registration.struct.tf getframe ]
- set registration(struct_costfn) mutualinfo
- set registration(struct_dof) 12
- set registration(struct_search) 90
- set registration(struct_yn) 0
-
- frame $w.registration.standard
- checkbutton $w.registration.standard.yn -variable registration(standard_yn) -command "registration_packframe $w"
- TitleFrame $w.registration.standard.tf -text "Standard space"
- label $w.registration.standard.lb -text "Standard space"
- optionMenu2 $w.registration.standard.tf.search registration(standard_search) 0 "No search" 90 "Normal search" 180 "Full search"
- optionMenu2 $w.registration.standard.tf.dof registration(standard_dof) 6 "6 DOF" 7 "7 DOF" 9 "9 DOF" 12 "12 DOF"
- optionMenu2 $w.registration.standard.tf.costfn registration(standard_costfn) corratio "Correlation ratio" mutualinfo "Mutual information"
- FileEntry $w.registration.standard.tf.file -textvariable registration(standard_image) -filetypes IMAGE -width 45
- pack $w.registration.standard.tf.file -side top -in [ $w.registration.standard.tf getframe ]
- pack $w.registration.standard.tf.search $w.registration.standard.tf.dof $w.registration.standard.tf.costfn -side left -in [ $w.registration.standard.tf getframe ]
- set registration(standard_yn) 1
- set registration(standard_dof) 12
- set registration(standard_search) 90
- set registration(standard_image) [ file join ${FSLDIR} etc standard avg152T1_brain ]
-
- pack $w.registration.directory $w.registration.struct $w.registration.standard -side top -padx 3 -pady 3 -anchor w
-
- proc registration_packframe { w } {
- global registration
- pack forget $w.registration.struct.yn $w.registration.struct.tf $w.registration.struct.yn $w.registration.struct.lb
- pack forget $w.registration.standard.yn $w.registration.standard.tf $w.registration.standard.yn $w.registration.standard.lb
- if {$registration(struct_yn)} { pack $w.registration.struct.yn $w.registration.struct.tf -side left -anchor w } else { pack $w.registration.struct.yn $w.registration.struct.lb -side left -anchor w}
- if {$registration(standard_yn)} { pack $w.registration.standard.yn $w.registration.standard.tf -side left -anchor w } else { pack $w.registration.standard.yn $w.registration.standard.lb -side left -anchor w}
- }
-
- registration_packframe $w
- #------- ECC --------
- frame $w.ecc
-
- proc ecc_update_files { w filename } {
- global eddy
- set eddy(output) [ file join [file dirname $eddy(input)] data ]
- }
-
- FileEntry $w.ecc.input -textvariable eddy(input) -label "Diffusion weighted data:" -title "Choose diffusion weighted image" -filetypes IMAGE -command "ecc_update_files $w"
-
- FileEntry $w.ecc.output -textvariable eddy(output) -label "Corrected output data:" -title "Choose output image name" -filetypes IMAGE -command "ecc_update_files $w"
-
- set eddy(refnum) 0
- LabelSpinBox $w.ecc.refnum -label "Reference volume" -textvariable eddy(refnum) -range {0 100 1 } -width 6
-
- pack $w.ecc.input $w.ecc.output $w.ecc.refnum -side top -padx 3 -pady 3 -expand yes -anchor w
-
- #------- DTIFit --------
-
- frame $w.dtifit
-
- FileEntry $w.dtifit.directory -textvariable dtifit(directory) -label "Input directory:" -title "Choose directory" -command "set_working_directory dtifit(cwd)"
-
- proc dtifit_toggle_expert { w } {
- global dtifit
-
- if { $dtifit(expert_yn) } {
- pack forget $w.dtifit.directory
- pack $w.dtifit.expert -in $w.dtifit -after $w.dtifit.expert_yn
- } else {
- pack forget $w.dtifit.expert
- pack $w.dtifit.directory -in $w.dtifit -before $w.dtifit.expert_yn
- }
- }
-
- checkbutton $w.dtifit.expert_yn -text "Specify input files manually" \
- -variable dtifit(expert_yn) -command "dtifit_toggle_expert $w"
-
- frame $w.dtifit.expert
-
- proc set_working_directory { cwd filename } {
- global dtifit
- set dirname [file dirname $filename]
- puts "switching from $dtifit(cwd) to $dirname"
- set dtifit(cwd) $dirname
- }
-
- proc dtifit_update_files { w filename } {
- global dtifit
-
- set dtifit(output) [ file join [file dirname $dtifit(input)] dti ]
- set_working_directory dtifit(cwd) $dtifit(input)
- }
-
- set dtifit(cwd) [ pwd ]
-
-#All the below orignally had -directory $dtifit(cwd)
- option add *dtifit.expert.FileEntry*labf*width 27
- FileEntry $w.dtifit.expert.input -textvariable dtifit(input) -label "Diffusion weighted data:" -title "Choose diffusion weighted image" -filetypes IMAGE -command "dtifit_update_files $w"
- FileEntry $w.dtifit.expert.mask -textvariable dtifit(mask) -label "BET binary brain mask:" -title "Choose BET brain mask file" -filetypes IMAGE -command "set_working_directory dtifit(cwd)"
- FileEntry $w.dtifit.expert.output -textvariable dtifit(output) -label "Output basename:" -title "Choose output base name" -filetypes * -command "set_working_directory dtifit(cwd)"
- FileEntry $w.dtifit.expert.bvecs -textvariable dtifit(bvecs) -label "Gradient directions:" -title "Choose bvecs file" -filetypes * -command "set_working_directory dtifit(cwd)"
- FileEntry $w.dtifit.expert.bvals -textvariable dtifit(bvals) -label "b values:" -title "Choose bvals file" -command "set_working_directory dtifit(cwd)"
-
- pack $w.dtifit.expert.input $w.dtifit.expert.mask $w.dtifit.expert.output \
- $w.dtifit.expert.bvecs $w.dtifit.expert.bvals \
- -side top -padx 3 -pady 3 -expand yes -anchor w
-
- pack $w.dtifit.directory $w.dtifit.expert_yn -side top -padx 3 -pady 3 -expand yes -anchor w
-
- #------- BEDPOST --------
-
- frame $w.bedpost
-
- FileEntry $w.bedpost.directory -textvariable bedpost(directory) -label "Input directory:" -title "Choose directory" -filetypes * -command "set_working_directory dtifit(cwd)"
-
- collapsible frame $w.bedpost.advanced -title "Advanced Options"
- set bedpost(nfibres) 2
- set bedpost(weight) 1
- set bedpost(burnin) 1000
- LabelSpinBox $w.bedpost.advanced.nfibres -label "Fibres " -textvariable bedpost(nfibres) -range {1 1000000000 1 }
- LabelSpinBox $w.bedpost.advanced.weight -label "Weight " -textvariable bedpost(weight) -range {0.0 100000000.0 1 }
- LabelSpinBox $w.bedpost.advanced.burnin -label "Burn In" -textvariable bedpost(burnin) -range {1 1000000000 1 }
-
- set bedpost(ecc_yn) 0
- pack $w.bedpost.advanced.nfibres $w.bedpost.advanced.weight $w.bedpost.advanced.burnin -in $w.bedpost.advanced.b -anchor w
- pack $w.bedpost.directory $w.bedpost.advanced -side top -padx 3 -pady 3 -expand yes -anchor w
-
- #-------- ProbTrack --------
- NoteBook $w.probtrack -bd 2 -tabpady {5 10} -arcradius 3
- $w.probtrack insert 0 data -text "Data"
- $w.probtrack insert 1 options -text "Options"
- #-------- Mode specific option --------
- frame $w.data
- FileEntry $w.data.directory -textvariable probtrack(bedpost_dir) -label "BEDPOST directory" -title "Choose BEDPOST directory" -filetypes * -command "probtrack_update_files $w"
-
- TitleFrame $w.data.seed -text "Seed Space"
- optionMenu2 $w.data.seed.menu probtrack(mode) -command "fdt:probtrack_mode $w" simple "Single voxel" seedmask "Single mask" network "Multiple masks"
- set probtrack(x) 0
- set probtrack(y) 0
- set probtrack(z) 0
- set probtrack(units) vox
- #Co-ordinate edit frame
- frame $w.data.seed.voxel
- LabelSpinBox $w.data.seed.voxel.x -label "X" -textvariable probtrack(x) -range {-1000000 1000000 1 }
- LabelSpinBox $w.data.seed.voxel.y -label "Y" -textvariable probtrack(y) -range {-1000000 1000000 1 }
- LabelSpinBox $w.data.seed.voxel.z -label "Z" -textvariable probtrack(z) -range {-1000000 1000000 1 }
- radiobutton $w.data.seed.voxel.vox -text "vox" -value vox -variable probtrack(units)
- radiobutton $w.data.seed.voxel.mm -text "mm" -value mm -variable probtrack(units)
- FileEntry $w.data.seed.reference -textvariable probtrack(reference) -label "Seed reference image:" -title "Choose reference image" -filetypes IMAGE
-
- option add *seed*FileEntry*labf*width 24
-
- frame $w.data.seed.ssf
- checkbutton $w.data.seed.ssf.ssd -text "Seed space is not diffusion" -variable probtrack(usereference_yn) -command " pack forget $w.data.seed.ssf.xfm ; if { \$probtrack(usereference_yn) } { pack $w.data.seed.ssf.xfm } ; $w.probtrack compute_size"
- FileEntry $w.data.seed.ssf.xfm -textvariable probtrack(xfm) -label "Select Seed to diff transform" -title "Select seed-space to DTI-space transformation matrix" -filetypes *
- pack $w.data.seed.ssf.ssd -side top -anchor nw
-
-
-
-
- frame $w.data.seed.bcf
- checkbutton $w.data.seed.bcf.bc -text "Blind Classification:" -variable probtrack(bcyn) -command " pack forget $w.data.seed.bcf.w ; if { \$probtrack(bcyn) } { pack $w.data.seed.bcf.w -side left} ; $w.probtrack compute_size"
- set probtrack(scale) 5
- LabelSpinBox $w.data.seed.bcf.w -label "Low resolution rescaling factor" -textvariable probtrack(scale) -range {1 1000000 1 }
- pack $w.data.seed.bcf.bc -side left -anchor w
-
- pack $w.data.seed.voxel.x $w.data.seed.voxel.y $w.data.seed.voxel.z $w.data.seed.voxel.vox $w.data.seed.voxel.mm -side left -padx 2
- pack $w.data.seed.voxel $w.data.seed.ssf -in $w.data.seed.f -side bottom -anchor w -pady 2
- pack $w.data.seed.menu $w.data.seed.reference -in $w.data.seed.f -side left -anchor w -pady 2
-
- TitleFrame $w.data.seed.target -text "Multiple Masks"
- listbox $w.data.seed.targets -height 6 -width 50 -yscrollcommand "$w.data.seed.sb set"
- scrollbar $w.data.seed.sb -command "$w.data.seed.targets yview "
- frame $w.data.seed.tb
- button $w.data.seed.tb.add -text "Add Image" -command "feat_file:setup_dialog $w a a a [namespace current] IMAGE {Select File} {fdt_add $w $w.data.seed.targets} {}"
- button $w.data.seed.tb.del -text "Remove Image" -command "fdt_sub $w $w.data.seed.targets"
- button $w.data.seed.tb.imp -text "Load List" -command "feat_file:setup_dialog $w a a a [namespace current] * {Select File} {fdt_imp $w $w.data.seed.targets} {}"
- button $w.data.seed.tb.exp -text "Save List" -command "feat_file:setup_dialog $w a a a [namespace current] * {Select File} {fdt_exp $w $w.data.seed.targets} {}"
- pack $w.data.seed.tb.add $w.data.seed.tb.del $w.data.seed.tb.imp $w.data.seed.tb.exp -side left
- pack $w.data.seed.tb -in [$w.data.seed.target getframe ] -side bottom -expand yes -fill x -anchor w -padx 3 -pady 3
- pack $w.data.seed.targets $w.data.seed.sb -in [$w.data.seed.target getframe ] -side left -expand yes -fill y -anchor w -padx 3 -pady 3
-
- TitleFrame $w.data.targets -text "Optional Targets"
-
- proc fdt_add { w listbox filename } {
- set filename [ fix_cygwin_filename $filename ]
- $listbox insert end $filename
- }
-
- proc fdt_sub { w listbox} {
- set count 0
- foreach file [ $listbox get 0 end ] {
- if { [ $listbox selection includes $count ] == 1 } {
- $listbox delete $count
- incr count -1
- }
- incr count
- }
- }
-
- proc fdt_imp { w listbox filename } {
- if { ![ file exists $filename ] } {
- MxPause "Warning: Bad or missing file!"
- return
- }
- set fd [ open $filename ]
- $listbox delete 0 end
- while { [ gets $fd file ] >= 0 } {
- $listbox insert end $file
- }
- close $fd
- }
-
- proc fdt_exp { w listbox filename } {
- set fd [ open $filename w ]
- foreach file [ $listbox get 0 end ] {
- puts $fd $file
- }
- close $fd
- }
-
- frame $w.data.targets.wf
- checkbutton $w.data.targets.wf.sct -text "Waypoints masks" -variable probtrack(waypoint_yn) -command " pack forget $w.data.targets.wf.tf ; if { \$probtrack(waypoint_yn) } { pack $w.data.targets.wf.tf } ; $w.probtrack compute_size"
- TitleFrame $w.data.targets.wf.tf -text "Waypoints"
- listbox $w.data.targets.wf.tf.targets -height 6 -width 50 -yscrollcommand "$w.data.targets.wf.tf.sb set"
- scrollbar $w.data.targets.wf.tf.sb -command "$w.data.targets.wf.tf.targets yview "
- frame $w.data.targets.wf.tf.tb
- button $w.data.targets.wf.tf.tb.add -text "Add Image" -command "feat_file:setup_dialog $w a a a [namespace current] IMAGE {Select File} {fdt_add $w $w.data.targets.wf.tf.targets} {}"
- button $w.data.targets.wf.tf.tb.del -text "Remove Image" -command "fdt_sub $w $w.data.targets.wf.tf.targets"
- button $w.data.targets.wf.tf.tb.imp -text "Load List" -command "feat_file:setup_dialog $w a a a [namespace current] * {Select File} {fdt_imp $w $w.data.targets.wf.tf.targets} {}"
- button $w.data.targets.wf.tf.tb.exp -text "Save List" -command "feat_file:setup_dialog $w a a a [namespace current] * {Select File} {fdt_exp $w $w.data.targets.wf.tf.targets} {}"
- pack $w.data.targets.wf.tf.tb.add $w.data.targets.wf.tf.tb.del $w.data.targets.wf.tf.tb.imp $w.data.targets.wf.tf.tb.exp -side left
- pack $w.data.targets.wf.tf.tb -in [$w.data.targets.wf.tf getframe ] -side bottom -expand yes -fill x -anchor w -padx 3 -pady 3
- pack $w.data.targets.wf.tf.targets $w.data.targets.wf.tf.sb -in [$w.data.targets.wf.tf getframe ] -side left -expand yes -fill y -anchor w -padx 3 -pady 3
- pack $w.data.targets.wf.sct -side top -anchor nw
- pack $w.data.targets.wf
-
- option add *targets*Checkbutton*width 18
- option add *targets*Checkbutton*anchor w
- frame $w.data.targets.ef
- checkbutton $w.data.targets.ef.srt -text "Exclusion mask" -variable probtrack(exclude_yn) -command " pack forget $w.data.targets.ef.rubbish ; if { \$probtrack(exclude_yn) } { pack $w.data.targets.ef.rubbish } ; $w.probtrack compute_size"
- FileEntry $w.data.targets.ef.rubbish -textvariable probtrack(exclude) -title "Select exclusion image" -filetypes IMAGE
- pack $w.data.targets.ef.srt -side left
-
- frame $w.data.targets.sf
- checkbutton $w.data.targets.sf.sst -text "Termination mask" -variable probtrack(terminate_yn) -command " pack forget $w.data.targets.sf.stop ; if { \$probtrack(terminate_yn) } { pack $w.data.targets.sf.stop } ; $w.probtrack compute_size"
- FileEntry $w.data.targets.sf.stop -textvariable probtrack(stop) -title "Select termination image" -filetypes IMAGE
- pack $w.data.targets.sf.sst -side left
-
- frame $w.data.targets.cf
- checkbutton $w.data.targets.cf.sct -text "Classification targets" -variable probtrack(classify_yn) -command " pack forget $w.data.targets.cf.tf ; if { \$probtrack(classify_yn) } { pack $w.data.targets.cf.tf } ; $w.probtrack compute_size"
- TitleFrame $w.data.targets.cf.tf -text "Classification"
- listbox $w.data.targets.cf.tf.targets -height 6 -width 50 -yscrollcommand "$w.data.targets.cf.tf.sb set"
- scrollbar $w.data.targets.cf.tf.sb -command "$w.data.targets.cf.tf.targets yview "
- frame $w.data.targets.cf.tf.tb
- button $w.data.targets.cf.tf.tb.add -text "Add Image" -command "feat_file:setup_dialog $w a a a [namespace current] IMAGE {Select File} {fdt_add $w $w.data.targets.cf.tf.targets} {}"
- button $w.data.targets.cf.tf.tb.del -text "Remove Image" -command "fdt_sub $w $w.data.targets.cf.tf.targets"
- button $w.data.targets.cf.tf.tb.imp -text "Load List" -command "feat_file:setup_dialog $w a a a [namespace current] * {Select File} {fdt_imp $w $w.data.targets.cf.tf.targets} {}"
- button $w.data.targets.cf.tf.tb.exp -text "Save List" -command "feat_file:setup_dialog $w a a a [namespace current] * {Select File} {fdt_exp $w $w.data.targets.cf.tf.targets} {}"
- pack $w.data.targets.cf.tf.tb.add $w.data.targets.cf.tf.tb.del $w.data.targets.cf.tf.tb.imp $w.data.targets.cf.tf.tb.exp -side left
- pack $w.data.targets.cf.tf.tb -in [$w.data.targets.cf.tf getframe ] -side bottom -expand yes -fill x -anchor w -padx 3 -pady 3
- pack $w.data.targets.cf.tf.targets $w.data.targets.cf.tf.sb -in [$w.data.targets.cf.tf getframe ] -side left -expand yes -fill y -anchor w -padx 3 -pady 3
- pack $w.data.targets.cf.sct -side top -anchor nw
- pack $w.data.targets.cf
-
-
- pack $w.data.targets.wf $w.data.targets.ef $w.data.targets.sf $w.data.targets.cf -in $w.data.targets.f -anchor w
-
-
-
-
- set probtrack(xfm) ""
- set probtrack(basename) "merged"
- set probtrack(mask) "nodif_brain_mask"
-
- proc probtrack_update_files { w filename } {
- global probtrack
- global FSLDIR
-
- if { ($probtrack(bedpost_dir) != "") && ($probtrack(reference) != "") } {
- set probtrack(output) \
- [ file join $probtrack(bedpost_dir) [ file tail [ exec $FSLDIR/bin/remove_ext $probtrack(reference) ] ] ]
- }
- }
-
- FileEntry $w.data.dir -textvariable probtrack(output) -label "Output directory:" -title "Name the output directory" -filetypes *
-
- pack $w.data.directory $w.data.seed $w.data.targets $w.data.dir -padx 3 -pady 3 -anchor nw
-
- pack $w.data -in [$w.probtrack getframe data] -padx 3 -pady 3 -anchor nw -expand yes -fill both
-
- #-------- ...Options... --------
- TitleFrame $w.options -text "Basic Options"
-
- checkbutton $w.options.verbose -text "Verbose" -variable probtrack(verbose_yn)
-
- set probtrack(nparticles) 5000
- LabelSpinBox $w.options.nparticles -label "Number of samples" -textvariable probtrack(nparticles) -range {1 1e24 100 } -width 6
-
- set probtrack(curvature) 0.2
- LabelSpinBox $w.options.curvature -label "Curvature threshold" -textvariable probtrack(curvature) -range {0.0 1.0 0.01 }
-
- set probtrack(loopcheck_yn) 1
- checkbutton $w.options.loopcheck -text "Loopcheck" -variable probtrack(loopcheck_yn)
-
- collapsible frame $w.advanced -title "Advanced Options" -command "$w.probtrack compute_size; set dummy"
-
- set probtrack(nsteps) 2000
- LabelSpinBox $w.advanced.nsteps -label "Maximum number of steps" -textvariable probtrack(nsteps) -range {2 1000000 10 } -width 6
-
- set probtrack(steplength) 0.5
- LabelSpinBox $w.advanced.steplength -label "Step length (mm)" -textvariable probtrack(steplength) -range {0.001 10000.0 0.1}
-
- set probtrack(modeuler_yn) 0
- checkbutton $w.advanced.modeuler -text "Use modified Euler streamlining" -variable probtrack(modeuler_yn)
-
- set probtrack(pd) 0
- checkbutton $w.advanced.pd -text "Use Distance correction" -variable probtrack(pd)
-
- set probtrack(usef_yn) 0
- checkbutton $w.advanced.usef -text "Use anisotropy to constrain tracking" -variable probtrack(usef_yn)
-
- pack $w.advanced.modeuler $w.advanced.nsteps $w.advanced.steplength $w.advanced.usef $w.advanced.pd -in $w.advanced.b -side top -pady 3 -padx 6 -anchor nw
-
- pack \
- $w.options.nparticles \
- $w.options.curvature \
- $w.options.verbose \
- $w.options.loopcheck \
- -in [$w.options getframe ] -side top -pady 3 -padx 6 -anchor nw
-
- pack $w.options $w.advanced -in [$w.probtrack getframe options] -side top -pady 3 -padx 6 -anchor nw -expand yes -fill both
-
- #-------- Buttons --------
-
- frame $w.btns
- frame $w.btns.b -relief raised -borderwidth 1
-
- button $w.apply -command "fdt:apply $w keep" \
- -text "Go" -width 5
- bind $w.apply <Return> {
- [winfo toplevel %W].apply invoke}
-
- button $w.cancel -command "fdt:destroy $w" \
- -text "Exit" -width 5
- bind $w.cancel <Return> {
- [winfo toplevel %W].cancel invoke}
-
- button $w.help -command "FmribWebHelp file: $HTMLPATH/index.html" \
- -text "Help" -width 5
- bind $w.help <Return> {
- [winfo toplevel %W].help invoke}
-
- pack $w.btns.b -side bottom -fill x -padx 3 -pady 5
- pack $w.apply $w.cancel $w.help -in $w.btns.b \
- -side left -expand yes -padx 3 -pady 10 -fill y
-
- pack $w.tool $w.opts $w.btns -side top -expand yes -fill both
-
-
-
- $w.probtrack raise data
- fdt:select_tool $w
- set probtrack(mode) simple
- fdt:probtrack_mode $w
-
- update idletasks
- if { $tclstartupfile != "" } {
- puts "Reading $tclstartupfile"
- source $tclstartupfile
- fdt:select_tool $w
- fdt:probtrack_mode $w
- }
-}
-
-proc fdt:probtrack_mode { w } {
- global probtrack
-
- pack forget $w.data.seed.voxel $w.data.seed.ssf $w.data.seed.menu $w.data.seed.reference $w.data.seed.bcf $w.data.seed.target $w.data.targets.cf
- $w.data.dir configure -label "Output directory:" -title "Name the output directory" -filetypes *
- switch -- $probtrack(mode) {
- simple {
- pack $w.data.seed.ssf $w.data.seed.voxel -in $w.data.seed.f -side bottom -anchor w -pady 2
- pack $w.data.seed.menu $w.data.seed.reference -in $w.data.seed.f -side left -anchor w -pady 2
- $w.data.seed.reference configure -label "Seed reference image:" -title "Choose reference image"
- $w.data.dir configure -label "Output file:" -title "Name the output file" -filetypes IMAGE
- }
- seedmask {
- pack $w.data.seed.ssf $w.data.seed.bcf -in $w.data.seed.f -side bottom -anchor w -pady 2
- pack $w.data.seed.menu $w.data.seed.reference -in $w.data.seed.f -side left -anchor w -pady 2
- pack $w.data.targets.cf -in $w.data.targets.f -anchor w
- $w.data.seed.reference configure -label "Mask image:" -title "Choose mask image"
- }
- network {
- pack $w.data.seed.target $w.data.seed.ssf $w.data.seed.menu -in $w.data.seed.f -side bottom -anchor w -pady 2
- }
- }
- $w.probtrack compute_size
-}
-
-proc fdt:select_tool { w } {
- global probtrack
- pack forget $w.ecc
- pack forget $w.probtrack
- pack forget $w.bedpost
- pack forget $w.registration
- pack forget $w.dtifit
- if {$probtrack(tool) == "bedpost"} {
- pack $w.bedpost -in $w.opts -side top -padx 3 -pady 3 -anchor nw
- } elseif {$probtrack(tool) == "probtrack"} {
- pack $w.probtrack -in $w.opts -side top -padx 3 -pady 3 -anchor nw
- } elseif {$probtrack(tool) == "dtifit"} {
- pack $w.dtifit -in $w.opts -side top -padx 3 -pady 3 -anchor nw
- } elseif {$probtrack(tool) == "eddy_current"} {
- pack $w.ecc -in $w.opts -side top -padx 3 -pady 3 -anchor nw
- } elseif {$probtrack(tool) == "registration"} {
- pack $w.registration -in $w.opts -side top -padx 3 -pady 3 -anchor nw
- }
-}
-proc fdt_monitor_short { w cmd } {
- global debugging OSFLAVOUR FSLPARALLEL
-
- puts "$cmd"
-
- if { $OSFLAVOUR != "cygwin" } {
- set oldcursor [ $w configure -cursor { watch red white } ]
-
- catch {
- update idletasks
- if { ! $debugging } {
- set fd [ open "|$cmd" r ]
-# set fd [ open "|qrsh -V -now n -q short.q $cmd" r ]
- while { ( [ gets $fd line ] >= 0 ) } {
- update idletasks
- puts $line
- }
- close $fd
- }
- } junk
-
- $w configure -cursor $oldcursor
-
- } else {
- catch { exec sh -c $cmd } junk
- }
-
- if { $junk != "" } {
- MxPause "Errors: $junk"
- }
-
- puts "Done!"
-}
-
-proc fdt_monitor { w cmd } {
- global debugging OSFLAVOUR
-
- puts "$cmd"
-
- if { $OSFLAVOUR != "cygwin" } {
- set oldcursor [ $w configure -cursor { watch red white } ]
-
- catch {
- update idletasks
- if { ! $debugging } {
- set fd [ open "|$cmd" r ]
-# set fd [ open "|qrsh -V -now n -q long.q $cmd" r ]
- while { ( [ gets $fd line ] >= 0 ) } {
- update idletasks
- puts $line
- }
- close $fd
- }
- } junk
-
- $w configure -cursor $oldcursor
-
- } else {
- catch { exec sh -c $cmd } junk
- }
-
- if { $junk != "" } {
- MxPause "Errors: $junk"
- }
-
- puts "Done!"
-}
-
-proc fdt:apply { w dialog } {
-
- global probtrack BINPATH FSLDIR FSLPARALLEL
-
- switch -- $probtrack(tool) {
- eddy_current {
- global eddy
-
- set errorStr ""
- if { $eddy(input) == "" } { set errorStr "You need to specify the input image! " }
- if { $eddy(output) == "" } { set errorStr "$errorStr You need to specify an output image!" }
- if { $errorStr != "" } {
- MxPause $errorStr
- return
- }
-
- # check output!=input
- set canwrite 1
- if { $eddy(input) == $eddy(output) } {
- set canwrite [ YesNoWidget "Output and input images have the same name. Overwrite input?" Yes No ]
- }
- if { $canwrite } {
- fdt_monitor $w "${FSLDIR}/bin/eddy_correct $eddy(input) $eddy(output) $eddy(refnum)"
- }
- }
- dtifit {
- global dtifit
-
- if { ! $dtifit(expert_yn) } {
- set dtifit(input) [ file join $dtifit(directory) data ]
- set dtifit(output) [ file join $dtifit(directory) dti ]
- set dtifit(mask) [ file join $dtifit(directory) nodif_brain_mask ]
- set dtifit(bvecs) [ file join $dtifit(directory) bvecs ]
- set dtifit(bvals) [ file join $dtifit(directory) bvals ]
- }
-
- set errorStr ""
- if { $dtifit(directory) == "" && ! $dtifit(expert_yn) } { set errorStr "You must specify the input directory!" }
- if { $dtifit(input) == "" } { set errorStr "You need to specify the diffusion weighted data image!" }
- if { $dtifit(output) == "" } { set errorStr "$errorStr You need to specify the output basename!" }
- if { $dtifit(mask) == "" } { set errorStr "$errorStr You need to specify a mask image!" }
- if { $dtifit(bvecs) == "" } { set errorStr "$errorStr Please select a gradient directions file!" }
- if { $dtifit(bvals) == "" } { set errorStr "$errorStr Please select a b values file!" }
- if { $errorStr != "" } {
- MxPause $errorStr
- return
- }
-
- set canwrite 1
- if { [file exists $dtifit(output) ] } {
- set canwrite [ YesNoWidget "Overwrite $dtifit(output)?" Yes No ]
- }
- if { $canwrite } {
- fdt_monitor_short $w "${FSLDIR}/bin/dtifit --data=$dtifit(input) --out=$dtifit(output) --mask=$dtifit(mask) --bvecs=$dtifit(bvecs) --bvals=$dtifit(bvals)"
- }
- }
- bedpost {
- global bedpost
-
- set errorStr ""
- if { $bedpost(directory) == "" } { set errorStr "You must specify the bedpost directory!" }
- if { $errorStr != "" } {
- MxPause $errorStr
- return
- }
-
- set canwrite 1
- if { [file exists ${bedpost(directory)}.bedpost ] } {
- set canwrite [ YesNoWidget "Overwrite ${bedpost(directory)}.bedpost?" Yes No ]
- if { $canwrite } {
- puts "rm -rf ${bedpost(directory)}.bedpost"
- catch { exec rm -rf ${bedpost(directory)}.bedpost } errmsg
- }
- }
- if { $canwrite } {
- puts "bedpostX $bedpost(directory) -n $bedpost(nfibres) -w $bedpost(weight) -b $bedpost(burnin)"
- fdt_monitor $w "${FSLDIR}/bin/bedpostX $bedpost(directory) -n $bedpost(nfibres) -w $bedpost(weight) -b $bedpost(burnin)"
- }
- }
- probtrack {
- global probtrack env
- set errorStr ""
- set FSLPARALLEL 0
- if { [ info exists env(SGE_ROOT) ] && $env(SGE_ROOT) != "" } { set FSLPARALLEL 1 }
- if { $probtrack(bedpost_dir) == "" } { set errorStr "You must specify the bedpost directory!" }
- if { $probtrack(mode) != "network" && $probtrack(reference) == "" } { set errorStr "$errorStr You must specify a reference image" }
- if { $probtrack(exclude_yn) && $probtrack(exclude) == "" } { set errorStr "$errorStr You must specify the exclusion mask!" }
- if { $probtrack(terminate_yn) && $probtrack(stop) == ""} { set errorStr "$errorStr You must specify the termination mask!" }
- if { $probtrack(output) == "" } { set errorStr "$errorStr You must specify the output basename!" }
- set flags ""
- if { $probtrack(verbose_yn) == 1 } { set flags "$flags -V 1" }
- if { $probtrack(loopcheck_yn) == 1 } { set flags "$flags -l" }
- if { $probtrack(usef_yn) == 1 } { set flags "$flags -f" }
- if { $probtrack(modeuler_yn) == 1 } { set flags "$flags --modeuler" }
- if { $probtrack(pd) } { set flags "$flags --pd" }
- set flags "$flags -c $probtrack(curvature) -S $probtrack(nsteps) --steplength=$probtrack(steplength) -P $probtrack(nparticles)"
-
- if { $errorStr != "" } {
- MxPause $errorStr
- return
- }
- set canwrite 1
- if { [ file exists $probtrack(output) ] } {
- set canwrite [ YesNoWidget "Overwrite $probtrack(output)?" Yes No ]
- }
- if { $canwrite } {
- puts "rm -rf $probtrack(output)"
- exec rm -rf $probtrack(output)
- puts "mkdir -p $probtrack(output)"
- exec mkdir -p $probtrack(output)
- }
-
- set filebase $probtrack(output)/fdtx
- set logfile "${filebase}_log.tcl"
- set log [open "$logfile" w]
- puts $log "set tool $probtrack(tool)"
- set copylog ""
-
- if { $probtrack(usereference_yn) } {
- set flags "$flags --xfm=$probtrack(xfm)"
- puts $log "set probtrack(xfm) $probtrack(xfm)"
- }
-
- if { $probtrack(exclude_yn) == 1 } {
- set flags "$flags --avoid=$probtrack(exclude)"
- puts $log "set probtrack(exclude) $probtrack(exclude)"
- }
-
- if { $probtrack(terminate_yn) == 1 } {
- set flags "$flags --stop=$probtrack(stop)"
- puts $log "set probtrack(stop) $probtrack(stop)"
- }
-
- set flags "$flags --forcedir --opd -s $probtrack(bedpost_dir)/merged -m $probtrack(bedpost_dir)/nodif_brain_mask --dir=$probtrack(output)"
- foreach entry {bedpost_dir xfm mode exclude_yn usereference_yn verbose_yn loopcheck_yn modeuler_yn curvature nsteps steplength nparticles} {
- puts $log "set probtrack($entry) $probtrack($entry)"
- }
- switch $probtrack(mode) {
- simple {
- set fd [ open "${filebase}_coordinates.txt" w ]
- set x $probtrack(x)
- set y $probtrack(y)
- set z $probtrack(z)
- if { $probtrack(units) == "mm" } {
- if { $probtrack(reference) != "" } {
- mm_to_voxels x y z $probtrack(reference)
- } else {
- mm_to_voxels x y z [ file join $probtrack(bedpost_dir) nodif_brain_mask ]
- }
- puts $fd "$x $y $z"
- puts "$probtrack(x) $probtrack(y) $probtrack(z) (mm) -> $x $y $z (voxels)"
- } else {
- puts $fd "$probtrack(x) $probtrack(y) $probtrack(z)"
- }
- close $fd
- puts $log "set probtrack(x) $probtrack(x)"
- puts $log "set probtrack(y) $probtrack(y)"
- puts $log "set probtrack(z) $probtrack(z)"
- puts $log "set probtrack(units) $probtrack(units)"
- set flags "--mode=simple --seedref=$probtrack(reference) -o $probtrack(output) -x ${filebase}_coordinates.txt $flags"
- }
- seedmask {
- if { $probtrack(bcyn) } {
- fdt_monitor_short $w "${FSLDIR}/bin/convert_xfm -omat $probtrack(output)/tmp_xfm_mat -inverse $probtrack(xfm)"
- fdt_monitor_short $w "${FSLDIR}/bin/flirt -in $probtrack(bedpost_dir)/nodif_brain_mask -ref $probtrack(reference) -applyxfm -init $probtrack(output)/tmp_xfm_mat -out $probtrack(output)/tmp_brain_mask"
- fdt_monitor_short $w "${FSLDIR}/bin/flirt -in $probtrack(output)/tmp_brain_mask -ref $probtrack(output)/tmp_brain_mask -applyisoxfm $probtrack(scale) -out $probtrack(output)/lowresmask"
- fdt_monitor_short $w "${FSLDIR}/bin/fslmaths $probtrack(output)/lowresmask -thr 0.5 -bin $probtrack(output)/lowresmask"
- set flags "$flags --lrmask=$probtrack(output)/lowresmask --omatrix2"
- fdt_monitor_short $w "${FSLDIR}/bin/imrm $probtrack(output)/tmp_brain_mask"
- fdt_monitor_short $w "/bin/rm $probtrack(output)/tmp_xfm_mat"
- }
- set flags "--mode=seedmask -x $probtrack(reference) $flags"
- }
- network {
- fdt_exp w $w.data.seed.targets $probtrack(output)/masks.txt
- set flags "--network --mode=seedmask -x $probtrack(output)/masks.txt $flags"
- }
- }
-
- if { $canwrite } {
- set copylog "fdt.log"
-
- if { $probtrack(waypoint_yn) == 1 } {
- fdt_exp w $w.data.targets.wf.tf.targets $probtrack(output)/waypoints.txt
- set flags "$flags --waypoints=$probtrack(output)/waypoints.txt "
- }
- if { $probtrack(classify_yn) == 1 } {
- fdt_exp w $w.data.targets.cf.tf.targets $probtrack(output)/targets.txt
- set flags "$flags --targetmasks=$probtrack(output)/targets.txt --os2t "
- }
-
- #TODO
-
-
- if { $FSLPARALLEL } {
- set script [open "${filebase}_script.sh" w]
- puts "${filebase}_script.sh"
- exec chmod 777 ${filebase}_script.sh
- puts $script "#!/bin/sh"
- puts $script "cd $probtrack(output)"
- puts $script "$FSLDIR/bin/probtrackx $flags"
- if { $probtrack(classify_yn) == 1 } {
- puts $script "$FSLDIR/bin/find_the_biggest seeds_to_* biggest >> fdt_seed_classification.txt"
- }
- if { $probtrack(mode) == "simple" } {
- puts $script "rm ${filebase}_coordinates.txt"
- }
- puts $script "mv $logfile $copylog"
- puts $script "rm ${filebase}_script.sh"
- close $script
- exec batch -q long.q ${filebase}_script.sh
- } else {
-
- fdt_monitor_short $w "$FSLDIR/bin/probtrackx $flags"
- if { $probtrack(classify_yn) == 1 } {
- fdt_monitor_short $w "$FSLDIR/bin/find_the_biggest ${logdir}/seeds_to_* biggest >> ${logdir}/fdt_seed_classification.txt"
- }
- set script [open "${filebase}_script.sh" w]
- puts "${filebase}_script.sh"
- exec chmod 777 ${filebase}_script.sh
- puts $script "#!/bin/sh"
- puts $script "$FSLDIR/bin/probtrackx $flags"
- if { $probtrack(classify_yn) == 1 } {
- puts $script "$FSLDIR/bin/find_the_biggest ${logdir}/seeds_to_* biggest >> ${logdir}/fdt_seed_classification.txt"
- }
- puts $script "rm ${filebase}_coordinates.txt"
- puts $script "mv $logfile $copylog"
- puts $script "rm ${filebase}_script.sh"
- close $script
- }
- }
- if { !$FSLPARALLEL } {
- if { $probtrack(mode) == "simple" } {
- puts "rm ${filebase}_coordinates.txt"
- exec rm ${filebase}_coordinates.txt
- }
- close $log
- if { $copylog != "" } {
- puts "mv $logfile $copylog"
- exec mv $logfile $copylog
- } else {
- puts "rm $logfile"
- exec rm $logfile
- }
- }
- }
- registration {
- global registration
-
- set errorStr ""
- if { $registration(directory) == "" } { set errorStr "You must specify the bedpost directory!" }
- if { $registration(struct_yn) && $registration(struct_image) == "" } { set errorStr "$errorStr You must specify the structural image!" }
- if { $registration(standard_yn) && $registration(standard_image) == "" } { set errorStr "$errorStr You must specify the standard image!" }
- if { $errorStr != "" } {
- MxPause $errorStr
- return
- }
-
- exec mkdir -p [ file join $registration(directory) xfms ]
- set eyefd [ open [ file join $registration(directory) xfms eye.mat ] w ]
- puts $eyefd "1 0 0 0"
- puts $eyefd "0 1 0 0"
- puts $eyefd "0 0 1 0"
- puts $eyefd "0 0 0 1"
- close $eyefd
-
- set diff2str [ file join $registration(directory) xfms diff2str.mat ]
- set str2diff [ file join $registration(directory) xfms str2diff.mat ]
- set str2stand [ file join $registration(directory) xfms str2standard.mat ]
- set stand2str [ file join $registration(directory) xfms standard2str.mat ]
- set diff2stand [ file join $registration(directory) xfms diff2standard.mat ]
- set stand2diff [ file join $registration(directory) xfms standard2diff.mat ]
- set diff [ file join $registration(directory) nodif_brain ]
- if { $registration(struct_yn) } {
- set searchrx "-searchrx -$registration(struct_search) $registration(struct_search)"
- set searchry "-searchry -$registration(struct_search) $registration(struct_search)"
- set searchrz "-searchrz -$registration(struct_search) $registration(struct_search)"
- set options "$searchrx $searchry $searchrz -dof $registration(struct_dof)"
- fdt_monitor $w "${FSLDIR}/bin/flirt -in $diff -ref $registration(struct_image) -omat $diff2str $options -cost $registration(struct_costfn)"
- fdt_monitor $w "${FSLDIR}/bin/convert_xfm -omat $str2diff -inverse $diff2str"
- if { $registration(standard_yn) } {
- set searchrx "-searchrx -$registration(standard_search) $registration(standard_search)"
- set searchry "-searchry -$registration(standard_search) $registration(standard_search)"
- set searchrz "-searchrz -$registration(standard_search) $registration(standard_search)"
- set options "$searchrx $searchry $searchrz -dof $registration(standard_dof)"
- fdt_monitor $w "${FSLDIR}/bin/flirt -in $registration(struct_image) -ref $registration(standard_image) -omat $str2stand $options -cost $registration(standard_costfn)"
- fdt_monitor $w "${FSLDIR}/bin/convert_xfm -omat $stand2str -inverse $str2stand"
- fdt_monitor $w "${FSLDIR}/bin/convert_xfm -omat $diff2stand -concat $str2stand $diff2str"
- fdt_monitor $w "${FSLDIR}/bin/convert_xfm -omat $stand2diff -inverse $diff2stand"
- }
- } elseif { $registration(standard_yn) } {
- set searchrx "-searchrx -$registration(standard_search) $registration(standard_search)"
- set searchry "-searchry -$registration(standard_search) $registration(standard_search)"
- set searchrz "-searchrz -$registration(standard_search) $registration(standard_search)"
- set options "$searchrx $searchry $searchrz -dof $registration(standard_dof)"
- fdt_monitor $w "${FSLDIR}/bin/flirt -in $diff -ref $registration(standard_image) -omat $diff2stand $options"
- fdt_monitor $w "${FSLDIR}/bin/convert_xfm -omat $stand2diff -inverse $diff2stand"
- }
- puts "Done!"
- # Fudge to make the logic work
- set canwrite 1
- }
- }
-
- if { $canwrite } {
- if { $FSLPARALLEL } { MxPause " Job submitted to queue" } else { MxPause " Done! " }
- update idletasks
- }
-
- if {$dialog == "destroy"} {
- fdt:destroy $w
- }
-}
-
-
-proc fdt:destroy { w } {
- destroy $w
-}
-
-set debugging 0
-
-while {[llength $argv] > 0 } {
- set flag [lindex $argv 0]
- switch -- $flag {
- "-debugging" {
- set debugging 1
- set argv [lrange $argv 1 end]
- puts "Debug mode!"
- }
- default { break }
- }
-}
-
-
-wm withdraw .
-if { [ info exists env(MRDATADIR) ] } {
- set MRDATADIR $env(MRDATADIR)
-} else {
- set MRDATADIR ~/MRdata
-}
-
-fdt:dialog .fdt $argv
-tkwait window .fdt