Skip to content
Snippets Groups Projects
Commit 7b52df83 authored by Matthew Webster's avatar Matthew Webster
Browse files

159 with fix for new probtrack

parent 63057ac9
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
Showing
with 23 additions and 58 deletions
fdt.tcl
+ 23
− 58
View file @ 7b52df83
...@@ -80,11 +80,6 @@ proc fdt:dialog { w tclstartupfile } { ...@@ -80,11 +80,6 @@ proc fdt:dialog { w tclstartupfile } {
checkbutton $w.registration.struct.yn -variable registration(struct_yn) -command "registration_packframe $w" checkbutton $w.registration.struct.yn -variable registration(struct_yn) -command "registration_packframe $w"
label $w.registration.struct.lb -text "Main structural image" label $w.registration.struct.lb -text "Main structural image"
TitleFrame $w.registration.struct.tf -text "Main structural image" TitleFrame $w.registration.struct.tf -text "Main structural image"
frame $w.registration.nonlin
checkbutton $w.registration.nonlin.yn -variable registration(nonlin_yn) -text "Non-betted structural" -command "registration_packframe $w"
FileEntry $w.registration.nonlin.file -textvariable registration(nonlin_image) -filetypes IMAGE
optionMenu2 $w.registration.struct.tf.search registration(struct_search) 0 "No search" 90 "Normal search" 180 "Full search" optionMenu2 $w.registration.struct.tf.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.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" optionMenu2 $w.registration.struct.tf.costfn registration(struct_costfn) corratio "Correlation ratio" mutualinfo "Mutual information"
...@@ -111,18 +106,14 @@ proc fdt:dialog { w tclstartupfile } { ...@@ -111,18 +106,14 @@ proc fdt:dialog { w tclstartupfile } {
set registration(standard_search) 90 set registration(standard_search) 90
set registration(standard_image) [ file join ${FSLDIR} data standard MNI152_T1_2mm_brain ] set registration(standard_image) [ file join ${FSLDIR} data standard MNI152_T1_2mm_brain ]
pack $w.registration.directory $w.registration.struct $w.registration.nonlin $w.registration.standard -side top -padx 3 -pady 3 -anchor w pack $w.registration.directory $w.registration.struct $w.registration.standard -side top -padx 3 -pady 3 -anchor w
proc registration_packframe { w } { proc registration_packframe { w } {
global registration global registration
pack forget $w.registration.struct.yn $w.registration.struct.tf $w.registration.struct.yn $w.registration.struct.lb $w.registration.nonlin.yn $w.registration.nonlin.file pack forget $w.registration.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 pack forget $w.registration.standard.yn $w.registration.standard.tf $w.registration.standard.yn $w.registration.standard.lb
if { $registration(struct_yn) } { pack $w.registration.struct.yn $w.registration.struct.tf -side left -anchor w } else { pack $w.registration.struct.yn $w.registration.struct.lb -side left -anchor w} if {$registration(struct_yn)} { pack $w.registration.struct.yn $w.registration.struct.tf -side left -anchor w } else { pack $w.registration.struct.yn $w.registration.struct.lb -side left -anchor w}
if { $registration(struct_yn) } { pack $w.registration.nonlin.yn -side left } if {$registration(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}
if { $registration(struct_yn) && $registration(nonlin_yn) } { pack $w.registration.nonlin.file -side left }
if { $registration(standard_yn) } { pack $w.registration.standard.yn $w.registration.standard.tf -side left -anchor w } else { pack $w.registration.standard.yn $w.registration.standard.lb -side left -anchor w}
} }
registration_packframe $w registration_packframe $w
...@@ -138,12 +129,10 @@ proc fdt:dialog { w tclstartupfile } { ...@@ -138,12 +129,10 @@ proc fdt:dialog { w tclstartupfile } {
FileEntry $w.ecc.output -textvariable eddy(output) -label "Corrected output data:" -title "Choose output image name" -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 set eddy(refnum) 0
LabelSpinBox $w.ecc.refnum -label "Reference volume" -textvariable eddy(refnum) -range { 0 100 1 } -width 6 LabelSpinBox $w.ecc.refnum -label "Reference volume" -textvariable eddy(refnum) -range {0 100 1 } -width 6
checkbutton $w.ecc.reorient -text "reorient bvecs" -variable eddy(reorientbVecs) -command " fdt:eddycorrect_mode $w "
FileEntry $w.ecc.bvecdata -textvariable eddy(bVecData) -label "bvecs file:" -title "Choose bvecs name" -filetypes IMAGE
pack $w.ecc.input $w.ecc.output $w.ecc.refnum $w.ecc.reorient -side top -padx 3 -pady 3 -expand yes -anchor w pack $w.ecc.input $w.ecc.output $w.ecc.refnum -side top -padx 3 -pady 3 -expand yes -anchor w
#------- DTIFit -------- #------- DTIFit --------
...@@ -470,14 +459,6 @@ proc fdt:dialog { w tclstartupfile } { ...@@ -470,14 +459,6 @@ proc fdt:dialog { w tclstartupfile } {
} }
} }
proc fdt:eddycorrect_mode { w } {
global eddy
pack forget $w.ecc.bvecdata
if { $eddy(reorientbVecs) } {
pack $w.ecc.bvecdata -side top -padx 3 -pady 3 -expand yes -anchor w
}
}
proc fdt:probtrack_mode { w } { proc fdt:probtrack_mode { w } {
global probtrack FSLDIR global probtrack FSLDIR
...@@ -487,13 +468,12 @@ proc fdt:probtrack_mode { w } { ...@@ -487,13 +468,12 @@ proc fdt:probtrack_mode { w } {
if { $probtrack(useNonlinear) && $probtrack(usereference_yn) } { pack $w.data.seed.ssf.invxfm -side bottom -anchor w -pady 2 } if { $probtrack(useNonlinear) && $probtrack(usereference_yn) } { pack $w.data.seed.ssf.invxfm -side bottom -anchor w -pady 2 }
switch -- $probtrack(mode) { switch -- $probtrack(mode) {
simple { simple {
pack $w.data.seed.voxel -in $w.data.seed.f -side bottom -anchor w -pady 2 pack $w.data.seed.voxel -in $w.data.seed.f -side bottom -anchor w -pady 2
if { $probtrack(usereference_yn) } { pack $w.data.seed.ssf.reference -side bottom -anchor w -pady 2 } if { $probtrack(usereference_yn) } { pack $w.data.seed.ssf.reference -side bottom -anchor w -pady 2 }
$w.data.seed.ssf.reference configure -label "Seed reference image:" -title "Choose reference image" $w.data.seed.ssf.reference configure -label "Seed reference image:" -title "Choose reference image"
$w.data.dir configure -label "Output file:" -title "Name the output file" -filetypes IMAGE $w.data.dir configure -label "Output file:" -title "Name the output file" -filetypes IMAGE
} }
seedmask { seedmask {
pack forget $w.data.seed.ssf.ssd pack forget $w.data.seed.ssf.ssd
if { [ file exists ${FSLDIR}/bin/reord_OM ] } { if { [ file exists ${FSLDIR}/bin/reord_OM ] } {
pack $w.data.seed.bcf -in $w.data.seed.f -side bottom -anchor w -pady 2 pack $w.data.seed.bcf -in $w.data.seed.f -side bottom -anchor w -pady 2
...@@ -504,12 +484,12 @@ proc fdt:probtrack_mode { w } { ...@@ -504,12 +484,12 @@ proc fdt:probtrack_mode { w } {
} }
network { network {
pack $w.data.seed.target -in $w.data.seed.f -side bottom -anchor w -pady 2 pack $w.data.seed.target -in $w.data.seed.f -side bottom -anchor w -pady 2
} }
} }
if { $probtrack(waypoint_yn) } { pack $w.data.targets.wf.tf } if { $probtrack(waypoint_yn) } { pack $w.data.targets.wf.tf }
if { $probtrack(classify_yn) } { pack $w.data.targets.cf.tf } if { $probtrack(classify_yn) } { pack $w.data.targets.cf.tf }
if { $probtrack(usereference_yn) } { pack $w.data.seed.ssf.nonlinear $w.data.seed.ssf.xfm -side top -anchor w -pady 2 } if { $probtrack(usereference_yn) } { pack $w.data.seed.ssf.nonlinear $w.data.seed.ssf.xfm -side top -anchor w -pady 2 }
$w.probtrack compute_size $w.probtrack compute_size
} }
...@@ -601,6 +581,7 @@ proc fdt_monitor { w cmd } { ...@@ -601,6 +581,7 @@ proc fdt_monitor { w cmd } {
} }
proc fdt:apply { w dialog } { proc fdt:apply { w dialog } {
global probtrack BINPATH FSLDIR FSLPARALLEL global probtrack BINPATH FSLDIR FSLPARALLEL
switch -- $probtrack(tool) { switch -- $probtrack(tool) {
...@@ -610,15 +591,10 @@ proc fdt:apply { w dialog } { ...@@ -610,15 +591,10 @@ proc fdt:apply { w dialog } {
set errorStr "" set errorStr ""
if { $eddy(input) == "" } { set errorStr "You need to specify the input image! " } 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 { $eddy(output) == "" } { set errorStr "$errorStr You need to specify an output image!" }
if { $eddy(reorientbVecs) } { set errorStr "$errorStr You need to specify a bvecs image!" }
if { $errorStr != "" } { if { $errorStr != "" } {
MxPause $errorStr MxPause $errorStr
return return
} }
set reorientCommand ""
if { $eddy(reorientbVecs) } {
set reorientCommand "; rotate_bvecs $eddy(bVecData) $eddy(output).ecclog"
}
# check output!=input # check output!=input
set canwrite 1 set canwrite 1
...@@ -626,7 +602,7 @@ proc fdt:apply { w dialog } { ...@@ -626,7 +602,7 @@ proc fdt:apply { w dialog } {
set canwrite [ YesNoWidget "Output and input images have the same name. Overwrite input?" Yes No ] set canwrite [ YesNoWidget "Output and input images have the same name. Overwrite input?" Yes No ]
} }
if { $canwrite } { if { $canwrite } {
fdt_monitor $w "${FSLDIR}/bin/eddy_correct $eddy(input) $eddy(output) $eddy(refnum) $reorientCommand" fdt_monitor $w "${FSLDIR}/bin/eddy_correct $eddy(input) $eddy(output) $eddy(refnum)"
} }
} }
dtifit { dtifit {
...@@ -744,11 +720,12 @@ proc fdt:apply { w dialog } { ...@@ -744,11 +720,12 @@ proc fdt:apply { w dialog } {
set flags "$flags --xfm=$probtrack(xfm)" set flags "$flags --xfm=$probtrack(xfm)"
puts $log "set probtrack(usereference_yn) $probtrack(usereference_yn)" puts $log "set probtrack(usereference_yn) $probtrack(usereference_yn)"
puts $log "set probtrack(xfm) $probtrack(xfm)" puts $log "set probtrack(xfm) $probtrack(xfm)"
if { $probtrack(useNonlinear) } { }
set flags "$flags --invxfm=$probtrack(invxfm)"
puts $log "set $probtrack(useNonlinear) $probtrack(useNonlinear)" if { $probtrack(useNonlinear) } {
puts $log "set probtrack(invxfm) $probtrack(invxfm)" set flags "$flags --invxfm=$probtrack(invxfm)"
} puts $log "set $probtrack(useNonlinear) $probtrack(useNonlinear)"
puts $log "set probtrack(invxfm) $probtrack(invxfm)"
} }
if { $probtrack(exclude_yn) == 1 } { if { $probtrack(exclude_yn) == 1 } {
...@@ -767,9 +744,8 @@ proc fdt:apply { w dialog } { ...@@ -767,9 +744,8 @@ proc fdt:apply { w dialog } {
foreach entry {bedpost_dir xfm mode exclude_yn usereference_yn verbose_yn loopcheck_yn modeuler_yn curvature nsteps steplength nparticles} { 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)" puts $log "set probtrack($entry) $probtrack($entry)"
} }
set singleFileName $probtrack(output) set singleFileName $probtrack(output)
switch $probtrack(mode) { switch $probtrack(mode) {
simple { simple {
set singleFileName [ file tail $probtrack(output) ] set singleFileName [ file tail $probtrack(output) ]
set fd [ open "${filebase}_coordinates.txt" w ] set fd [ open "${filebase}_coordinates.txt" w ]
...@@ -884,8 +860,7 @@ proc fdt:apply { w dialog } { ...@@ -884,8 +860,7 @@ proc fdt:apply { w dialog } {
set errorStr "" set errorStr ""
if { $registration(directory) == "" } { set errorStr "You must specify the bedpostX directory!" } if { $registration(directory) == "" } { set errorStr "You must specify the bedpostX directory!" }
if { $registration(struct_yn) && $registration(struct_image) == "" } { set errorStr "$errorStr You must specify the structural image!" } if { $registration(struct_yn) && $registration(struct_image) == "" } { set errorStr "$errorStr You must specify the structural image!" }
if { $registration(struct_yn) && $registration(nonlin_yn) && $registration(nonlin_image) == "" } { set errorStr "$errorStr You must specify the non-betted structural image!" } if { $registration(standard_yn) && $registration(standard_image) == "" } { set errorStr "$errorStr You must specify the standard image!" }
if { $registration(standard_yn) && == "" } { set errorStr "$errorStr You must specify the standard image!" }
if { $errorStr != "" } { if { $errorStr != "" } {
MxPause $errorStr MxPause $errorStr
return return
...@@ -902,13 +877,9 @@ proc fdt:apply { w dialog } { ...@@ -902,13 +877,9 @@ proc fdt:apply { w dialog } {
set diff2str [ file join $registration(directory) xfms diff2str.mat ] set diff2str [ file join $registration(directory) xfms diff2str.mat ]
set str2diff [ file join $registration(directory) xfms str2diff.mat ] set str2diff [ file join $registration(directory) xfms str2diff.mat ]
set str2stand [ file join $registration(directory) xfms str2standard.mat ] set str2stand [ file join $registration(directory) xfms str2standard.mat ]
set str2stand_warp [ file join $registration(directory) xfms str2standard_warp ]
set stand2str [ file join $registration(directory) xfms standard2str.mat ] set stand2str [ file join $registration(directory) xfms standard2str.mat ]
set stand2str_warp [ file join $registration(directory) xfms standard2str_warp ]
set diff2stand [ file join $registration(directory) xfms diff2standard.mat ] set diff2stand [ file join $registration(directory) xfms diff2standard.mat ]
set diff2stand_warp [ file join $registration(directory) xfms diff2standard_warp ]
set stand2diff [ file join $registration(directory) xfms standard2diff.mat ] set stand2diff [ file join $registration(directory) xfms standard2diff.mat ]
set stand2diff_warp [ file join $registration(directory) xfms standard2diff_warp ]
set diff [ file join $registration(directory) nodif_brain ] set diff [ file join $registration(directory) nodif_brain ]
if { $registration(struct_yn) } { if { $registration(struct_yn) } {
set searchrx "-searchrx -$registration(struct_search) $registration(struct_search)" set searchrx "-searchrx -$registration(struct_search) $registration(struct_search)"
...@@ -926,12 +897,6 @@ proc fdt:apply { w dialog } { ...@@ -926,12 +897,6 @@ proc fdt:apply { w dialog } {
fdt_monitor $w "${FSLDIR}/bin/convert_xfm -omat $stand2str -inverse $str2stand" 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 $diff2stand -concat $str2stand $diff2str"
fdt_monitor $w "${FSLDIR}/bin/convert_xfm -omat $stand2diff -inverse $diff2stand" fdt_monitor $w "${FSLDIR}/bin/convert_xfm -omat $stand2diff -inverse $diff2stand"
if { $registration(nonlin_yn) } {
fdt_monitor $w "${FSLDIR}/bin/fnirt --in=$registration(nonlin_image) --aff=$str2strand --cout=$str2stand_warp --config=T1_2_MNI152_2mm"
fdt_monitor $w "${FSLDIR}/bin/invwarp -w $str2stand_warp -o standard2str_warp -r ${diff}_mask"
fdt_monitor $w "${FSLDIR}/bin/convertwarp -o $diff2stand_warp -r ${FSLDIR}/data/standard/MNI152_T1_2mm -m $diff2str -w $str2stand_warp"
fdt_monitor $w "${FSLDIR}/bin/convertwarp -o $stand2diff_warp -r ${diff}_mask -w $stand2str_warp --postmat=$str2diff"
}
} }
} elseif { $registration(standard_yn) } { } elseif { $registration(standard_yn) } {
set searchrx "-searchrx -$registration(standard_search) $registration(standard_search)" set searchrx "-searchrx -$registration(standard_search) $registration(standard_search)"
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment