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Commit 6ee00ae6 authored by Saad Jbabdi's avatar Saad Jbabdi
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change default for dti->struct

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fdt.tcl
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......@@ -80,19 +80,14 @@ proc fdt:dialog { w tclstartupfile } {
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"
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.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_costfn) corratio
set registration(struct_dof) 6
set registration(struct_search) 90
set registration(struct_yn) 0
......@@ -111,18 +106,14 @@ proc fdt:dialog { w tclstartupfile } {
set registration(standard_search) 90
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 } {
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
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(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 $w.registration.standard.lb -side left -anchor w}
if {$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
......@@ -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"
set eddy(refnum) 0
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
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 $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 --------
......@@ -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 } {
global probtrack FSLDIR
......@@ -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 }
switch -- $probtrack(mode) {
simple {
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 }
$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
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 }
$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
}
seedmask {
pack forget $w.data.seed.ssf.ssd
if { [ file exists ${FSLDIR}/bin/reord_OM ] } {
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 } {
}
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(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
}
......@@ -601,6 +581,7 @@ proc fdt_monitor { w cmd } {
}
proc fdt:apply { w dialog } {
global probtrack BINPATH FSLDIR FSLPARALLEL
switch -- $probtrack(tool) {
......@@ -610,15 +591,10 @@ proc fdt:apply { w dialog } {
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 { $eddy(reorientbVecs) } { set errorStr "$errorStr You need to specify a bvecs image!" }
if { $errorStr != "" } {
MxPause $errorStr
return
}
set reorientCommand ""
if { $eddy(reorientbVecs) } {
set reorientCommand "; rotate_bvecs $eddy(bVecData) $eddy(output).ecclog"
}
# check output!=input
set canwrite 1
......@@ -626,7 +602,7 @@ proc fdt:apply { w dialog } {
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) $reorientCommand"
fdt_monitor $w "${FSLDIR}/bin/eddy_correct $eddy(input) $eddy(output) $eddy(refnum)"
}
}
dtifit {
......@@ -744,11 +720,12 @@ proc fdt:apply { w dialog } {
set flags "$flags --xfm=$probtrack(xfm)"
puts $log "set probtrack(usereference_yn) $probtrack(usereference_yn)"
puts $log "set probtrack(xfm) $probtrack(xfm)"
if { $probtrack(useNonlinear) } {
set flags "$flags --invxfm=$probtrack(invxfm)"
puts $log "set $probtrack(useNonlinear) $probtrack(useNonlinear)"
puts $log "set probtrack(invxfm) $probtrack(invxfm)"
}
}
if { $probtrack(useNonlinear) } {
set flags "$flags --invxfm=$probtrack(invxfm)"
puts $log "set $probtrack(useNonlinear) $probtrack(useNonlinear)"
puts $log "set probtrack(invxfm) $probtrack(invxfm)"
}
if { $probtrack(exclude_yn) == 1 } {
......@@ -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} {
puts $log "set probtrack($entry) $probtrack($entry)"
}
set singleFileName $probtrack(output)
set singleFileName $probtrack(output)
switch $probtrack(mode) {
simple {
set singleFileName [ file tail $probtrack(output) ]
set fd [ open "${filebase}_coordinates.txt" w ]
......@@ -884,8 +860,7 @@ proc fdt:apply { w dialog } {
set errorStr ""
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(nonlin_yn) && $registration(nonlin_image) == "" } { set errorStr "$errorStr You must specify the non-betted structural image!" }
if { $registration(standard_yn) && == "" } { set errorStr "$errorStr You must specify the standard image!" }
if { $registration(standard_yn) && $registration(standard_image) == "" } { set errorStr "$errorStr You must specify the standard image!" }
if { $errorStr != "" } {
MxPause $errorStr
return
......@@ -902,13 +877,9 @@ proc fdt:apply { w dialog } {
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 str2stand_warp [ file join $registration(directory) xfms str2standard_warp ]
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_warp [ file join $registration(directory) xfms diff2standard_warp ]
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 ]
if { $registration(struct_yn) } {
set searchrx "-searchrx -$registration(struct_search) $registration(struct_search)"
......@@ -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 $diff2stand -concat $str2stand $diff2str"
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 { $registration(standard_yn) } {
set searchrx "-searchrx -$registration(standard_search) $registration(standard_search)"
......
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