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Commit ca3716ea authored by David Flitney's avatar David Flitney
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Changes to support Tim's new waypoints and extended registration functionality.

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with 30 additions and 22 deletions
fdt.tcl
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......@@ -18,7 +18,7 @@ tixWidgetClass registrationImageSelect {
-classname RegistrationImageSelect
-flag {
-variable -filename -labelwidth -label -search -dof -pattern -filterhist
-variable -filename -labelwidth -label -search -dof -pattern -filterhist -costfn
}
-configspec {
......@@ -30,6 +30,7 @@ tixWidgetClass registrationImageSelect {
{-filename filename Filename {}}
{-search search Search N}
{-dof dof DOF N}
{-costfn costfn Costfn N}
{-pattern pattern Pattern "*.{hdr,hdr.gz,nii,nii.gz}"}
}
}
......@@ -65,14 +66,17 @@ proc registrationImageSelect:ConstructWidget { w } {
$w.frame.options.search add command 180 -label "Full search"
tixOptionMenu $w.frame.options.dof -variable $data(-dof)
$w.frame.options.dof add command 3 -label "3 DOF (translation-only)"
$w.frame.options.dof add command 6 -label "6 DOF"
$w.frame.options.dof add command 7 -label "7 DOF"
$w.frame.options.dof add command 9 -label "9 DOF"
$w.frame.options.dof add command 12 -label "12 DOF"
tixOptionMenu $w.frame.options.costfn -variable $data(-costfn)
$w.frame.options.costfn add command corratio -label "Correlation ratio"
$w.frame.options.costfn add command mutualinfo -label "Mutual information"
pack $w.frame.options.f -in [$w.frame.options subwidget frame] -side top -expand yes -fill x
pack $w.frame.options.dof $w.frame.options.search -in [$w.frame.options subwidget frame] -side right
pack $w.frame.options.costfn $w.frame.options.dof $w.frame.options.search -in [$w.frame.options subwidget frame] -side right
pack $w.frame.visible_yn $w.frame.label -in $w.frame -side left -expand yes -padx 3
pack $w.frame -in $w
......@@ -188,7 +192,7 @@ proc multiFileSelect:load { w filename } {
upvar #0 $w data
if { ![ file exists $filename ] } {
MxPause "Warning: Bad or missing targets file!"
MxPause "Warning: Bad or missing file!"
return
}
set fd [ open $filename ]
......@@ -393,6 +397,7 @@ proc fdt:dialog { w tclstartupfile } {
-filename registration(struct_image) \
-dof registration(struct_dof) \
-search registration(struct_search) \
-costfn registration(struct_costfn) \
-directory $PWD \
-label "Main structural image" \
-labelwidth $LWIDTH \
......@@ -406,6 +411,7 @@ proc fdt:dialog { w tclstartupfile } {
-filename registration(standard_image) \
-dof registration(standard_dof) \
-search registration(standard_search) \
-costfn registration(standard_costfn) \
-directory $PWD \
-label "Standard space" \
-labelwidth $LWIDTH \
......@@ -593,7 +599,7 @@ proc fdt:dialog { w tclstartupfile } {
$w.data.mode add command xtitlex -label "Path distribution estimation" -state disabled
$w.data.mode add command simple -label " Single seed voxel"
$w.data.mode add command all -label " Seed mask"
$w.data.mode add command maska -label " Seed mask and target mask"
$w.data.mode add command maska -label " Seed mask and waypoint masks"
$w.data.mode add command masks -label " Two masks - symmetric"
$w.data.mode add separator xseedsx
$w.data.mode add command seeds -label "Connectivity-based seed classification"
......@@ -630,9 +636,7 @@ proc fdt:dialog { w tclstartupfile } {
-filterhist VARS(history)
tixLabelFrame $w.data.target -label "Target list"
multiFileSelect $w.data.targets -label "Target file: " -labelwidth $LWIDTH -directory $PWD
pack $w.data.targets -in [$w.data.target subwidget frame] \
-side top -anchor w -padx 3 -pady 3
......@@ -660,6 +664,11 @@ proc fdt:dialog { w tclstartupfile } {
-command "probtrack_update_files $w" \
-filterhist VARS(history)
tixLabelFrame $w.data.waypoint -label "Waypoint masks"
multiFileSelect $w.data.waypoints -label "Waypoint mask file: " -labelwidth $LWIDTH -directory $PWD
pack $w.data.waypoints -in [$w.data.waypoint subwidget frame] \
-side top -anchor w -padx 3 -pady 3
set probtrack(x) 0
set probtrack(y) 0
set probtrack(z) 0
......@@ -826,11 +835,11 @@ proc fdt:dialog { w tclstartupfile } {
-selectmode immediate -options { entry.width 4 }
$w.advanced.steplength subwidget label config -width $LWIDTH
set probtrack(usef_yn) 0
checkbutton $w.advanced.usef \
-text "Use anisotropy constraints" \
-variable probtrack(usef_yn) \
-command "if { \$probtrack(usef_yn) } { puts yes; set probtrack(nsteps) 20000 } else { puts no; set probtrack(nsteps) 1000 }"
# set probtrack(usef_yn) 0
# checkbutton $w.advanced.usef \
# -text "Use anisotropy constraints" \
# -variable probtrack(usef_yn) \
# -command "if { \$probtrack(usef_yn) } { set probtrack(nsteps) 20000 } else { set probtrack(nsteps) 1000 }"
set probtrack(modeuler_yn) 0
checkbutton $w.advanced.modeuler \
......@@ -838,7 +847,6 @@ proc fdt:dialog { w tclstartupfile } {
-variable probtrack(modeuler_yn)
pack \
$w.advanced.usef \
$w.advanced.modeuler \
$w.advanced.nsteps \
$w.advanced.steplength \
......@@ -906,6 +914,7 @@ proc fdt:probtrack_mode { w mode } {
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 \
......@@ -921,8 +930,7 @@ proc fdt:probtrack_mode { w mode } {
pack forget $w.data.seed
}
maska {
pack $w.data.seed2 -in $seedspacef -side top -after $w.data.seed
[$w.data.seed2 subwidget label] configure -text "Target image:"
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
......@@ -1076,7 +1084,7 @@ proc fdt:apply { w dialog } {
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" }
set flags "$flags -c $probtrack(curvature) -S $probtrack(nsteps) --steplength=$probtrack(steplength) -P $probtrack(nparticles)"
......@@ -1097,7 +1105,7 @@ proc fdt:apply { w dialog } {
}
set basics "--forcedir -s $probtrack(bedpost_dir)/merged -m $probtrack(bedpost_dir)/nodif_brain_mask"
foreach entry {bedpost_dir xfm mode exclude_yn usereference_yn verbose_yn loopcheck_yn usef_yn modeuler_yn \
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)"
}
......@@ -1214,14 +1222,12 @@ proc fdt:apply { w dialog } {
}
maska {
if { $probtrack(seed) == "" } { set errorStr "$errorStr You must specify a seed image!" }
if { $probtrack(seed2) == "" } { set errorStr "$errorStr You must select a target image!" }
if { $probtrack(dir) == "" } { set errorStr "$errorStr You must specify the output directory!" }
if { $errorStr != "" } {
MxPause $errorStr
return
}
puts $log "set probtrack(seed) $probtrack(seed)"
puts $log "set probtrack(seed2) $probtrack(seed2)"
puts $log "set probtrack(dir) $probtrack(dir)"
set canwrite 1
......@@ -1235,8 +1241,10 @@ proc fdt:apply { w dialog } {
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=twomasks_asymm --seed=$probtrack(seed) --mask2=$probtrack(seed2) $basics $ssopts $flags -o fdt_paths --dir=$probtrack(dir)"
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 {
......@@ -1386,14 +1394,14 @@ proc fdt:apply { w dialog } {
set searchry "-searchry -$registration(struct_search) $registration(struct_search)"
set searchrz "-searchrz -$registration(struct_search) $registration(struct_search)"
set options "$searchrx $searchry $searchrz -dof $registration(struct_dof)"
fdt_monitor $w "flirt -in $diff -ref $registration(struct_image) -omat $diff2str $options"
fdt_monitor $w "flirt -in $diff -ref $registration(struct_image) -omat $diff2str $options -cost $registration(struct_costfn)"
fdt_monitor $w "convert_xfm -omat $str2diff -inverse $diff2str"
if { $registration(standard_yn) } {
set searchrx "-searchrx -$registration(standard_search) $registration(standard_search)"
set searchry "-searchry -$registration(standard_search) $registration(standard_search)"
set searchrz "-searchrz -$registration(standard_search) $registration(standard_search)"
set options "$searchrx $searchry $searchrz -dof $registration(standard_dof)"
fdt_monitor $w "flirt -in $registration(struct_image) -ref $registration(standard_image) -omat $str2stand $options"
fdt_monitor $w "flirt -in $registration(struct_image) -ref $registration(standard_image) -omat $str2stand $options $registration(standard_costfn)"
fdt_monitor $w "convert_xfm -omat $stand2str -inverse $str2stand"
fdt_monitor $w "convert_xfm -omat $diff2stand -concat $str2stand $diff2str"
fdt_monitor $w "convert_xfm -omat $stand2diff -inverse $diff2stand"
......
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