From 848c5cc2e18f21a51d66b3d19753fef98035f391 Mon Sep 17 00:00:00 2001
From: David Flitney <dave.flitney@ndcn.ox.ac.uk>
Date: Fri, 25 Jun 2004 17:12:54 +0000
Subject: [PATCH] Fixes RT1127 FDT ProbTrack rubbish...
---
fdt.tcl | 70 ++++++++++++++++++++++++++++++++++++---------------------
1 file changed, 44 insertions(+), 26 deletions(-)
diff --git a/fdt.tcl b/fdt.tcl
index 9fc7110..de08756 100644
--- a/fdt.tcl
+++ b/fdt.tcl
@@ -964,20 +964,20 @@ proc fdt:select_tool { w tool } {
proc fdt_monitor { w cmd } {
puts "$cmd"
- set oldcursor [ $w configure -cursor { watch red white } ]
- catch {
- update idletasks
- set fd [ open "|$cmd" r ]
- while { ( [ gets $fd line ] >= 0 ) } {
- update idletasks
- puts $line
- }
- close $fd
- } junk
- $w configure -cursor $oldcursor
- if { $junk != "" } {
- MxPause "Errors: $junk"
- }
+# set oldcursor [ $w configure -cursor { watch red white } ]
+# catch {
+# update idletasks
+# set fd [ open "|$cmd" r ]
+# while { ( [ gets $fd line ] >= 0 ) } {
+# update idletasks
+# puts $line
+# }
+# close $fd
+# } junk
+# $w configure -cursor $oldcursor
+# if { $junk != "" } {
+# MxPause "Errors: $junk"
+# }
puts "Done!"
}
@@ -1077,6 +1077,14 @@ proc fdt:apply { w dialog } {
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)"
+
+ set tn [open "| $BINPATH/tmpnam"]
+ gets $tn filebase
+ close $tn
+ set logfile "${filebase}_log.tcl"
+ set log [open "$logfile" w]
+ puts $log "set tool $tool"
+ set copylog ""
set ssopts ""
if { $probtrack(usereference_yn) } {
set ssopts "--xfm=$probtrack(xfm)"
@@ -1087,13 +1095,6 @@ proc fdt:apply { w dialog } {
}
set basics "--forcedir -s $probtrack(bedpost_dir)/merged -m $probtrack(bedpost_dir)/nodif_brain_mask"
- set tn [open "| $BINPATH/tmpnam"]
- gets $tn filebase
- close $tn
- set logfile "${filebase}_log.tcl"
- set log [open "$logfile" w]
- puts $log "set tool $tool"
- set copylog ""
foreach entry {bedpost_dir xfm mode exclude_yn usereference_yn verbose_yn loopcheck_yn usef_yn modeuler_yn \
curvature nsteps steplength nparticles} {
puts $log "set probtrack($entry) $probtrack($entry)"
@@ -1112,6 +1113,9 @@ proc fdt:apply { w dialog } {
} else {
set ssopts ""
}
+ if { $probtrack(exclude_yn) == 1 } {
+ set ssopts "$ssopts --rubbish=$probtrack(exclude)"
+ }
set fd [ open "${filebase}_coordinates.txt" w ]
$w.data.seedxyz update
if { $probtrack(units) == "mm" } {
@@ -1140,8 +1144,18 @@ proc fdt:apply { w dialog } {
return
}
- fdt_monitor $w "$FSLDIR/bin/probtrack --mode=simple -x ${filebase}_coordinates.txt $basics $ssopts $flags -o $probtrack(output)"
-
+ 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 $w "$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
}
@@ -1279,12 +1293,14 @@ proc fdt:apply { w dialog } {
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 $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) ] } {
@@ -1298,7 +1314,7 @@ proc fdt:apply { w dialog } {
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 $flags -o fdt_matrix --dir=$probtrack(dir)"
+ fdt_monitor $w "$FSLDIR/bin/probtrack --mode=matrix2 -x $probtrack(seed) $basics $ssopts --lrmask=$probtrack(lrmask) $flags -o fdt_matrix --dir=$probtrack(dir)"
}
}
mskmat {
@@ -1392,8 +1408,10 @@ proc fdt:apply { w dialog } {
}
}
- MxPause " Done! "
- update idletasks
+ if { $canwrite } {
+ MxPause " Done! "
+ update idletasks
+ }
if {$dialog == "destroy"} {
fdt:destroy $w
--
GitLab