From 70dade3a77a4a424fb4356bcfac4564f76fd8acb Mon Sep 17 00:00:00 2001
From: Mark Jenkinson <mark@fmrib.ox.ac.uk>
Date: Tue, 31 Aug 2004 11:53:29 +0000
Subject: [PATCH] Use environment variables in script calls
---
lesions_0.1 | 2 +-
lesions_0.2 | 2 +-
lesions_0.3 | 2 +-
siena_flirt | 2 +-
4 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/lesions_0.1 b/lesions_0.1
index 71ca63e..92db43f 100755
--- a/lesions_0.1
+++ b/lesions_0.1
@@ -80,7 +80,7 @@ ${FSLDIR}/bin/slicer $1_lesions_render -A 400 $1_lesions_render
${FSLDIR}/bin/slicer $1_brain_seg strucseg_2_$1_brain -A 400 $1_brain_seg
${FSLDIR}/bin/slicer $1 -A 400 $1
${FSLDIR}/bin/slicer $1_lesions+ucsf -i 0 1 -A 400 $1_lesions+ucsf
-${FSLDIR}/bin/convert -colors 200 +append $2 $2_brain_seg $1_lesions_render $1_brain_seg $1 $1_lesions+ucsf $1_lesions.gif
+${FSLCONVERT} -colors 200 +append $2 $2_brain_seg $1_lesions_render $1_brain_seg $1 $1_lesions+ucsf $1_lesions.gif
diff --git a/lesions_0.2 b/lesions_0.2
index a97e8d3..0f104ab 100755
--- a/lesions_0.2
+++ b/lesions_0.2
@@ -92,7 +92,7 @@ echo "$A `cat ${A}_lesions.txt`"
${FSLDIR}/bin/flirt -in $B -ref $A -out ${B}_grot -applyxfm -init ${B}_to_${A}.mat ; ${FSLDIR}/bin/slicer ${B}_grot -A 400 $B
${FSLDIR}/bin/flirt -in ${B}_brain_seg -ref $A -out ${B}_grot -applyxfm -init ${B}_to_${A}.mat ; ${FSLDIR}/bin/slicer ${B}_grot -i 0 $nclasses -A 400 ${B}_brain_seg
${FSLDIR}/bin/overlay 0 1 $A -a ${A}_lesions $lesion_thr 1 ${A}_lesions_render ; ${FSLDIR}/bin/slicer ${A}_lesions_render -A 400 ${A}_lesions_render
-${FSLDIR}/bin/convert -colors 200 +append $A ${A}_brain_seg $B ${B}_brain_seg ${A}_lesions_render ${A}_lesions.gif
+${FSLCONVERT} -colors 200 +append $A ${A}_brain_seg $B ${B}_brain_seg ${A}_lesions_render ${A}_lesions.gif
diff --git a/lesions_0.3 b/lesions_0.3
index c415dec..4de092e 100644
--- a/lesions_0.3
+++ b/lesions_0.3
@@ -92,7 +92,7 @@ echo "$A `cat ${A}_lesions.txt`"
${FSLDIR}/bin/flirt -in $B -ref $A -out ${B}_grot -applyxfm -init ${B}_to_${A}.mat ; ${FSLDIR}/bin/slicer ${B}_grot -A 400 $B
${FSLDIR}/bin/flirt -in ${B}_brain_seg -ref $A -out ${B}_grot -applyxfm -init ${B}_to_${A}.mat ; ${FSLDIR}/bin/slicer ${B}_grot -i 0 $nclasses -A 400 ${B}_brain_seg
${FSLDIR}/bin/overlay 0 1 $A -a ${A}_lesions $lesion_thr 1 ${A}_lesions_render ; ${FSLDIR}/bin/slicer ${A}_lesions_render -A 400 ${A}_lesions_render
-${FSLDIR}/bin/convert -colors 200 +append $A ${A}_brain_seg $B ${B}_brain_seg ${A}_lesions_render ${A}_lesions.gif
+${FSLCONVERT} -colors 200 +append $A ${A}_brain_seg $B ${B}_brain_seg ${A}_lesions_render ${A}_lesions.gif
diff --git a/siena_flirt b/siena_flirt
index 929f61b..a4aa650 100755
--- a/siena_flirt
+++ b/siena_flirt
@@ -48,6 +48,6 @@ ${FSLDIR}/bin/extracttxt Backward ${A2}_to_${A1}.mat_avscale 4 1 > ${A1}_halfway
${FSLDIR}/bin/flirt -out ${A1}_halfwayto_${A2} -applyxfm -init ${A1}_halfwayto_${A2}.mat -ref ${A1} -in ${A1}_brain
${FSLDIR}/bin/flirt -out ${A2}_halfwayto_${A1} -applyxfm -init ${A2}_halfwayto_${A1}.mat -ref ${A1} -in ${A2}_brain
${FSLDIR}/bin/slicer ${A2}_halfwayto_${A1} ${A1}_halfwayto_${A2} -s 1 -x 0.4 gr${A1}${A2}a -x 0.5 gr${A1}${A2}b -x 0.6 gr${A1}${A2}c -y 0.4 gr${A1}${A2}d -y 0.5 gr${A1}${A2}e -y 0.6 gr${A1}${A2}f -z 0.4 gr${A1}${A2}g -z 0.5 gr${A1}${A2}h -z 0.6 gr${A1}${A2}i
-${FSLDIR}/bin/convert -colors 100 +append gr${A1}${A2}a gr${A1}${A2}b gr${A1}${A2}c gr${A1}${A2}d gr${A1}${A2}e gr${A1}${A2}f gr${A1}${A2}g gr${A1}${A2}h gr${A1}${A2}i ${A2}_regto_${A1}.gif
+${FSLCONVERT} -colors 100 +append gr${A1}${A2}a gr${A1}${A2}b gr${A1}${A2}c gr${A1}${A2}d gr${A1}${A2}e gr${A1}${A2}f gr${A1}${A2}g gr${A1}${A2}h gr${A1}${A2}i ${A2}_regto_${A1}.gif
/bin/rm gr${A1}${A2}a gr${A1}${A2}b gr${A1}${A2}c gr${A1}${A2}d gr${A1}${A2}e gr${A1}${A2}f gr${A1}${A2}g gr${A1}${A2}h gr${A1}${A2}i `$FSLDIR/bin/imglob ${A2}_halfwayto_${A1}.* ${A1}_halfwayto_${A2}.*`
--
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