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Commit bf13acdf authored by Sam Harrison's avatar Sam Harrison
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BUGFIX: Missing variable expansion

parent f367b0ad
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1 merge request!5Fix ordering issues with --thr flag
......@@ -127,7 +127,7 @@ if [ $NAF2 -eq 1 ] ; then
$FSLDIR/bin/fslmaths ${OUTPUT}/MM_${s}/stats/thresh2_negative -uthr -2 ${OUTPUT}/MM_${s}/stats/thresh2_negative ; \
$FSLDIR/bin/fslmaths ${OUTPUT}/MM_${s}/stats/thresh2_positive -thr 2 ${OUTPUT}/MM_${s}/stats/thresh2_positive ; \
$FSLDIR/bin/fslmaths ${OUTPUT}/MM_${s}/stats/thresh2_negative -add ${OUTPUT}/MM_${s}/stats/thresh2_positive ${OUTPUT}/MM_${s}/stats/thresh2 ; \
$FSLDIR/bin/imrm \`\$FSLDIR/bin/imglob ${OUTPUT}/MM_{s}/stats/thresh2_*.*\` ; \
$FSLDIR/bin/imrm \`\$FSLDIR/bin/imglob ${OUTPUT}/MM_${s}/stats/thresh2_*.*\` ; \
$FSLDIR/bin/fsl_glm -i $i -d ${OUTPUT}/MM_${s}/stats/thresh2 -o $OUTPUT/dr_stage4_${s}.txt --demean -m $OUTPUT/mask" >> ${LOGDIR}/drD2
j=`echo "$j 1 + p" | dc -`
done
......
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