From 958e6f5df142d583937d57ad8e526ce549d15d10 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <paulmc@fmrib.ox.ac.uk>
Date: Thu, 25 Oct 2018 17:17:56 +0100
Subject: [PATCH] Fix path in fdt2 test
---
fsl_course/fdt2/feedsRun6.sh | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/fsl_course/fdt2/feedsRun6.sh b/fsl_course/fdt2/feedsRun6.sh
index 0db0913..52e9be9 100755
--- a/fsl_course/fdt2/feedsRun6.sh
+++ b/fsl_course/fdt2/feedsRun6.sh
@@ -9,8 +9,11 @@ outdir=$1
datadir=$2
subdatadir=$datadir/fsl_course_data/fdt2
+cat ${subdatadir}/LGNTracts/waypoints.txt | sed -e "s|/vols/Data/fsldev/dataSets/fsl_course_data|$datadir|g" > ${outdir}/waypoints.txt
+
+
# Tracking from voxels in MNI152 standard space
-probtrackx2 -x ${subdatadir}/subj1_2fibres.bedpostX/SEED_LGN_LEFT.nii.gz -l --onewaycondition -c 0.2 -S 2000 --steplength=0.5 -P 5000 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --xfm=${subdatadir}/subj1_2fibres.bedpostX/xfms/standard2diff_warp.nii.gz --invxfm=${subdatadir}/subj1_2fibres.bedpostX/xfms/diff2standard_warp.nii.gz --avoid=${subdatadir}/subj1_2fibres.bedpostX/EXCLUSION.nii.gz --stop=${subdatadir}/subj1_2fibres.bedpostX/TARGET_V1_LEFT.nii.gz --forcedir --opd -s ${subdatadir}/subj1_2fibres.bedpostX/merged -m ${subdatadir}/subj1_2fibres.bedpostX/nodif_brain_mask --dir=${outdir}/LGNTracts --waypoints=${subdatadir}/LGNTracts/waypoints.txt --waycond=AND --rseed=10
+probtrackx2 -x ${subdatadir}/subj1_2fibres.bedpostX/SEED_LGN_LEFT.nii.gz -l --onewaycondition -c 0.2 -S 2000 --steplength=0.5 -P 5000 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --xfm=${subdatadir}/subj1_2fibres.bedpostX/xfms/standard2diff_warp.nii.gz --invxfm=${subdatadir}/subj1_2fibres.bedpostX/xfms/diff2standard_warp.nii.gz --avoid=${subdatadir}/subj1_2fibres.bedpostX/EXCLUSION.nii.gz --stop=${subdatadir}/subj1_2fibres.bedpostX/TARGET_V1_LEFT.nii.gz --forcedir --opd -s ${subdatadir}/subj1_2fibres.bedpostX/merged -m ${subdatadir}/subj1_2fibres.bedpostX/nodif_brain_mask --dir=${outdir}/LGNTracts --waypoints=${outdir}/waypoints.txt --waycond=AND --rseed=10
exit 0
--
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