Fix path in fdt2 test

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