diff --git a/fsl_course/fdt1/test_topup_eddy.sh b/fsl_course/fdt1/test_topup_eddy.sh index 448b656d097c9464fe7ab25fb06157670a9a1aa3..414d491f42816afb595ae9087ace28a54851627d 100755 --- a/fsl_course/fdt1/test_topup_eddy.sh +++ b/fsl_course/fdt1/test_topup_eddy.sh @@ -4,6 +4,8 @@ # Tests topup, eddy, and gps. set -e +# -m needed for correct jobs control +set -m set -x outdir=$1 @@ -40,15 +42,18 @@ if which eddy_openmp &> /dev/null; then --index=$subdatadir/index.txt --acqp=$subdatadir/acqparams.txt \ --bvecs=$subdatadir/bvecs --bvals=$subdatadir/bvals \ --fwhm=0 --topup=$outdir/topup_AP_PA_b0 --flm=quadratic \ - --out=$outdir/eddy_unwarped_images & sleep 10; kill -s TERM $! + --out=$outdir/eddy_unwarped_images & elif which eddy &> /dev/null; then eddy --imain=$subdatadir/dwidata --mask=$outdir/hifi_nodif_brain_mask \ --index=$subdatadir/index.txt --acqp=$subdatadir/acqparams.txt \ --bvecs=$subdatadir/bvecs --bvals=$subdatadir/bvals \ --fwhm=0 --topup=$outdir/topup_AP_PA_b0 --flm=quadratic \ - --out=$outdir/eddy_unwarped_image & sleep 10; kill -s TERM $! + --out=$outdir/eddy_unwarped_images & fi +sleep 10 +kill %1 + cp $subdatadir/pre_baked/eddy_unwarped_images* $outdir # Finally, test the gps command, for generating bvecs