From cd2f484ec1686bc3b0ff18958dfa54066d2293cc Mon Sep 17 00:00:00 2001
From: Matthew Webster <mwebster@jalapeno19.cluster.fmrib.ox.ac.uk>
Date: Tue, 18 Mar 2025 17:27:45 +0000
Subject: [PATCH] BF: Correctly kill the background eddy process(es)
---
fsl_course/fdt1/test_topup_eddy.sh | 9 +++++++--
1 file changed, 7 insertions(+), 2 deletions(-)
diff --git a/fsl_course/fdt1/test_topup_eddy.sh b/fsl_course/fdt1/test_topup_eddy.sh
index 448b656..414d491 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
--
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