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Commit d8e44c98 authored by Paul McCarthy's avatar Paul McCarthy :mountain_bicyclist:
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Fix eddy call

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fsl_course/fdt1/test_topup_eddy.sh
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...@@ -42,7 +42,7 @@ eddy_openmp --imain=$subdatadir/dwidata --mask=$outdir/hifi_nodif_brain_mask \ ...@@ -42,7 +42,7 @@ eddy_openmp --imain=$subdatadir/dwidata --mask=$outdir/hifi_nodif_brain_mask \
--fwhm=0 --topup=$outdir/topup_AP_PA_b0 --flm=quadratic \ --fwhm=0 --topup=$outdir/topup_AP_PA_b0 --flm=quadratic \
--out=$outdir/eddy_unwarped_images & sleep 10; kill -TERM $! --out=$outdir/eddy_unwarped_images & sleep 10; kill -TERM $!
elif [ `bash -c "test -e eddy; echo \$?; exit 0"` -eq "0" ]; then elif [ `bash -c "test -e eddy; echo \$?; exit 0"` -eq "0" ]; then
eddy_openmp --imain=$subdatadir/dwidata --mask=$outdir/hifi_nodif_brain_mask \ eddy --imain=$subdatadir/dwidata --mask=$outdir/hifi_nodif_brain_mask \
--index=$subdatadir/index.txt --acqp=$subdatadir/acqparams.txt \ --index=$subdatadir/index.txt --acqp=$subdatadir/acqparams.txt \
--bvecs=$subdatadir/bvecs --bvals=$subdatadir/bvals \ --bvecs=$subdatadir/bvecs --bvals=$subdatadir/bvals \
--fwhm=0 --topup=$outdir/topup_AP_PA_b0 --flm=quadratic \ --fwhm=0 --topup=$outdir/topup_AP_PA_b0 --flm=quadratic \
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