diff --git a/fsl_course/fdt1/test_topup_eddy.sh b/fsl_course/fdt1/test_topup_eddy.sh index 8777b26ac6523c8596f67c3e248e0426f9d4af7f..c03aa2c8dcf23aa49276a7ff7d2e7fd8b5db112d 100755 --- a/fsl_course/fdt1/test_topup_eddy.sh +++ b/fsl_course/fdt1/test_topup_eddy.sh @@ -35,18 +35,18 @@ applytopup --imain=$outdir/nodif,$subdatadir/nodif_PA --topup=$outdir/topup_AP_P bet $outdir/hifi_nodif $outdir/hifi_nodif_brain -m -f 0.2 # Correct for eddy currents, actually just make sure eddy ( both pre- and post- 5.0.9 naming scheme) runs and then simulate CTRL+C ( as per course instructions ) -if [ `which -s eddy_openmp; echo \$?; exit 0` -eq "0" ]; then -eddy_openmp --imain=$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_images & sleep 10; kill -TERM $! -elif [ `which -s eddy; echo \$?; exit 0` -eq "0" ]; then -eddy --imain=$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 -TERM $! +if which eddy_openmp &> /dev/null; then + eddy_openmp --imain=$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_images & sleep 10; kill -TERM $! +elif which eddy_openmp &> /dev/null; then + eddy --imain=$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 -TERM $! fi cp $subdatadir/pre_baked/eddy_unwarped_images* $outdir