diff --git a/README b/README index c4ded7a4176235949168e916321f6d78e0c792dc..29b53c70e42135961b8759dda88c8ed678e20bfc 100644 --- a/README +++ b/README @@ -8,4 +8,8 @@ Run the tests from the repository root as follows: pyfeeds -c pyfeeds_config.cfg -o /path/to/output_direcfory . Before running the tests, make sure to update the paths in -`pyfeeds_config.cfg`. \ No newline at end of file +`pyfeeds_config.cfg`. + + +Note that some tests (e.g. `fsl_course/fdt/bedpostx_gpu/`) need to be run on a +CUDA-capable machine. \ No newline at end of file diff --git a/fsl_course/fdt/bedpostx_cpu/feedsInputs b/fsl_course/fdt/bedpostx_cpu/feedsInputs new file mode 100644 index 0000000000000000000000000000000000000000..12c24c115e9953bd130625f26ffc8c5d006407fb --- /dev/null +++ b/fsl_course/fdt/bedpostx_cpu/feedsInputs @@ -0,0 +1 @@ +fsl_course_data/fdt2/subj1 diff --git a/fsl_course/fdt/bedpostx_cpu/feedsRun b/fsl_course/fdt/bedpostx_cpu/feedsRun new file mode 100755 index 0000000000000000000000000000000000000000..7108e45432093ebb7e8bd86110fd90403dccc469 --- /dev/null +++ b/fsl_course/fdt/bedpostx_cpu/feedsRun @@ -0,0 +1,23 @@ +#!/bin/bash + +set -e + +unset SGE_ROOT + +outdir=$1 +datadir=$2 + +basedir=$datadir/fsl_course_data/fdt2/subj1 + +# make a cut-down data set, +# with just one slice +mkdir $outdir/subj1 +cp $basedir/bvals $outdir/subj1/ +cp $basedir/bvecs $outdir/subj1/ +fslroi $basedir/data $outdir/subj1/data 0 -1 0 -1 31 1 +fslroi $basedir/nodif_brain_mask $outdir/subj1/nodif_brain_mask 0 -1 0 -1 31 1 + +bedpostx $outdir/subj1 --nf=2 --fudge=1 --bi=1000 --seed=1234 + +chmod -R u+w $outdir/subj1 +rm -r $outdir/subj1 diff --git a/fsl_course/fdt/bedpostx_gpu/feedsInputs b/fsl_course/fdt/bedpostx_gpu/feedsInputs new file mode 100644 index 0000000000000000000000000000000000000000..12c24c115e9953bd130625f26ffc8c5d006407fb --- /dev/null +++ b/fsl_course/fdt/bedpostx_gpu/feedsInputs @@ -0,0 +1 @@ +fsl_course_data/fdt2/subj1 diff --git a/fsl_course/fdt/bedpostx_gpu/feedsRun b/fsl_course/fdt/bedpostx_gpu/feedsRun new file mode 100755 index 0000000000000000000000000000000000000000..2c1b1e69b296ef6994a19a96ffacf483338cdb61 --- /dev/null +++ b/fsl_course/fdt/bedpostx_gpu/feedsRun @@ -0,0 +1,18 @@ +#!/bin/bash + +# This test needs to be executed +# on a CUDA-capable machine + +set -e + +unset SGE_ROOT + +outdir=$1 +datadir=$2 + +cp -r $datadir/fsl_course_data/fdt2/subj1 $outdir/ + +bedpostx_gpu $outdir/subj1 --nf=2 --fudge=1 --bi=1000 --seed=1234 + +chmod -R u+w $outdir/subj1 +rm -r $outdir/subj1