diff --git a/subcorticalparc_smk/workflow/rules/tractmap.smk b/subcorticalparc_smk/workflow/rules/tractmap.smk index 7fc1eeb..54c5222 100644 --- a/subcorticalparc_smk/workflow/rules/tractmap.smk +++ b/subcorticalparc_smk/workflow/rules/tractmap.smk @@ -218,7 +218,7 @@ rule track_from_clusters: "diffparc_participant2" shell: "mkdir -p {output.probtrack_dir} && " - "{params.extract_seed_cmd} && singularity exec -e --nv {params.container} " + "singularity exec -e {params.container} {params.extract_seed_cmd} && singularity exec -e --nv {params.container} " "probtrackx2_gpu --samples={params.bedpost_merged} --mask={input.mask} --seed={output.probtrack_dir}/in_seed.nii.gz " "--seedref={output.probtrack_dir}/in_seed.nii.gz --nsamples={params.nsamples} " "--dir={output.probtrack_dir} {params.probtrack_opts} -V 2 &> {log}"