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Add singularity call to track_from_clusters rule #6

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Add singularity call to track_from_clusters rule #6

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f7f94fd
Add singularity call to fslmaths
kaitj Dec 20, 2023
ec2668b
Add missing container call
kaitj Dec 20, 2023
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2 changes: 1 addition & 1 deletion subcorticalparc_smk/workflow/rules/tractmap.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -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}"
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