diff --git a/hippunfold/workflow/envs/env12.yaml b/hippunfold/workflow/envs/env12.yaml new file mode 100644 index 00000000..2d9b595c --- /dev/null +++ b/hippunfold/workflow/envs/env12.yaml @@ -0,0 +1,9 @@ +name: env2 +channels: + - conda-forge + - khanlab + - defaults +dependencies: + - python=3.9 + - convert3d + - greedyreg \ No newline at end of file diff --git a/hippunfold/workflow/rules/subfields.smk b/hippunfold/workflow/rules/subfields.smk index c2a37782..fa5d4133 100644 --- a/hippunfold/workflow/rules/subfields.smk +++ b/hippunfold/workflow/rules/subfields.smk @@ -37,14 +37,14 @@ rule resample_unfoldreg_subfields: container: config["singularity"]["autotop"] conda: - "../envs/env2.yaml" + "../envs/env12.yaml" shadow: "minimal" group: "subj" shell: "c3d {input.label_nii} -slice z 0:15 -oo tmp0%d.nii.gz && " - "for fn in $(ls tmp*.nii.gz); do antsApplyTransforms -d 2 -i $fn -r $fn -o $fn -n MultiLabel -t {input.warp}; done && " + "for fn in $(ls tmp*.nii.gz); do greedy -d 2 -rf $fn -rm $fn $fn -r {input.warp}; done && " "c3d tmp*.nii.gz -tile z -o recombined.nii.gz && " "c3d {input.label_nii} recombined.nii.gz -copy-transform -o {output}"