diff --git a/hippunfold/workflow/rules/download.smk b/hippunfold/workflow/rules/download.smk index 6424a100..ce3a2c6a 100644 --- a/hippunfold/workflow/rules/download.smk +++ b/hippunfold/workflow/rules/download.smk @@ -67,8 +67,6 @@ rule import_template_dseg: ), group: "subj" - container: - config["singularity"]["autotop"] shell: "cp {params.template_seg} {output.template_seg}" @@ -122,8 +120,6 @@ rule import_template_coords: ), group: "subj" - container: - config["singularity"]["autotop"] shell: "cp {params.template_coords} {output.template_coords}" @@ -161,7 +157,6 @@ rule flip_template_coords: "c3d {input.template_coords} -flip x -o {output.template_coords} " - rule import_template_anat: input: template_dir=Path(download_dir) / "template" / config["template"], @@ -183,8 +178,6 @@ rule import_template_anat: ), group: "subj" - container: - config["singularity"]["autotop"] shell: "cp {params.template_anat} {output.template_anat}" @@ -218,4 +211,3 @@ rule flip_template_anat: "subj" shell: "c3d {input.template_anat} -flip x -o {output.template_anat} " - diff --git a/hippunfold/workflow/rules/templateseg.smk b/hippunfold/workflow/rules/templateseg.smk index 65ca96e8..cd7348c8 100644 --- a/hippunfold/workflow/rules/templateseg.smk +++ b/hippunfold/workflow/rules/templateseg.smk @@ -6,6 +6,7 @@ def get_smoothing_opt(wildcards): return f"-s {gradient_sigma}vox {warp_sigma}vox" + rule template_reg: input: fixed_img=bids(