diff --git a/snakedwi/workflow/Snakefile b/snakedwi/workflow/Snakefile index 3cd3789..e8770ff 100644 --- a/snakedwi/workflow/Snakefile +++ b/snakedwi/workflow/Snakefile @@ -21,13 +21,24 @@ rule all: **get_eddy_quad_all(), **get_bedpost_all(), mask_qc=expand( - bids(root=root,datatype='qc', suffix="mask.png", desc="brain", **subj_wildcards), + bids( + root=root, + datatype="qc", + suffix="mask.png", + desc="brain", + **subj_wildcards + ), zip, **input_zip_lists["dwi"] ), reg_qc=expand( bids( - root=root,datatype='qc', suffix="reg.png", from_="dwiref", to="T1w", **subj_wildcards + root=root, + datatype="qc", + suffix="reg.png", + from_="dwiref", + to="T1w", + **subj_wildcards ), zip, **input_zip_lists["dwi"] diff --git a/snakedwi/workflow/rules/prepdwi.smk b/snakedwi/workflow/rules/prepdwi.smk index fe81d3b..6cfc781 100644 --- a/snakedwi/workflow/rules/prepdwi.smk +++ b/snakedwi/workflow/rules/prepdwi.smk @@ -719,11 +719,23 @@ rule qc_brainmask_for_eddy: seg=get_mask_for_eddy(), output: png=report( - bids(root=root,datatype='qc', suffix="mask.png", desc="brain", **subj_wildcards), + bids( + root=root, + datatype="qc", + suffix="mask.png", + desc="brain", + **subj_wildcards + ), caption="../report/brainmask_dwi.rst", category="Brainmask", ), - html=bids(root=root,datatype='qc', suffix="mask.html", desc="brain", **subj_wildcards), + html=bids( + root=root, + datatype="qc", + suffix="mask.html", + desc="brain", + **subj_wildcards + ), group: "subj" container: diff --git a/snakedwi/workflow/rules/reg_dwi_to_t1.smk b/snakedwi/workflow/rules/reg_dwi_to_t1.smk index e081b3d..1412bcd 100644 --- a/snakedwi/workflow/rules/reg_dwi_to_t1.smk +++ b/snakedwi/workflow/rules/reg_dwi_to_t1.smk @@ -103,13 +103,23 @@ rule qc_reg_dwi_t1: output: png=report( bids( - root=root,datatype='qc', suffix="reg.png", **subj_wildcards, from_="dwiref", to="T1w" + root=root, + datatype="qc", + suffix="reg.png", + **subj_wildcards, + from_="dwiref", + to="T1w" ), caption="../report/reg_dwi_t1.rst", category="B0 T1w registration", ), html=bids( - root=root,datatype='qc', suffix="reg.html", from_="dwiref", to="T1w", **subj_wildcards + root=root, + datatype="qc", + suffix="reg.html", + from_="dwiref", + to="T1w", + **subj_wildcards ), group: "subj" diff --git a/snakedwi/workflow/rules/visqc.smk b/snakedwi/workflow/rules/visqc.smk index a872c02..0cb1d17 100644 --- a/snakedwi/workflow/rules/visqc.smk +++ b/snakedwi/workflow/rules/visqc.smk @@ -12,7 +12,8 @@ rule qc_reg: output: png=report( bids( - root=root,datatype='qc', + root=root, + datatype="qc", subject="{subject}", suffix="regqc.png", from_="subject", @@ -24,7 +25,8 @@ rule qc_reg: subcategory="{desc} {template}", ), html=bids( - root=root,datatype='qc', + root=root, + datatype="qc", subject="{subject}", suffix="regqc.html", from_="subject", @@ -51,7 +53,8 @@ rule qc_probseg: output: png=report( bids( - root=root,datatype='qc', + root=root, + datatype="qc", subject="{subject}", suffix="probseg.png", desc="atropos3seg", @@ -82,7 +85,8 @@ rule qc_dseg: output: png=report( bids( - root=root,datatype='qc', + root=root, + datatype="qc", subject="{subject}", suffix="dseg.png", atlas="{atlas}", @@ -93,7 +97,8 @@ rule qc_dseg: subcategory="{atlas} Atlas from {template}", ), html=bids( - root=root,datatype='qc', + root=root, + datatype="qc", subject="{subject}", suffix="dseg.html", atlas="{atlas}",