update config wildcards and filtering

Previously, the usage of `wildcards` was vast in the config file,
allowing for wildcards for all sorts of entities. This PR constrains the
wildcards to just subject, session, and run (can consider others in the
future, but these make the most sense at the moment).

Dwi filters are constrained to be in the "T1w" space, as we assume dwi
processing should be performed in the same space as T1w. Alternatively,
can consider "orig" space as well, but will need to think about to
handle transformations to the T1w in that case.

If multiple entities are found (e.g. "res"), Snakebids will throw an
error reflecting the files found and suggest to the user to make use of
the `--filter` option to constrain the files.

scattr/config/snakebids.yml

@@ -30,9 +30,6 @@ pybids_inputs:
     wildcards:
       - subject
       - session
-      - acquisition
-      - part
-      - reconstruction
       - run
 pybids_inputs_dwi:
   dwi:
@@ -41,27 +38,19 @@ pybids_inputs_dwi:
       extension: ".nii.gz"
       datatype: "dwi"
       space: "T1w"
-      part: ["mag", false]
     wildcards:
       - subject
       - session
-      - acquisition
-      - direction
-      - part
-      - reconstruction
       - run
-      - res
   mask:
     filters:
       suffix: "mask"
       extension: ".nii.gz"
       datatype: "dwi"
-      space: ["orig", "scanner", "individual", "T1w"]
+      space: "T1w"
     wildcards:
       - subject
       - session
-      - acquisition
-      - res
       - run
 
 # Configuration for the command-line parameters to make available

scattr/workflow/Snakefile

@@ -26,7 +26,9 @@ inputs_dwi = generate_inputs(
     bids_dir=config["dwi_dir"] if config["dwi_dir"] else config["bids_dir"],
     pybids_inputs=config["pybids_inputs_dwi"],
     pybids_config=["bids", "derivatives"],
-    pybidsdb_dir=config.get("pybidsdb_dwi_dir") if config["pybidsdb_dwi_dir"] else config.get("pybidsdb_dir"),
+    pybidsdb_dir=config.get("pybidsdb_dwi_dir")
+    if config["pybidsdb_dwi_dir"]
+    else config.get("pybidsdb_dir"),
     pybidsdb_reset=config.get("pybidsdb_reset"),
     derivatives=config["derivatives"],
     participant_label=config["participant_label"],

scattr/workflow/rules/freesurfer.smk

@@ -76,7 +76,9 @@ rule thalamic_segmentation:
         subj_dir=str(Path(bids(**inputs_t1w.subj_wildcards)).parent),
     output:
         thal_seg=str(
-            Path(bids(root=freesurfer_dir, **inputs_t1w.subj_wildcards)).parent
+            Path(
+                bids(root=freesurfer_dir, **inputs_t1w.subj_wildcards)
+            ).parent
             / "mri"
             / "ThalamicNuclei.v12.T1.mgz"
         ),
@@ -113,7 +115,9 @@ rule mgz2nii:
         if not config.get("skip_thal_seg")
         else [],
         aparcaseg=str(
-            Path(bids(root=freesurfer_dir, **inputs_t1w.subj_wildcards)).parent
+            Path(
+                bids(root=freesurfer_dir, **inputs_t1w.subj_wildcards)
+            ).parent
             / "mri"
             / "aparc+aseg.mgz"
         ),

scattr/workflow/rules/mrtpipelines.smk

@@ -58,7 +58,7 @@ bids_labelmerge = partial(
 bids_log = partial(
     bids,
     root=log_dir,
-    **inputs_t1w.subj_wildcards,
+    **inputs_dwi.subj_wildcards,
 )
 
 """Mrtrix3 reference (additional citations are included per rule as necessary):

scattr/workflow/rules/mrtpipelines/preproc.smk

@@ -14,15 +14,16 @@ rule nii2mif:
         mask=bids(
             root=mrtrix_dir,
             datatype="dwi",
-            suffix="brainmask.mif",
+            desc="brain",
+            suffix="mask.mif",
             **inputs_dwi.subj_wildcards
         ),
     threads: 4
     resources:
         mem_mb=16000,
         time=10,
     log:
-        bids_log(suffix="nii2mif.log"),
+        bids_log(suffix="nii2mif.log", **inputs_dwi.subj_wildcards),
     group:
         "dwiproc"
     container:

scattr/workflow/rules/zona_bb_subcortex.smk

@@ -71,7 +71,9 @@ rule reg2native:
             / Path(config["zona_bb_subcortex"][config["Space"]]["dir"])
             / Path(config["zona_bb_subcortex"][config["Space"]]["T1w"])
         ),
-        target=lambda wildcards: inputs_t1w["T1w"].filter(**wildcards).expand()[0],
+        target=lambda wildcards: inputs_t1w["T1w"]
+        .filter(**wildcards)
+        .expand()[0],
     params:
         out_dir=directory(str(Path(bids_anat()).parent)),
         out_prefix=bids_anat(