use single pybids_inputs instead of two

.github/dependabot.yml

@@ -1,15 +1,15 @@
+---
 version: 2
 updates:
-  - package-ecosystem: "github-actions"
+  - package-ecosystem: github-actions
     # Workflow files stored in the default location of `.github/workflows`. 
     # (You don't need to specify `/.github/workflows` for `directory`. 
     # You can use `directory: "/"`.)
-    directory: "/"
+    directory: /
     # Run on first of each month
     schedule:
-      interval: "monthly"
+      interval: monthly
     # Group to submit a single PR if possible
     groups:
       github-actions:
-        patterns:
-          - "*"
+        patterns: ['*']

docs/getting_started/installation.md

@@ -12,7 +12,9 @@ supported**. We do not have a Docker arm64 container yet._
 
 ### Notes
 * Inputs to SCATTR should be a BIDS dataset, including processed Freesurfer
-and DWI derivatives (which can be stored separately). 
+and DWI derivatives. If any BIDS files are stored separately, you can point to these using the
+relevant `--path-{component}` CLI option. The Freesurfer folder is specified with a separate 
+CLI option `--freesurfer-dir`(which can be stored separately). 
 
 ## Docker on Windows / Mac (Intel) / Linux
 
@@ -49,4 +51,4 @@ Instructions can be found in the [Contributing](https://scattr.readthedocs.io/en
 * Flexibility to modify code
 
 ### Cons
-* Only compatible on systems with Singularity for external dependencies
+* Only compatible on systems with Singularity for external dependencies

docs/outputs/output_files.md

@@ -126,6 +126,3 @@ Workflow steps that write logs to file are stored in the hidden `.logs`
 subfolder, with the file names based on the tools used (e.g. `mrtrix`) and rule
 wildcards (e.g. `subject`).
 
-If the app is run in workflow mode (`--workflow-mode` / `-W`), which enables
-direct use of the Snakemake CLI to run scattr, output folders (e.g. `work`) will
-be placed in a `results` folder.

docs/requirements.txt

@@ -1,5 +1,5 @@
 docutils<0.18
-sphinx-argparse
+sphinx-argparse<0.5.0
 sphinx_rtd_theme
 sphinxcontrib-asciinema
-myst-parser
+myst-parser

docs/usage/faq.md

@@ -21,7 +21,7 @@ the dataset, so we suggest using the
 your dataset has no errors.
 
 If you passed Freesurfer or diffusion derivative locations (`--freesurfer-dir` 
-or `--dwi-dir`), you may get get this message as the files are a different
+or `--path-dwi`), you may get get this message as the files are a different
 location than in the input directory provided.
 
 ### 2. What if I want to use merge two different atlases?

docs/usage/useful_options.md

@@ -44,11 +44,19 @@ Similarly, subjects can be excluded from processing using the
 ## Alternate Freesurfer / derived-diffusion data locations
 
 By default, SCATTR attempts to locate Freesurfer and derived diffusion data 
-locations. Users can overwrite these options, by passing along the actual 
-location of each using either `--freesurfer_dir` or `--dwi_dir`, respectively.
+locations. Users can overwrite the Freesurfer location by passing `--freesurfer_dir`, 
+e.g.: 
 
 ```
---freesurfer_dir /path/to/fs_dir --dwi_dir /path/to/dwi_dir
+--freesurfer_dir /path/to/fs_dir
+```
+
+The paths to any of the BIDS files (T1w, dwi, dwi mask) can always be customized
+using the `--path-T1w`, `--path-dwi`, or `--path-mask` options. Note, you must
+include generic wildcards in any path you specify, e.g.:
+
+```
+--path-T1w /mydata/project1/sub-{subject}/T1.nii.gz`
 ```
 
 ## Pre-generated average response function
@@ -121,4 +129,4 @@ filter out extra files, but for now, if your dataset has these issues, you will
 need to rename or remove extraneous files.
 
 More example of possible BIDS-compliant datasets can be found in 
-`scattr/test/data`.
+`scattr/test/data`.

pyproject.toml

@@ -85,14 +85,20 @@ python ./scattr/run.py ./test/data/bids test/data/derivatives/ participant \
 [tool.poe.tasks.test_dwi]
 shell = """
 python ./scattr/run.py ./test/data/bids_nodwi test/data/derivatives/ \
-    participant --dwi_dir ./test/data/derivatives/prepdwi \
+    participant --path-dwi \
+    ./test/data/derivatives/prepdwi/sub-{subject}/dwi/sub-{subject}_space-T1w_desc-preproc_dwi.nii.gz \
+    --path-mask \
+    ./test/data/derivatives/prepdwi/sub-{subject}/dwi/sub-{subject}_space-T1w_desc-preproc_mask.nii.gz \
     --fs-license ./test/.fs_license -np --force-output
 """
 
 [tool.poe.tasks.test_snakedwi]
 shell = """
 python ./scattr/run.py ./test/data/bids_nodwi test/data/derivatives/ \
-    participant --dwi_dir ./test/data/derivatives/snakedwi \
+    participant --path-dwi \
+    ./test/data/derivatives/snakedwi/sub-{subject}/dwi/sub-{subject}_space-T1w_desc-eddy_res-orig_dwi.nii.gz \
+    --path-dwi-mask \
+    ./test/data/derivatives/snakedwi/sub-{subject}/dwi/sub-{subject}_space-T1w_desc-eddy_res-orig_mask.nii.gz \
     --fs-license ./test/.fs_license -np --force-output
 """
 

scattr/config/snakebids.yml

@@ -26,12 +26,10 @@ pybids_inputs:
       extension: ".nii.gz"
       datatype: "anat"
       desc: "brain" # Require a skull-stripped brain
-      part: ["mag", false]
     wildcards:
       - subject
       - session
       - run
-pybids_inputs_dwi:
   dwi:
     filters:
       suffix: "dwi"
@@ -102,18 +100,6 @@ parse_args:
     nargs: "?"
     type: Path
 
-  --dwi_dir:
-    help: "The path to the directory containing pre-processed dwi data
-      transformed to subject T1w space. If not provided, workflow assumes
-      this data exists in <bids_dir>/<subject>/dwi."
-    nargs: "?"
-    type: Path
-
-  --pybidsdb_dwi_dir:
-    help: "The path to the pybids database associated with provided dwi_dir"
-    nargs: "?"
-    type: Path
-
   --responsemean_dir:
     help: "The path to the directory containing average response functions. If
       not provided, one will be computed from the subjects in the input

scattr/workflow/Snakefile

@@ -12,7 +12,7 @@ configfile: "config/snakebids.yml"
 
 
 # writes inputs_config.yml and updates config dict
-inputs_t1w = generate_inputs(
+inputs = generate_inputs(
     bids_dir=config["bids_dir"],
     pybids_inputs=config["pybids_inputs"],
     pybids_config=["bids", "derivatives"],
@@ -22,18 +22,6 @@ inputs_t1w = generate_inputs(
     participant_label=config["participant_label"],
     exclude_participant_label=config["exclude_participant_label"],
 )
-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["dwi_dir"]
-    else config.get("pybidsdb_dir"),
-    pybidsdb_reset=config.get("pybidsdb_reset"),
-    derivatives=config["derivatives"],
-    participant_label=config["participant_label"],
-    exclude_participant_label=config["exclude_participant_label"],
-)
 
 
 # this adds constraints to the bids naming
@@ -56,7 +44,7 @@ if config.get("labelmerge_base_dir") or config.get("labelmerge_overlay_dir"):
     """
     )
 
-if len(inputs_dwi.sessions) > 1 and not config.get("responsemean_ses"):
+if len(inputs.sessions) > 1 and not config.get("responsemean_ses"):
     print(
         """
     WARNING: Multiple sessions detected - average response function will be 
@@ -75,10 +63,10 @@ include: "rules/qc.smk"
 
 rule all:
     input:
-        tck_files=inputs_t1w["T1w"].expand(
+        tck_files=inputs["T1w"].expand(
             rules.filtered_tck2connectome.output.sl_assignment
         ),
-        dti_files=inputs_t1w["T1w"].expand(rules.dwi2tensor.output.dti),
+        dti_files=inputs["T1w"].expand(rules.dwi2tensor.output.dti),
         qc_files=rules.gather_qc.input,
     params:
         mrtrix_dir=mrtrix_dir,

scattr/workflow/rules/freesurfer.smk

@@ -19,13 +19,13 @@ bids_fs_out = partial(
     bids,
     root=freesurfer_dir,
     datatype="anat",
-    **inputs_t1w.subj_wildcards,
+    **inputs.subj_wildcards,
 )
 
 bids_log = partial(
     bids,
     root=log_dir,
-    **inputs_t1w.subj_wildcards,
+    **inputs.subj_wildcards,
 )
 
 """Freesurfer references (with additional in rules as necessary)
@@ -73,12 +73,10 @@ rule thalamic_segmentation:
         freesurfer_dir=freesurfer_dir,
     params:
         fs_license=fs_license,
-        subj_dir=str(Path(bids(**inputs_t1w.subj_wildcards)).parent),
+        subj_dir=str(Path(bids(**inputs.subj_wildcards)).parent),
     output:
         thal_seg=str(
-            Path(
-                bids(root=freesurfer_dir, **inputs_t1w.subj_wildcards)
-            ).parent
+            Path(bids(root=freesurfer_dir, **inputs.subj_wildcards)).parent
             / "mri"
             / "ThalamicNuclei.v12.T1.mgz"
         ),
@@ -115,9 +113,7 @@ 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.subj_wildcards)).parent
             / "mri"
             / "aparc+aseg.mgz"
         ),
@@ -162,7 +158,7 @@ rule fs_xfm_to_native:
     input:
         thal=rules.mgz2nii.output.thal,
         aparcaseg=rules.mgz2nii.output.aparcaseg,
-        ref=lambda wildcards: inputs_t1w["T1w"].filter(**wildcards).expand()[0],
+        ref=lambda wildcards: inputs["T1w"].filter(**wildcards).expand()[0],
     output:
         thal=bids_fs_out(
             space="T1w",

scattr/workflow/rules/mrtpipelines.smk

@@ -30,35 +30,35 @@ bids_dti_out = partial(
     root=mrtrix_dir,
     datatype="dti",
     model="dti",
-    **inputs_dwi.subj_wildcards,
+    **inputs.subj_wildcards,
 )
 
 bids_tractography_out = partial(
     bids,
     root=mrtrix_dir,
     datatype="tractography",
-    **inputs_dwi.subj_wildcards,
+    **inputs.subj_wildcards,
 )
 
 bids_anat_out = partial(
     bids,
     root=mrtrix_dir,
     datatype="anat",
-    **inputs_t1w.subj_wildcards,
+    **inputs.subj_wildcards,
 )
 
 bids_labelmerge = partial(
     bids,
     root=str(Path(labelmerge_dir) / "combined")
     if not config.get("skip_labelmerge")
     else config.get("labelmerge_base_dir") or zona_dir,
-    **inputs_t1w.subj_wildcards,
+    **inputs.subj_wildcards,
 )
 
 bids_log = partial(
     bids,
     root=log_dir,
-    **inputs_dwi.subj_wildcards,
+    **inputs.subj_wildcards,
 )
 
 """Mrtrix3 reference (additional citations are included per rule as necessary):