update docs and add pybidsdb options

docs/outputs/output_files.md

@@ -1,9 +1,9 @@
 # Output Files
 
-After running the workflow, the `/path/to/output/dir` folder will contain a 
-hidden `.logs` folder for troubleshooting, as well as additional folders 
-associated with the tools that were used to generate files (e.g. `freesurfer`, 
-`labelmerge`), but for most purposes, all the primary outputs of interest will 
+After running the workflow, the `/path/to/output/dir` folder will contain a
+hidden `.logs` folder for troubleshooting, as well as additional folders
+associated with the tools that were used to generate files (e.g. `freesurfer`,
+`labelmerge`), but for most purposes, all the primary outputs of interest will
 be in the `mrtrix` directory with the following structure:
 
 ```
@@ -15,16 +15,16 @@ mrtrix/
     └── tractography
 ```
 
-Briefly, `dti` contains processed diffusion tensor images along with 
+Briefly, `dti` contains processed diffusion tensor images along with
 quantitative maps (e.g. `FA`, `MD`, etc.), `dwi` contains images that were
-converted from Nifti (`.nii.gz`) to the MRtrix imaging format (`.mif`), 
+converted from Nifti (`.nii.gz`) to the MRtrix imaging format (`.mif`),
 `response` contains subject-specific response functions, and `tractography`
 contains tractogram files.
 
 ## dti
 
-This folder contains processed diffusion tensor images (DTI) that were used to 
-compute quantitative maps (stored in the MRtrix imaging format - `.mif`), also 
+This folder contains processed diffusion tensor images (DTI) that were used to
+compute quantitative maps (stored in the MRtrix imaging format - `.mif`), also
 found within the folder:
 
 ```
@@ -38,20 +38,20 @@ sub-{subject}
 ```
 
 As per the BIDS extension proposal, `model-dti` denotes to the DTI model used to
-process the data, and the suffix (`ad`, `fa`, `md`, `rd`, `tensor`) describes 
+process the data, and the suffix (`ad`, `fa`, `md`, `rd`, `tensor`) describes
 the imaging data.
 
 ## dwi
 
-This folder contains the input diffusion weighted image (dwi) and brain mask 
+This folder contains the input diffusion weighted image (dwi) and brain mask
 converted from Nifti (`.nii.gz`) to the MRtrix imaging format (`.mif`) used in
 downstream processing. It also contains an intensity normalized dwi image used
 for DTI:
 
 ```
 sub-{subject}
 └── dwi
-    ├── sub-{subject}_brainmask.mif
+    ├── sub-{subject}_desc-brain_mask.mif
     ├── sub-{subject}_desc-normalized_dwi.mif
     └── sub-{subject}_dwi.mif
 ```
@@ -60,7 +60,7 @@ sub-{subject}
 
 This folder contains the subject-specific response functions that were estimated
 from the input diffusion data, as well as both the normalized and unnormalized
-versions of the estimated fibre orientation distribution (FOD) maps. Both 
+versions of the estimated fibre orientation distribution (FOD) maps. Both
 response functions and FOD maps are estimated for the three different tissue
 types: white matter (wm), grey matter (gm), and corticospinal fluid (csf):
 
@@ -96,19 +96,20 @@ sub-{subject}
     ├── sub-{subject}_desc-subcortical_nodeWeights.csv
 ```
 
-The `desc-filteredsubcortical` entity pair describes associated tractogram 
-files that have been filtered to only pass through WM and connect two GM 
+The `desc-filteredsubcortical` entity pair describes associated tractogram
+files that have been filtered to only pass through WM and connect two GM
 structures, while the `desc-subcortical` entity pair denotes files associated
 with the unfiltered subcortical connectome. Whole-brain tractogram associated
 files are denoted by `desc-iFOD2`, which describes the tractography algorithm
 used to perform tractograpy.
 
-_Note: As the BIDS extension proposal has not been finalized, the naming of 
+_Note: As the BIDS extension proposal has not been finalized, the naming of
 such files may be subject to change_
 
 ## Additional Files
 
 The top-level `/path/to/output/dir` contains additional files / folders:
+
 ```
 /path/to/output/dir
 ├── ...
@@ -118,13 +119,13 @@ The top-level `/path/to/output/dir` contains additional files / folders:
 └── .snakemake
 ```
 
-The `config` folder, along with the hidden `.snakebids` and `.snakemake` folders 
+The `config` folder, along with the hidden `.snakebids` and `.snakemake` folders
 contain a record of the code and parameters used, and paths to the inputs.
 
-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`). 
+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 
+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.
+be placed in a `results` folder.

scattr/config/snakebids.yml

@@ -50,6 +50,7 @@ pybids_inputs_dwi:
       - part
       - reconstruction
       - run
+      - res
   mask:
     filters:
       suffix: "mask"
@@ -119,6 +120,11 @@ parse_args:
     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

@@ -16,6 +16,8 @@ inputs_t1w = generate_inputs(
     bids_dir=config["bids_dir"],
     pybids_inputs=config["pybids_inputs"],
     pybids_config=["bids", "derivatives"],
+    pybidsdb_dir=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"],
@@ -24,6 +26,8 @@ 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_reset=config.get("pybidsdb_reset"),
     derivatives=config["derivatives"],
     participant_label=config["participant_label"],
     exclude_participant_label=config["exclude_participant_label"],