Add qsiprep/qsirecon bids app options

src/simbids/cli/parser.py

@@ -147,7 +147,7 @@ def _bids_filter(value, parser):
     )
 
     parser.add_argument(
-        'bids_app',
+        '--bids-app',
         choices=['qsiprep', 'qsirecon', 'xcp_d', 'fmriprep'],
         help=('BIDS-App to be simulated'),
     )

src/simbids/utils/bids.py

@@ -39,6 +39,75 @@
 from simbids.data import load as load_data
 
 
+def write_derivative_description(input_dir, output_dir):
+    """Write dataset_description.json file for derivatives.
+
+    Parameters
+    ----------
+    input_dir : :obj:`str`
+        Path to the primary input dataset being ingested.
+        This may be a raw BIDS dataset (in the case of raw+derivatives workflows)
+        or a preprocessing derivatives dataset (in the case of derivatives-only workflows).
+    output_dir : :obj:`str`
+        Path to the output xcp-d dataset.
+    dataset_links : :obj:`dict`, optional
+        Dictionary of dataset links to include in the dataset description.
+    """
+
+    DOWNLOAD_URL = 'https://github.com/nipreps/simbids/archive/0.1.0.tar.gz'
+
+    input_dir = Path(input_dir)
+    output_dir = Path(output_dir)
+
+    orig_dset_description = os.path.join(input_dir, 'dataset_description.json')
+    if not os.path.isfile(orig_dset_description):
+        raise FileNotFoundError(f'Dataset description does not exist: {orig_dset_description}')
+
+    with open(orig_dset_description) as fobj:
+        desc = json.load(fobj)
+
+    # Update dataset description
+    desc['Name'] = 'fMRIPost-AROMA- ICA-AROMA Postprocessing Outputs'
+    desc['BIDSVersion'] = '1.9.0dev'
+    desc['DatasetType'] = 'derivative'
+    desc['HowToAcknowledge'] = 'Include the generated boilerplate in the methods section.'
+
+    # Start with GeneratedBy from the primary input dataset's dataset_description.json
+    desc['GeneratedBy'] = desc.get('GeneratedBy', [])
+
+    # Add GeneratedBy from fMRIPost-AROMA
+    desc['GeneratedBy'].insert(
+        0,
+        {
+            'Name': 'SimBIDS',
+            'Version': '0.1.0',
+            'CodeURL': DOWNLOAD_URL,
+        },
+    )
+
+    # Keys that can only be set by environment
+    if 'SIMBIDS_SINGULARITY_URL' in os.environ:
+        desc['GeneratedBy'][0]['Container'] = {
+            'Type': 'singularity',
+            'URI': os.getenv('SIMBIDS_SINGULARITY_URL'),
+        }
+
+    # Replace local templateflow path with URL
+    dataset_links = {}
+    dataset_links['templateflow'] = 'https://github.com/templateflow/templateflow'
+
+    # Add DatasetLinks
+    desc['DatasetLinks'] = desc.get('DatasetLinks', {})
+    for k, v in dataset_links.items():
+        if k in desc['DatasetLinks'].keys() and str(desc['DatasetLinks'][k]) != str(v):
+            print(f'"{k}" is already a dataset link. Overwriting.')
+
+        desc['DatasetLinks'][k] = str(v)
+
+    out_desc = Path(output_dir / 'dataset_description.json')
+    out_desc.write_text(json.dumps(desc, indent=4))
+
+
 def collect_derivatives(
     raw_dataset: Path | BIDSLayout | None,
     derivatives_dataset: Path | BIDSLayout | None,

src/simbids/workflows/base.py

@@ -36,6 +36,8 @@
 
 from simbids import config
 
+from ..utils.bids import write_derivative_description
+
 
 def init_simbids_wf():
     """Build *SimBIDS*'s pipeline.
@@ -61,7 +63,7 @@ def init_simbids_wf():
 
     simbids_wf = Workflow(name=f'simbids_{ver.major}_{ver.minor}_wf')
     simbids_wf.base_dir = config.execution.work_dir
-
+    write_derivative_description(config.execution.bids_dir, config.execution.output_dir)
     for subject_id in config.execution.participant_label:
         single_subject_wf = init_single_subject_wf(subject_id)
 
@@ -114,5 +116,13 @@ def init_single_subject_wf(subject_id: str):
         from simbids.workflows.qsiprep import init_single_subject_qsiprep_wf
 
         return init_single_subject_qsiprep_wf(subject_id)
+    elif config.workflow.bids_app == 'qsirecon':
+        from simbids.workflows.qsirecon import (
+            init_single_subject_qsirecon_wf,
+            write_root_level_atlases,
+        )
+
+        write_root_level_atlases(config.execution.output_dir)
+        return init_single_subject_qsirecon_wf(subject_id)
     else:
-        raise ValueError(f'Unknown application: {config.workflow.simulated_app}')
+        raise ValueError(f'Unknown application: {config.workflow.bids_app}')

src/simbids/workflows/qsiprep/qsiprep.py

@@ -313,134 +313,120 @@ def init_single_subject_qsiprep_wf(subject_id: str):
 
     # Create the anatomical datasinks
     anatomical_template = 'MNI152NLin6Asym'
-    for anat_file in subject_data['t1w']:
-        workflow.add_nodes(
-            [
-                pe.Node(
-                    DerivativesDataSink(
-                        compress=True,
-                        in_file=anat_file,
-                        source_file=anat_file,
-                        base_directory=config.execution.output_dir,
-                        space='ACPC',
-                        desc='preproc',
-                        keep_dtype=True,
-                    ),
-                    name=_get_wf_name(anat_file, 'ds_t1_preproc'),
-                    run_without_submitting=True,
+    anat_file = (subject_data['t1w'] + subject_data['t2w'])[0]
+    workflow.add_nodes(
+        [
+            pe.Node(
+                DerivativesDataSink(
+                    compress=True,
+                    in_file=anat_file,
+                    source_file=anat_file,
+                    base_directory=config.execution.output_dir,
+                    space='ACPC',
+                    desc='preproc',
+                    keep_dtype=True,
                 ),
-                pe.Node(
-                    DerivativesDataSink(
-                        compress=True,
-                        in_file=anat_file,
-                        source_file=anat_file,
-                        base_directory=config.execution.output_dir,
-                        space='ACPC',
-                        desc='brain',
-                        suffix='mask',
-                    ),
-                    name=_get_wf_name(anat_file, 'ds_t1_mask'),
-                    run_without_submitting=True,
+                name=_get_wf_name(anat_file, 'ds_t1_preproc'),
+                run_without_submitting=True,
+            ),
+            pe.Node(
+                DerivativesDataSink(
+                    compress=True,
+                    in_file=anat_file,
+                    source_file=anat_file,
+                    base_directory=config.execution.output_dir,
+                    space='ACPC',
+                    desc='brain',
+                    suffix='mask',
                 ),
-                pe.Node(
-                    DerivativesDataSink(
-                        compress=True,
-                        in_file=anat_file,
-                        source_file=anat_file,
-                        base_directory=config.execution.output_dir,
-                        space='ACPC',
-                        suffix='dseg',
-                    ),
-                    name=_get_wf_name(anat_file, 'ds_t1_seg'),
-                    run_without_submitting=True,
+                name=_get_wf_name(anat_file, 'ds_t1_mask'),
+                run_without_submitting=True,
+            ),
+            pe.Node(
+                DerivativesDataSink(
+                    compress=True,
+                    in_file=anat_file,
+                    source_file=anat_file,
+                    base_directory=config.execution.output_dir,
+                    space='ACPC',
+                    suffix='dseg',
                 ),
-                pe.Node(
-                    DerivativesDataSink(
-                        compress=True,
-                        in_file=anat_file,
-                        source_file=anat_file,
-                        base_directory=config.execution.output_dir,
-                        space='ACPC',
-                        desc='aseg',
-                        suffix='dseg',
-                    ),
-                    name=_get_wf_name(anat_file, 'ds_t1_aseg'),
-                    run_without_submitting=True,
+                name=_get_wf_name(anat_file, 'ds_t1_seg'),
+                run_without_submitting=True,
+            ),
+            pe.Node(
+                DerivativesDataSink(
+                    compress=True,
+                    in_file=anat_file,
+                    source_file=anat_file,
+                    base_directory=config.execution.output_dir,
+                    space='ACPC',
+                    desc='aseg',
+                    suffix='dseg',
                 ),
-                pe.Node(
-                    DerivativesDataSink(
-                        in_file=anat_file,
-                        source_file=anat_file,
-                        base_directory=config.execution.output_dir,
-                        to='ACPC',
-                        mode='image',
-                        suffix='xfm',
-                        **{'from': anatomical_template},
-                    ),
-                    name=_get_wf_name(anat_file, 'ds_t1_mni_inv_warp'),
-                    run_without_submitting=True,
+                name=_get_wf_name(anat_file, 'ds_t1_aseg'),
+                run_without_submitting=True,
+            ),
+            pe.Node(
+                DerivativesDataSink(
+                    in_file=anat_file,
+                    source_file=anat_file,
+                    base_directory=config.execution.output_dir,
+                    suffix='xfm',
+                    extension='.h5',
+                    **{'from': anatomical_template, 'to': 'ACPC', 'mode': 'image'},
                 ),
-                pe.Node(
-                    DerivativesDataSink(
-                        source_file=anat_file,
-                        in_file=anat_file,
-                        base_directory=config.execution.output_dir,
-                        to='ACPC',
-                        mode='image',
-                        suffix='xfm',
-                        **{'from': 'anat'},
-                    ),
-                    name=_get_wf_name(anat_file, 'ds_t1_template_acpc_transforms'),
-                    run_without_submitting=True,
+                name=_get_wf_name(anat_file, 'ds_t1_mni_inv_warp'),
+                run_without_submitting=True,
+            ),
+            pe.Node(
+                DerivativesDataSink(
+                    source_file=anat_file,
+                    in_file=text_file,
+                    base_directory=config.execution.output_dir,
+                    to='ACPC',
+                    mode='image',
+                    suffix='xfm',
+                    extension='.mat',
+                    **{'from': 'anat'},
                 ),
-                pe.Node(
-                    DerivativesDataSink(
-                        in_file=anat_file,
-                        source_file=anat_file,
-                        base_directory=config.execution.output_dir,
-                        to='anat',
-                        mode='image',
-                        suffix='xfm',
-                        **{'from': 'ACPC'},
-                    ),
-                    name=_get_wf_name(anat_file, 'ds_t1_template_acpc_inv_transforms'),
-                    run_without_submitting=True,
+                name=_get_wf_name(anat_file, 'ds_t1_template_acpc_transforms'),
+                run_without_submitting=True,
+            ),
+            pe.Node(
+                DerivativesDataSink(
+                    in_file=text_file,
+                    source_file=anat_file,
+                    base_directory=config.execution.output_dir,
+                    to='anat',
+                    mode='image',
+                    suffix='xfm',
+                    extension='.mat',
+                    **{'from': 'ACPC'},
                 ),
-                pe.Node(
-                    DerivativesDataSink(
-                        in_file=anat_file,
-                        source_file=anat_file,
-                        base_directory=config.execution.output_dir,
-                        to=anatomical_template,
-                        mode='image',
-                        suffix='xfm',
-                        **{'from': 'ACPC'},
-                    ),
-                    name=_get_wf_name(anat_file, 'ds_t1_mni_warp'),
-                    run_without_submitting=True,
+                name=_get_wf_name(anat_file, 'ds_t1_template_acpc_inv_transforms'),
+                run_without_submitting=True,
+            ),
+            pe.Node(
+                DerivativesDataSink(
+                    in_file=anat_file,
+                    source_file=anat_file,
+                    base_directory=config.execution.output_dir,
+                    to=anatomical_template,
+                    mode='image',
+                    suffix='xfm',
+                    extension='.h5',
+                    **{'from': 'ACPC'},
                 ),
-            ]
-        )
+                name=_get_wf_name(anat_file, 'ds_t1_mni_warp'),
+                run_without_submitting=True,
+            ),
+        ]
+    )
 
     return clean_datasinks(workflow)
 
 
-def init_single_dwi_run_wf(dwi_file: str):
-    """Set up a single-run workflow for SimBIDS."""
-    from niworkflows.engine.workflows import LiterateWorkflow as Workflow
-
-    workflow = Workflow(name=_get_wf_name(dwi_file, 'single_run'))
-    workflow.__desc__ = ''
-
-    # Fill in datasinks seen so far
-    for node in workflow.list_node_names():
-        if node.split('.')[-1].startswith('ds_'):
-            workflow.get_node(node).inputs.base_directory = config.execution.output_dir
-            workflow.get_node(node).inputs.source_file = dwi_file
-
-    return workflow
-
-
 def clean_datasinks(workflow: pe.Workflow) -> pe.Workflow:
     """Overwrite ``out_path_base`` of DataSinks."""
     for node in workflow.list_node_names():

src/simbids/workflows/qsirecon/__init__.py

@@ -0,0 +1,3 @@
+from .qsirecon import init_single_subject_qsirecon_wf, write_root_level_atlases
+
+__all__ = ['init_single_subject_qsirecon_wf', 'write_root_level_atlases']