Add fmriprep bids app

src/simbids/cli/parser.py

@@ -151,6 +151,11 @@ def _bids_filter(value, parser):
         choices=['qsiprep', 'qsirecon', 'xcp_d', 'fmriprep'],
         help=('BIDS-App to be simulated'),
     )
+    parser.add_argument(
+        '--anat-only',
+        action='store_true',
+        help=('Only run the anatomical workflow'),
+    )
 
     g_bids = parser.add_argument_group('Options for filtering BIDS queries')
     g_bids.add_argument(

src/simbids/config.py

@@ -541,6 +541,8 @@ class workflow(_Config):
     """Ignore particular steps for *SimBIDS*."""
     bids_app = 'qsiprep'
     """The BIDS App to simulate."""
+    anat_only = False
+    """Only run the anatomical workflow."""
 
 
 class loggers:

src/simbids/data/nipreps.json

@@ -0,0 +1,185 @@
+{
+    "name": "nipreps",
+    "entities": [
+      {
+        "name": "subject",
+        "pattern": "[/\\\\]+sub-([a-zA-Z0-9+]+)",
+        "directory": "{subject}"
+      },
+      {
+        "name": "session",
+        "pattern": "[_/\\\\]+ses-([a-zA-Z0-9+]+)",
+        "mandatory": false,
+        "directory": "{subject}{session}"
+      },
+      {
+        "name": "task",
+        "pattern": "[_/\\\\]+task-([a-zA-Z0-9+]+)"
+      },
+      {
+        "name": "acquisition",
+        "pattern": "[_/\\\\]+acq-([a-zA-Z0-9+]+)"
+      },
+      {
+        "name": "ceagent",
+        "pattern": "[_/\\\\]+ce-([a-zA-Z0-9+]+)"
+      },
+      {
+        "name": "reconstruction",
+        "pattern": "[_/\\\\]+rec-([a-zA-Z0-9+]+)"
+      },
+      {
+        "name": "direction",
+        "pattern": "[_/\\\\]+dir-([a-zA-Z0-9+]+)"
+      },
+      {
+        "name": "run",
+        "pattern": "[_/\\\\]+run-(\\d+)",
+        "dtype": "int"
+      },
+      {
+        "name": "proc",
+        "pattern": "[_/\\\\]+proc-([a-zA-Z0-9+]+)"
+      },
+      {
+        "name": "modality",
+        "pattern": "[_/\\\\]+mod-([a-zA-Z0-9+]+)"
+      },
+      {
+        "name": "echo",
+        "pattern": "[_/\\\\]+echo-([0-9]+)"
+      },
+      {
+        "name": "flip",
+        "pattern": "[_/\\\\]+flip-([0-9]+)"
+      },
+      {
+        "name": "inv",
+        "pattern": "[_/\\\\]+inv-([0-9]+)"
+      },
+      {
+        "name": "mt",
+        "pattern": "[_/\\\\]+mt-(on|off)"
+      },
+      {
+        "name": "part",
+        "pattern": "[_/\\\\]+part-(mag|phase|real|imag)"
+      },
+      {
+        "name": "recording",
+        "pattern": "[_/\\\\]+recording-([a-zA-Z0-9+]+)"
+      },
+      {
+        "name": "space",
+        "pattern": "[_/\\\\]+space-([a-zA-Z0-9+]+)"
+      },
+      {
+        "name": "suffix",
+        "pattern": "[._]*([a-zA-Z0-9]*?)\\.[^/\\\\]+$"
+      },
+      {
+        "name": "scans",
+        "pattern": "(.*\\_scans.tsv)$"
+      },
+      {
+        "name": "fmap",
+        "pattern": "(phasediff|magnitude[1-2]|phase[1-2]|fieldmap|epi)\\.nii"
+      },
+      {
+        "name": "datatype",
+        "pattern": "[/\\\\]+(func|anat|fmap|dwi|meg|eeg|perf|figures)[/\\\\]+"
+      },
+      {
+        "name": "extension",
+        "pattern": "[._]*[a-zA-Z0-9]*?(\\.[^/\\\\]+)$"
+      },
+      {
+        "name": "atlas",
+        "pattern": "[_/\\\\]+atlas-([a-zA-Z0-9+]+)"
+      },
+      {
+        "name": "roi",
+        "pattern": "[_/\\\\]+roi-([a-zA-Z0-9+]+)"
+      },
+      {
+        "name": "label",
+        "pattern": "[_/\\\\]+label-([a-zA-Z0-9+]+)"
+      },
+      {
+        "name": "fmapid",
+        "pattern": "[_/\\\\]+fmapid-([a-zA-Z0-9+]+)"
+      },
+      {
+        "name": "desc",
+        "pattern": "[_/\\\\]+desc-([a-zA-Z0-9+]+)"
+      },
+      {
+        "name": "from",
+        "pattern": "(?:^|_)from-([a-zA-Z0-9+]+).*xfm"
+      },
+      {
+        "name": "to",
+        "pattern": "(?:^|_)to-([a-zA-Z0-9+]+).*xfm"
+      },
+      {
+        "name": "mode",
+        "pattern": "(?:^|_)mode-(image|points).*xfm"
+      },
+      {
+        "name": "hemi",
+        "pattern": "hemi-(L|R)"
+      },
+      {
+        "name": "model",
+        "pattern": "model-([a-zA-Z0-9+]+)"
+      },
+      {
+        "name": "subset",
+        "pattern": "subset-([a-zA-Z0-9+]+)"
+      },
+      {
+        "name": "resolution",
+        "pattern": "res-([a-zA-Z0-9+]+)"
+      },
+      {
+        "name": "density",
+        "pattern": "res-([a-zA-Z0-9+]+)"
+      },
+      {
+        "name": "cohort",
+        "pattern": "[_/\\\\]+cohort-0*(\\d+)",
+        "dtype": "int"
+      }
+    ],
+    "default_path_patterns": [
+      "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2starmap|FLAIR|FLASH|PDmap|PD|PDT2|dseg|inplaneT[12]|angio|T2starw|MTw|TSE>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
+      "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_hemi-{hemi<L|R>}]_from-{from}_to-{to}_mode-{mode<image|points>|image}_{suffix<xfm>|xfm}{extension<.txt|.h5>}",
+      "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}]_hemi-{hemi<L|R>}[_space-{space}][_cohort-{cohort}][_den-{density}][_desc-{desc}]_{suffix<white|smoothwm|pial|midthickness|inflated|vinflated|sphere|flat|sulc|curv|thickness>}{extension<.surf.gii|.shape.gii>}",
+      "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_den-{density}][_desc-{desc}]_{suffix<sulc|curv|thickness>}{extension<.dscalar.nii|.json>}",
+      "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_desc-{desc}_{suffix<mask>|mask}{extension<.nii|.nii.gz|.json>|.nii.gz}",
+      "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_label-{label}[_desc-{desc}]_{suffix<probseg>|probseg}{extension<.nii|.nii.gz|.json>|.nii.gz}",
+      "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<bold|cbv|sbref|boldref|boldmap|dseg>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
+      "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<phase>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
+      "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_hemi-{hemi<L|R>}]_from-{from}_to-{to}_mode-{mode<image|points>|image}[_desc-{desc}]_{suffix<xfm>|xfm}{extension<.txt|.h5>}",
+      "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_desc-{desc}_{suffix<mask>|mask}{extension<.nii|.nii.gz|.json>|.nii.gz}",
+      "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<AROMAnoiseICs>|AROMAnoiseICs}{extension<.csv|.tsv>|.csv}",
+      "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<timeseries|regressors>|timeseries}{extension<.json|.tsv>|.tsv}",
+      "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<components|mixing>|components}{extension<.json|.tsv|.nii|.nii.gz>|.tsv}",
+      "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<decomposition>|decomposition}{extension<.json>|.json}",
+      "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_hemi-{hemi<L|R>}][_space-{space}][_cohort-{cohort}][_den-{density}][_desc-{desc}]_{suffix<bold|boldmap>}{extension<.dtseries.nii|.dtseries.json|.func.gii|.func.json>}",
+      "sub-{subject}[/ses-{session}]/{datatype<func>}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<T2starmap>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
+      "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<dwi|dwiref|epiref|lowb|dseg>}{extension<.json|.nii.gz|.nii>|.nii.gz}",
+      "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_desc-{desc}_{suffix<mask>}{extension<.json|.nii.gz|.nii>|.nii.gz}",
+      "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<dwi>}{extension<.tsv|.bval|.bvec|.b>|.tsv}",
+      "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_rec-{reconstruction}][_dir-{direction}][_run-{run}]_from-{from}_to-{to}_mode-{mode<image|points>|image}[_desc-{desc}]_{suffix<xfm>|xfm}{extension<.txt|.h5>}",
+      "sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_rec-{reconstruction}][_dir-{direction}][_run-{run}]_{suffix<aslcontext>}{extension<.tsv|.json>|.tsv}",
+      "sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}]_from-{from}_to-{to}_mode-{mode<image|points>|image}_{suffix<xfm>|xfm}{extension<.txt|.h5>}",
+      "sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix<timeseries>}{extension<.json|.tsv>|.tsv}",
+      "sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix<asl|aslref|att|cbf|coverage|mask>}{extension<.nii|.nii.gz|.json|.tsv>|.tsv}",
+      "sub-{subject}[/ses-{session}]/{datatype<fmap>|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_run-{run}][_part-{part}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_fmapid-{fmapid}][_desc-{desc}]_{suffix<fieldmap>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
+      "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio|dseg|mask|T2starw|MTw|TSE>}{extension<.html|.svg>|.svg}",
+      "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_fmapid-{fmapid}][_desc-{desc}]_{suffix<fieldmap>}{extension<.html|.svg>|.svg}",
+      "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<dwi|epi|epiref>}{extension<.html|.svg>|.svg}",
+      "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<bold|boldmap>}{extension<.html|.svg>|.svg}"
+    ]
+  }

src/simbids/interfaces/bids.py

@@ -78,3 +78,27 @@ class QSIReconDerivativesDataSink(BaseDerivativesDataSink):
     _config_entities = config_entities
     _config_entities_dict = merged_entities
     _file_patterns = simbids_spec['default_path_patterns']
+
+
+class NiPrepsDerivativesDataSink(BaseDerivativesDataSink):
+    """Store derivative files.
+
+    A child class of the niworkflows DerivativesDataSink,
+    using simbids's configuration files.
+    """
+
+    simbids_spec = loads(load_data('nipreps.json').read_text())
+    bids_config = Config.load('bids')
+    deriv_config = Config.load('derivatives')
+
+    simbids_entities = {v['name']: v['pattern'] for v in simbids_spec.get('entities', {})}
+    merged_entities = {**bids_config.entities, **deriv_config.entities}
+    merged_entities = {k: v.pattern for k, v in merged_entities.items()}
+    merged_entities = {**merged_entities, **simbids_entities}
+    merged_entities = [{'name': k, 'pattern': v} for k, v in merged_entities.items()]
+    config_entities = frozenset({e['name'] for e in merged_entities})
+    out_path_base = ''
+    _allowed_entities = set(config_entities)
+    _config_entities = config_entities
+    _config_entities_dict = merged_entities
+    _file_patterns = simbids_spec['default_path_patterns']

src/simbids/workflows/base.py

@@ -124,5 +124,9 @@ def init_single_subject_wf(subject_id: str):
 
         write_root_level_atlases(config.execution.output_dir)
         return init_single_subject_qsirecon_wf(subject_id)
+    elif config.workflow.bids_app == 'fmriprep':
+        from simbids.workflows.fmriprep import init_single_subject_fmriprep_wf
+
+        return init_single_subject_fmriprep_wf(subject_id)
     else:
         raise ValueError(f'Unknown application: {config.workflow.bids_app}')