Merge branch 'develop'

Dockerfile

@@ -250,9 +250,11 @@ RUN mkdir /bids_input /output /atlases /config
 
 # include bidsapp interface
 COPY ["app", "/app"]
+RUN chmod -R 775 /app
 RUN pip3 install -r /app/requirements.txt
 # setup entrypoint
 COPY ["./entrypoint.sh", "/entrypoint.sh"]
+RUN chmod -R 775 /entrypoint.sh
 COPY ["LICENSE", "/LICENSE"]
 ENTRYPOINT ["/entrypoint.sh"]
 WORKDIR /

app/helpers.py

@@ -6,13 +6,14 @@
 from bids.layout import BIDSLayout
 
 
-def read_bids_dataset(bids_input, subject_list=None, collect_on_subject=False):
+def read_bids_dataset(bids_input, subject_list=None, session_list=None, collect_on_subject=False):
     """
     extracts and organizes relevant metadata from a bids dataset necessary
     for the dcan-modified hcp fmri processing pipeline.
     :param bids_input: path to input bids folder
     :param subject_list: EITHER, a list of subject ids to filter on,
     OR a dictionary of subject id: list of sessions to filter on.
+    :param session_list: a list of session ids to filter on.
     :param collect_on_subject: collapses all sessions, for cases with
     non-longitudinal data spread across scan sessions.
     :return: bids data struct (nested dict)
@@ -48,6 +49,11 @@ def read_bids_dataset(bids_input, subject_list=None, collect_on_subject=False):
     # filter session list
     for s in subjects:
         sessions = layout.get_sessions(subject=s)
+
+        # filter sessions_list
+        if isinstance(session_list, list):
+            sessions = [t for t in sessions if t in session_list]
+
         if not sessions:
             subsess += [(s, None)]
         elif collect_on_subject:

app/run.py

@@ -50,6 +50,7 @@ def _cli():
         'bids_dir': args.bids_dir,
         'output_dir': args.output_dir,
         'subject_list': args.subject_list,
+        'session_list': args.session_list,
         'collect': args.collect,
         'ncpus': args.ncpus,
         'stages': args.stages,
@@ -103,6 +104,13 @@ def generate_parser(parser=None):
              'found under the BIDS input directory. The participant label '
              'does not include the "sub-" prefix'
     )
+    parser.add_argument(
+        '--session-id', dest='session_list', nargs='*',
+        metavar='LABEL',
+        help='filter input dataset by session id. Default is all ids '
+             'found under the subject input directory(s).  A session id '
+             'does not include "ses-"'
+    )
     parser.add_argument(
         '--freesurfer-license', dest='freesurfer_license',
         metavar='LICENSE_FILE',
@@ -219,14 +227,15 @@ def interface(bids_dir, output_dir, subject_list=None, collect=False, ncpus=1,
               stages=None, bandstop_params=None, check_only=False,
               run_abcd_task=False, study_template=None, cleaning_json=None,
               print_commands=False, ignore_expected_outputs=False,
-              ignore_modalities=[], freesurfer_license=None):
+              ignore_modalities=[], freesurfer_license=None, session_list=None):
     """
     main application interface
     :param bids_dir: input bids dataset see "helpers.read_bids_dataset" for
     more information.
     :param output_dir: output folder
     :param subject_list: subject and session list filtering.  See
     "helpers.read_bids_dataset" for more information.
+    :param session_list: session list filtering. See "helpers.read_bids_dataset".
     :param collect: treats each subject as having only one session.
     :param ncpus: number of cores for parallelized processing.
     :param stages: only run a subset of stages.
@@ -241,7 +250,8 @@ def interface(bids_dir, output_dir, subject_list=None, collect=False, ncpus=1,
     if not os.path.isdir(output_dir):
         os.makedirs(output_dir)
     session_generator = read_bids_dataset(
-        bids_dir, subject_list=subject_list, collect_on_subject=collect
+        bids_dir, subject_list=subject_list, 
+        collect_on_subject=collect, session_list=session_list
     )
 
     # run each session in serial