Merge pull request #9 from DCAN-Labs/develop

Sync dev and master

Dockerfile

@@ -18,7 +18,7 @@ RUN python3 -m pip install -r "/app/requirements.txt"
 
 # insert pipeline code
 ADD https://github.com/DCAN-Labs/dcan-infant-pipeline.git version.json
-RUN git clone -b 'v0.0.1' --single-branch --depth 1 https://github.com/DCAN-Labs/dcan-infant-pipeline.git /opt/pipeline
+RUN git clone -b 'v0.0.2' --single-branch --depth 1 https://github.com/DCAN-Labs/dcan-infant-pipeline.git /opt/pipeline
 
 # unless otherwise specified...
 ENV OMP_NUM_THREADS=1

app/helpers.py

@@ -328,3 +328,25 @@ def validate_config(bids_spec, anat_only):
     assert ('bold' in modes) or anat_only, 'Must provide functional data or specify --ignore-func or --anat-only.'
 
 
+def validate_license(freesurfer_license):
+    fshome = os.environ['FREESURFER_HOME']
+    license_txt = os.path.join(fshome, 'license.txt')
+    if freesurfer_license is None:
+        print('DEBUG:')
+        print('default path: %s' % license_txt)
+        assert os.path.exists(license_txt), \
+            'freesurfer license.txt not located. You can provide a license ' \
+            'file using the --freesurfer-license <LICENSE> argument.'
+    elif os.path.normpath(license_txt) == os.path.normpath(freesurfer_license):
+        print('DEBUG:')
+        print('these must be the same:')
+        print('first: %s' % os.path.normpath(license_txt))
+        print('second: %s' % os.path.normpath(freesurfer_license))
+        pass
+    else:
+        import shutil
+        print('DEBUG:')
+        print('copying: %s' % freesurfer_license)
+        print('to: %s' % license_txt)
+        shutil.copy(freesurfer_license, license_txt)
+

app/run.py

@@ -29,7 +29,7 @@
 import argparse
 import os
 
-from helpers import (read_bids_dataset, validate_config)
+from helpers import (read_bids_dataset, validate_config, validate_license)
 from pipelines import (ParameterSettings, PreFreeSurfer, FreeSurfer,
                        PostFreeSurfer, FMRIVolume, FMRISurface,
                        DCANBOLDProcessing, ExecutiveSummary, CustomClean,
@@ -52,6 +52,7 @@ def _cli():
         'atropos_range': args.atropos_range,
         'bandstop_params': args.bandstop,
         'dcmethod': args.dcmethod,
+        'freesurfer_license': args.freesurfer_license,
         'hyper_norm_method': args.hyper_norm_method,
         'jlf_method': args.jlf_method,
         'max_cortical_thickness': args.max_cortical_thickness,
@@ -108,7 +109,8 @@ def generate_parser(parser=None):
     # Optional args (now sorted alphabetically:
     parser.add_argument(
         '--aseg', type=str, dest='aseg',
-        default="DEFAULT",
+        default='DEFAULT',
+        metavar='PATH',
         help='specify path to the aseg file to be used by FreeSurfer. '
              'Default: aseg generated by PreFreeSurfer. '
     )
@@ -148,22 +150,30 @@ def generate_parser(parser=None):
         help='specify a distortion correction method. Default: use auto-'
              'detection. '
     )
+    parser.add_argument(
+        '--freesurfer-license', dest='freesurfer_license',
+        metavar='PATH',
+        help='If using docker or singularity, you will need to acquire and '
+             'provide your own FreeSurfer license. The license can be '
+             'acquired by filling out this form: '
+             'https://surfer.nmr.mgh.harvard.edu/registration.html '
+    )
     parser.add_argument(
         '--hyper-normalization-method', dest='hyper_norm_method',
         default='ADULT_GM_IP',
         choices=['ADULT_GM_IP', 'ROI_IPS', 'NONE'],
         help='specify the intensity profiles to use for the hyper-'
-             'normalization step in FreeSurfer: '
+             'normalization step in FreeSurfer: \n'
              'ADULT_GM_IP adjusts the entire base image such that the IP '
              'of GM in the target roughly matches the IP of GM of the '
              'reference (i.e., the adult freesurfer atlas). Then the WM '
              'is shifted in the target image to match the histogram of WM '
-             'in the reference. '
+             'in the reference. \n'
              'ROI_IPS adjusts the intensity profiles of each ROI (GM, WM, '
              'CSF) separately and reassembles the parts. '
              'NONE skips hyper-normalization step. This allows the user '
              'to run PreFreeSurfer, apply new, experimental hyper-'
-             'normalization methods and then restart at FreeSurfer. '
+             'normalization methods and then restart at FreeSurfer. \n'
              'Default: ADULT_GM_IP.'
     )
     parser.add_argument(
@@ -176,25 +186,28 @@ def generate_parser(parser=None):
     parser.add_argument(
         '--max-cortical-thickness', type=int, dest='max_cortical_thickness',
         default=5,
+        metavar='MM',
         help='maximum cortical thickness to allow in FreeSurfer. '
              'Default: 5 mm. '
 
     )
     parser.add_argument(
         '--motion-control-frame', '--mc-frame', dest='mc_frame',
         default=17,
-        metavar="FRAME",
+        metavar='FRAME',
         help='frame to be used when computing motion-control values. This '
              'choosing different frames to see what works best for a run. In '
              'future, will add an algorithm to determine best frame(s). '
              'Default: 17'
     )
     parser.add_argument(
         '--multi-masking-dir', dest='multi_masking_dir',
+        metavar='PATH',
         help='directory for joint label fusion masks.'
     )
     parser.add_argument(
         '--multi-template-dir', dest='multi_template_dir',
+        metavar='PATH',
         help='directory for joint label fusion templates. It should contain '
              'only folders which each contain a "T1w_brain.nii.gz" and a '
              '"Segmentation.nii.gz". Each subdirectory may have any name and '
@@ -208,14 +221,14 @@ def generate_parser(parser=None):
     )
     parser.add_argument(
         '--participant-label', dest='subject_list', nargs='+',
-        metavar='PARTICIPANT_LABEL',
+        metavar='LABEL',
         help='optional list of participant ids to run. Default is all ids '
              'found under the bids input directory.  A participant label '
              'does not include "sub-"'
     )
     parser.add_argument(
         '--session-id', dest='session_list', nargs='*',
-        metavar='SESSION_ID',
+        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-"'
@@ -236,9 +249,10 @@ def generate_parser(parser=None):
     parser.add_argument(
         '--T1-brain-mask', type=str, dest='t1_brain_mask',
         default=None,
+        metavar='PATH',
         help='specify the path to the mask file. The file specified will replace '
              'T1w_acpc_brain_mask.nii.gz. '
-             'Tip: when supplying a brain-mask, you _may_ want to set '
+             'Tip: when supplying a brain-mask, you may want to set '
              '--atropos-mask-method to NONE. '
              'Default: mask generated by PreFreeSurfer. '
     )
@@ -276,14 +290,14 @@ def generate_parser(parser=None):
     )
     extras.add_argument(
         '--custom-clean', dest='cleaning_json',
-        metavar='CC_JSON',
+        metavar='PATH',
         help='runs dcan cleaning script after the pipeline completes '
              'successfully, to delete pipeline outputs based on the file '
              'structure specified in the custom-clean json.'
     )
     extras.add_argument(
         '--file-mapper-json', dest='file_mapper_json',
-        metavar='FM_JSON',
+        metavar='PATH',
         help='runs dcan file-mapper after the pipeline completes '
              'successfully, to copy pipeline outputs to BIDS-formatted '
              'derivatives files based on the file-mapper json.'
@@ -318,6 +332,7 @@ def generate_parser(parser=None):
     )
     runopts.add_argument(
         '--stage','--stages', dest='stages',
+        metavar='STAGE',
         help='specify a subset of stages to run.'
              'If a single stage name is given, the pipeline with be '
              'started at that stage. If a string with a ":" is given, '
@@ -356,7 +371,8 @@ def generate_parser(parser=None):
 
 def interface(bids_dir, output_dir, subject_list=None, session_list=None,
               aseg="DEFAULT", atropos_mask_method=None, atropos_range=None,
-              bandstop_params=None, dcmethod=None, hyper_norm_method=None,
+              bandstop_params=None, dcmethod=None, freesurfer_license=None,
+              hyper_norm_method=None,
               jlf_method=None, max_cortical_thickness=5, mc_frame=17,
               multi_masking_dir=None, multi_template_dir=None, no_crop=False,
               smoothing_iterations=10,
@@ -376,6 +392,7 @@ def interface(bids_dir, output_dir, subject_list=None, session_list=None,
     :param atropos_range: tuple of lower and upper bounds for ANTs/Atropos labels.
     :param bandstop_params: tuple of lower and upper bounds for stop-band filter.
     :param dcmethod: which method will be used for distortion correction.
+    :param freesurfer_license: path to license to use FreeSurfer.
     :param hyper_norm_method: which method will be used for hyper-normalization step.
     :param jlf_method: which method to use for joint label fusion.
     :param max_cortical_thickness: maximum cortical thickness allowed in FreeSurfer.
@@ -398,6 +415,8 @@ def interface(bids_dir, output_dir, subject_list=None, session_list=None,
     :param stages: only run a subset of stages.
     :return:
     """
+    if not check_only and not print_commands:
+        validate_license(freesurfer_license)
     # Read from bids dataset.
     assert os.path.isdir(bids_dir), bids_dir + ' is not a directory!'
     if not os.path.isdir(output_dir):