Add --fs-license-file option

freesurfer_post/__init__.py

@@ -6,4 +6,4 @@
 
 __version__ = '0.1.0'
 __author__ = 'Your Name'
-__email__ = 'your.email@example.com'
+__email__ = 'your.email@example.com'

freesurfer_post/cli.py

@@ -17,7 +17,18 @@
 @click.option('--subject-id', '-s', help='Subject ID to process')
 @click.option('--session-id', '-x', help='Session ID to process')
 @click.option('--working-dir', '-w', help='Path to working directory')
-def main(verbose, input_path, output_path, processing_level, subjects_dir, subject_id, session_id, working_dir):
+@click.option('--fs-license-file', '-l', help='Path to license file')
+def main(
+    verbose,
+    input_path,
+    output_path,
+    processing_level,
+    subjects_dir,
+    subject_id,
+    session_id,
+    working_dir,
+    fs_license_file,
+):
     """FreeSurfer Post-processing Tools.
 
     A command line interface for post-processing FreeSurfer outputs.
@@ -41,6 +52,7 @@ def main(verbose, input_path, output_path, processing_level, subjects_dir, subje
     click.echo(f'Subject directory: {subject_fs_dir}')
     click.echo(f'Processing level: {processing_level}')
     click.echo(f'Working directory: {working_dir}')
+    click.echo(f'FreeSurfer license file: {fs_license_file}')
 
     workflow = build_workflow(
         subject_id=subject_id,
@@ -50,8 +62,10 @@ def main(verbose, input_path, output_path, processing_level, subjects_dir, subje
         working_dir=working_dir,
     )
 
-    workflow.config['execution'] = {
-        'stop_on_first_crash': 'true'}
+    import os
+
+    os.environ['FS_LICENSE'] = fs_license_file
+    workflow.config['execution'] = {'stop_on_first_crash': 'true'}
     workflow.run()
 
 

freesurfer_post/interfaces/interfaces.py

@@ -7,12 +7,14 @@ class _WaitingInputSpec(TraitedSpec):
         mandatory=True,
     )
 
+
 class _WaitingOutputSpec(TraitedSpec):
     no_args = traits.Str(
         desc='No args',
         mandatory=True,
     )
 
+
 class Waiting(SimpleInterface):
     # Force a bunch of nodes to finish and then retuen an empty string
     # to put in "args" of the dependent workflow

freesurfer_post/interfaces/tabular.py

@@ -15,10 +15,10 @@
 
 
 def statsfile_to_df(stats_fname, hemi, atlas, column_suffix=''):
-    with open(stats_fname, 'r') as fo:
+    with open(stats_fname) as fo:
         data = fo.readlines()
 
     idx = [i for i, l in enumerate(data) if l.startswith('# ColHeaders ')]
     assert len(idx) == 1
     idx = idx[0]
 
@@ -137,7 +137,9 @@
         output_dir = Path(self.inputs.output_dir) / subject_id
         output_dir.mkdir(parents=True, exist_ok=True)
         output_prefix = f'{subject_id}_{session_id}' if session_id else subject_id
-        cleaned_atlas_name = atlas.replace('.', '').replace('_order', '').replace('_', '')
+        cleaned_atlas_name = (
+            atlas.replace('.', '').replace('_order', '').replace('_', '')
+        )
         out_df.to_csv(
             output_dir / f'{output_prefix}_atlas-{cleaned_atlas_name}_surfacestats.tsv',
             sep='\t',
@@ -204,7 +206,7 @@
     (header,) = [line for line in lines if header_tag in line]
     header = header[len(header_tag) :].strip().split()
 
-    stats_df = pd.read_csv(str(stats_file), sep='\s+', comment='#', names=header).melt(
+    stats_df = pd.read_csv(str(stats_file), sep=r'\s+', comment='#', names=header).melt(
         id_vars=['StructName'], ignore_index=True
     )
     stats_df = stats_df[stats_df['variable'] != 'Index']

freesurfer_post/utils.py

@@ -1,9 +1,12 @@
 """Utility functions for FreeSurfer post-processing."""
+
 import warnings
 from pathlib import Path
 
 
-def find_freesurfer_dir(subjects_dir: str | Path, subject_id: str, session_id: str | None = None) -> Path:
+def find_freesurfer_dir(
+    subjects_dir: str | Path, subject_id: str, session_id: str | None = None
+) -> Path:
     """Find a valid FreeSurfer subject directory in a directory.
 
     Parameters
@@ -27,8 +30,8 @@ def find_freesurfer_dir(subjects_dir: str | Path, subject_id: str, session_id: s
 
     warn_no_session = False
     if session_id is not None:
-        if (subjects_dir / f"{subject_id}_{session_id}").exists():
-            return subjects_dir / f"{subject_id}_{session_id}"
+        if (subjects_dir / f'{subject_id}_{session_id}').exists():
+            return subjects_dir / f'{subject_id}_{session_id}'
         warn_no_session = True
 
     if (subjects_dir / subject_id).exists():
@@ -39,4 +42,6 @@ def find_freesurfer_dir(subjects_dir: str | Path, subject_id: str, session_id: s
                 stacklevel=2,
             )
         return subjects_dir / subject_id
-    raise FileNotFoundError(f'No directory found for subject: {subject_id}, session: {session_id}')
+    raise FileNotFoundError(
+        f'No directory found for subject: {subject_id}, session: {session_id}'
+    )

freesurfer_post/workflows.py

@@ -59,7 +59,8 @@ def build_workflow(
 
     inputnode = pe.Node(
         niu.IdentityInterface(
-            fields=['subject_id', 'session_id', 'fs_subjects_dir', 'output_dir']),
+            fields=['subject_id', 'session_id', 'fs_subjects_dir', 'output_dir']
+        ),
         name='inputnode',
     )
     inputnode.inputs.subject_id = subject_id
@@ -73,29 +74,44 @@ def build_workflow(
             subject_freesurfer_dir=subject_freesurfer_dir,
             parc_name=parc_name,
         )
-        workflow.connect([
-            (inputnode, parc_wf, [('subject_id', 'inputnode.subject_id'),
-                                  ('session_id', 'inputnode.session_id'),
-                                  ('fs_subjects_dir', 'inputnode.fs_subjects_dir'),
-                                  ('output_dir', 'inputnode.output_dir')]),
-        ])
+        workflow.connect(
+            [
+                (
+                    inputnode,
+                    parc_wf,
+                    [
+                        ('subject_id', 'inputnode.subject_id'),
+                        ('session_id', 'inputnode.session_id'),
+                        ('fs_subjects_dir', 'inputnode.fs_subjects_dir'),
+                        ('output_dir', 'inputnode.output_dir'),
+                    ],
+                ),
+            ]
+        )
 
     # Get the segmentation stats and euler number
     fs_stats = pe.Node(FSStats(), name='fs_stats')
-    workflow.connect([
-        (inputnode, fs_stats, [('subject_id', 'subject_id'),
-                               ('session_id', 'session_id'),
-                               ('fs_subjects_dir', 'subjects_dir'),
-                               ('output_dir', 'output_dir')]),
-    ])
+    workflow.connect(
+        [
+            (
+                inputnode,
+                fs_stats,
+                [
+                    ('subject_id', 'subject_id'),
+                    ('session_id', 'session_id'),
+                    ('fs_subjects_dir', 'subjects_dir'),
+                    ('output_dir', 'output_dir'),
+                ],
+            ),
+        ]
+    )
 
     return workflow
 
 
 def init_parcellation_wf(
-        subject_id: str,
-        subject_freesurfer_dir: str | Path,
-        parc_name: str):
+    subject_id: str, subject_freesurfer_dir: str | Path, parc_name: str
+):
     """
     Initialize a workflow to process a single parcellation.
 
@@ -126,7 +142,8 @@ def init_parcellation_wf(
     """
     inputnode = pe.Node(
         niu.IdentityInterface(
-            fields=['subject_id', 'session_id', 'fs_subjects_dir', 'output_dir']),
+            fields=['subject_id', 'session_id', 'fs_subjects_dir', 'output_dir']
+        ),
         name='inputnode',
     )
     clean_parc_name = parc_name.replace('.', '').replace('_', '')
@@ -138,25 +155,32 @@ def init_parcellation_wf(
         ),
         name='collect_stats',
     )
-    workflow.connect([
-        (inputnode, collect_stats, [
-            ('subject_id', 'subject_id'),
-            ('session_id', 'session_id'),
-            ('fs_subjects_dir', 'subjects_dir'),
-            ('output_dir', 'output_dir'),
-        ]),
-    ])
+    workflow.connect(
+        [
+            (
+                inputnode,
+                collect_stats,
+                [
+                    ('subject_id', 'subject_id'),
+                    ('session_id', 'session_id'),
+                    ('fs_subjects_dir', 'subjects_dir'),
+                    ('output_dir', 'output_dir'),
+                ],
+            ),
+        ]
+    )
     transform_nodes = {}
     parc_stats_nodes = {}
     gwr_seg_stats_nodes = {}
     for hemi in ['lh', 'rh']:
-
         fsaverage_annot = ANNOTS_DIR / f'{hemi}.{parc_name}.annot'
         # native annot is created by SurfaceTransform if it's not a NATIVE_PARCELLATION
         # otherwise it's already present in the subject's directory
         native_annot = subject_freesurfer_dir / 'label' / f'{hemi}.{parc_name}.annot'
         stats_file = subject_freesurfer_dir / 'stats' / f'{hemi}.{parc_name}.stats'
-        gwr_stats_file = subject_freesurfer_dir / 'stats' / f'{hemi}.{parc_name}.g-w.pct.stats'
+        gwr_stats_file = (
+            subject_freesurfer_dir / 'stats' / f'{hemi}.{parc_name}.g-w.pct.stats'
+        )
         if parc_name in AVAILABLE_PARCELLATIONS:
             transform_nodes[hemi] = pe.Node(
                 fs.SurfaceTransform(
@@ -229,7 +253,3 @@ def init_parcellation_wf(
         ])  # fmt: off
 
     return workflow
-
-
-
-

tests/test.sh

@@ -3,7 +3,7 @@ docker run --rm -ti --entrypoint /bin/bash \
    -v /Users/mcieslak/Desktop/fmriprep_anat:/data \
    -v /Users/mcieslak/Desktop/freesurfer_post:/output \
    -v /Users/mcieslak/Desktop/fspost_work:/work \
-   --mount type=bind,source=/Users/mcieslak/Desktop/license.txt,target=/opt/freesurfer/license.txt \
+   --mount type=bind,source=/Users/mcieslak/Desktop/license.txt,target=/opt/fs_license.txt \
    -v /Users/mcieslak/projects/freesurfer-post/freesurfer_post:/opt/conda/envs/freesurfer-post/lib/python3.12/site-packages/freesurfer_post \
    pennlinc/freesurfer-post:unstable \
        /data \
@@ -18,5 +18,7 @@ freesurfer-post \
        participant \
        --subjects-dir /data/sourcedata/freesurfer \
        --subject-id sub-colornest001 \
+       --fs-license-file /opt/fs_license.txt \
+       --session-id ses-01 \
        -w /work