Merge pull request #2014 from oesteban/fix/fs-license-path-parsing

FIX: fMRIPrep crashes whenever ``FREESURFER_HOME`` is not set

Author: mgxd

fmriprep/cli/run.py

@@ -316,17 +316,23 @@ def main():
               "cases).")
         validate_input_dir(exec_env, opts.bids_dir, opts.participant_label)
 
-    # FreeSurfer license
-    default_license = str(Path(os.getenv('FREESURFER_HOME')) / 'license.txt')
     # Precedence: --fs-license-file, $FS_LICENSE, default_license
-    license_file = opts.fs_license_file or Path(os.getenv('FS_LICENSE', default_license))
-    if not license_file.exists():
+    license_file = opts.fs_license_file
+
+    if license_file is None and os.getenv("FS_LICENSE"):
+        license_file = Path(os.getenv("FS_LICENSE"))
+
+    if license_file is None and os.getenv("FREESURFER_HOME"):
+        license_file = Path(os.getenv("FREESURFER_HOME")) / "license.txt"
+
+    # FreeSurfer license
+    if license_file is None or not license_file.exists():
         raise RuntimeError("""\
 ERROR: a valid license file is required for FreeSurfer to run. fMRIPrep looked for an existing \
 license file at several paths, in this order: 1) command line argument ``--fs-license-file``; \
 2) ``$FS_LICENSE`` environment variable; and 3) the ``$FREESURFER_HOME/license.txt`` path. Get it \
 (for free) by registering at https://surfer.nmr.mgh.harvard.edu/registration.html""")
-    os.environ['FS_LICENSE'] = str(license_file.resolve())
+    os.environ["FS_LICENSE"] = str(license_file.absolute())
 
     # Retrieve logging level
     log_level = int(max(25 - 5 * opts.verbose_count, logging.DEBUG))