Added function to test for FastSurfer files in --fs-subjects-dir

Checks FreeSurfer subjects dir for presence of files in mri/ with names indicating processing with FastSurfer, and returns a boolean fastsurfer_bool to indicate that FastSurfer is being used instead of Freesurfer. For development purposes, this also touches files that are expected outputs of Freesurfer, but not produced by default in FastSurfer. (Addresses nipreps#278 & Deep-MI/FastSurfer#21)

smriprep/utils/misc.py

@@ -95,3 +95,44 @@ def fs_isRunning(subjects_dir, subject_id, mtime_tol=86400, logger=None):
     if logger:
         logger.warn(f'Removed "IsRunning*" files found under {subj_dir}')
     return subjects_dir
+
+def check_fastsurfer(subjects_dir, subject_id):
+    """
+    Checks FreeSurfer subjects dir for presence of files in mri/ with names indicating processing with FastSurfer,
+    and returns a boolean fastsurfer_bool to indicate that FastSurfer is being used instead of Freesurfer.
+    
+    For development purposes, this also touches files that are expected outputs of Freesurfer, 
+    but not produced by default in FastSurfer.
+
+    Parameters
+    ----------
+    subjects_dir : os.PathLike or None
+        Existing FreeSurfer subjects directory
+    subject_id : str
+        Subject label
+
+    Returns
+    -------
+    fastsurfer_bool : Boolean
+    subjects_dir : os.PathLike or None
+
+
+    """
+    from pathlib import Path
+
+    if subjects_dir is None:
+        return subjects_dir
+    subj_dir = Path(subjects_dir) / subject_id
+    if not subj_dir.exists():
+
+        return subjects_dir
+
+    fastsurferfiles = tuple(subj_dir.glob("mri/*deep*mgz"))
+    if not fastsurferfiles:
+        fastsurfer_bool = False
+        return fastsurfer_bool, subjects_dir
+    else:
+        fastsurfer_bool = True
+        noCCseglabel = Path(subj_dir / 'mri/aseg.auto_noCCseg.label_intensities.txt')
+        noCCseglabel.touch(exist_ok=False)
+        return fastsurfer_bool, subjects_dir