Added exclusive group to prevent two fs flags not running simultaneously

Author: baej3

petprep/cli/parser.py

@@ -509,25 +509,39 @@ def _bids_filter(value, parser):
         help='Path to FreeSurfer license key file. Get it (for free) by registering'
         ' at https://surfer.nmr.mgh.harvard.edu/registration.html',
     )
+    # g_fs.add_argument(
+    #     '--fs-subjects-dir',
+    #     metavar='PATH',
+    #     type=Path,
+    #     help='Path to existing FreeSurfer subjects directory to reuse. '
+    #     '(default: OUTPUT_DIR/freesurfer)',
+    # )
     g_fs.add_argument(
+        '--no-submm-recon',
+        action='store_false',
+        dest='hires',
+        help='Disable sub-millimeter (hires) reconstruction',
+    )
+    fs_mutex = g_fs.add_mutually_exclusive_group()
+    fs_mutex.add_argument(
         '--fs-subjects-dir',
         metavar='PATH',
         type=Path,
         help='Path to existing FreeSurfer subjects directory to reuse. '
         '(default: OUTPUT_DIR/freesurfer)',
     )
-    g_fs.add_argument(
-        '--no-submm-recon',
-        action='store_false',
-        dest='hires',
-        help='Disable sub-millimeter (hires) reconstruction',
-    )
-    g_fs.add_argument(
+    fs_mutex.add_argument(
         '--fs-no-reconall',
         action='store_false',
         dest='run_reconall',
         help='Disable FreeSurfer surface preprocessing.',
     )
+    # g_fs.add_argument(
+    #     '--fs-no-reconall',
+    #     action='store_false',
+    #     dest='run_reconall',
+    #     help='Disable FreeSurfer surface preprocessing.',
+    # )
     g_fs.add_argument(
         '--fs-no-resume',
         action='store_true',