Add quick fix check for FastSurfer

Adds the check_fastsurfer function call to log FastSurfer outputs detected in subjects_dir and touch mri/aseg.auto_noCCseg.label_intensities.txt to prevent failure in surfaces.py as a temporary fix for nipreps#278

smriprep/workflows/anatomical.py

@@ -47,7 +47,7 @@
 from niworkflows.utils.misc import fix_multi_T1w_source_name, add_suffix
 from niworkflows.anat.ants import init_brain_extraction_wf, init_n4_only_wf
 from ..utils.bids import get_outputnode_spec
-from ..utils.misc import apply_lut as _apply_bids_lut, fs_isRunning as _fs_isRunning
+from ..utils.misc import apply_lut as _apply_bids_lut, fs_isRunning as _fs_isRunning, check_fastsurfer as _check_fastsurfer
 from .norm import init_anat_norm_wf
 from .outputs import init_anat_reports_wf, init_anat_derivatives_wf
 from .surfaces import init_surface_recon_wf
@@ -514,14 +514,24 @@ def _check_img(img):
         niu.Function(function=_fs_isRunning), overwrite=True, name="fs_isrunning"
     )
     fs_isrunning.inputs.logger = LOGGER
-
+
+    # check for FastSurfer .mgz files and 
+    #   touch mri/aseg.auto_noCCseg.label_intensities.txt to prevent failure in surfaces.py (temporary fix)
+    check_fastsurfer = pe.Node(
+        niu.Function(function=_check_fastsurfer), overwrite=True, name="check_fastsurfer"
+    )
+    check_fastsurfer.inputs.logger = LOGGER
+
     # 5. Surface reconstruction (--fs-no-reconall not set)
     surface_recon_wf = init_surface_recon_wf(
         name="surface_recon_wf", omp_nthreads=omp_nthreads, hires=hires
     )
     applyrefined = pe.Node(fsl.ApplyMask(), name="applyrefined")
     # fmt:off
     workflow.connect([
+        (inputnode, check_fastsurfer, [
+            ('subjects_dir', 'subjects_dir'),
+            ('subject_id', 'subject_id')]),
         (inputnode, fs_isrunning, [
             ('subjects_dir', 'subjects_dir'),
             ('subject_id', 'subject_id')]),