ENH: Add option to use recon-all instead of infant_recon_all (#214)

* ENH: Add option to force traditional reconall

* ENH: Add anatomical pathway for `recon-all`

RF: `infant_surface_recon_wf` inputs were renamed to synchronize with existing workflow.

* FIX: Forgotten renamed field

* FIX: Missing output files

* RF: IRCA/RCA input/output field convergence

* ENH: Update FS build to include RCA

* FIX: Missing aseg connection to outputnode

Author: mgxd

Dockerfile

@@ -208,7 +208,7 @@ ENV FSLDIR="/opt/fsl" \
     LD_LIBRARY_PATH="/opt/fsl/lib:$LD_LIBRARY_PATH"
 
 # Install FreeSurfer
-COPY --from=nipreps/freesurfer@sha256:2ddc13f0a07b09e282a85d0a1aa715967841b1f4b734371dde98da1d1e87bed8 /opt/freesurfer /opt/freesurfer
+COPY --from=nipreps/freesurfer@sha256:7a750b97e276008030bfc68ffad3266a8838c4767398d82b25b539d389c8688e /opt/freesurfer /opt/freesurfer
 ENV FREESURFER_HOME="/opt/freesurfer"
 ENV SUBJECTS_DIR="$FREESURFER_HOME/subjects" \
     FUNCTIONALS_DIR="$FREESURFER_HOME/sessions" \

nibabies/cli/parser.py

@@ -655,6 +655,12 @@ def _slice_time_ref(value, parser):
         metavar="FILE",
         help="A JSON file for customizing the derivatives queries.",
     )
+    g_baby.add_argument(
+        "--force-reconall",
+        default=False,
+        action="store_true",
+        help="Force traditional FreeSurfer surface reconstruction.",
+    )
     return parser
 
 

nibabies/config.py

@@ -543,6 +543,8 @@ class workflow(_Config):
     """Remove the mean from fieldmaps."""
     force_syn = None
     """Run *fieldmap-less* susceptibility-derived distortions estimation."""
+    force_reconall = False
+    """Force traditional FreeSurfer surface reconstruction instead of infant version."""
     hires = None
     """Run FreeSurfer ``recon-all`` with the ``-hires`` flag."""
     ignore = None

nibabies/workflows/anatomical/base.py

@@ -15,6 +15,7 @@ def init_infant_anat_wf(
     bids_root,
     existing_derivatives,
     freesurfer,
+    hires,
     longitudinal,
     omp_nthreads,
     output_dir,
@@ -65,10 +66,10 @@ def init_infant_anat_wf(
         Inverse transform of the above.
     subject_id
         FreeSurfer subject ID
-    anat2fsnative_xfm
+    t1w2fsnative_xfm
         LTA-style affine matrix translating from T1w to
         FreeSurfer-conformed subject space
-    fsnative2anat_xfm
+    fsnative2t1w_xfm
         LTA-style affine matrix translating from FreeSurfer-conformed
         subject space to T1w
     surfaces
@@ -91,7 +92,6 @@ def init_infant_anat_wf(
     from .preproc import init_anat_average_wf
     from .registration import init_coregistration_wf
     from .segmentation import init_anat_segmentations_wf
-    from .surfaces import init_infant_surface_recon_wf
 
     # for now, T1w only
     num_t1w = len(t1w) if t1w else 0
@@ -138,8 +138,8 @@ def init_infant_anat_wf(
                 "subject_id",
                 "anat2std_xfm",
                 "std2anat_xfm",
-                "anat2fsnative_xfm",
-                "fsnative2anat_xfm",
+                "t1w2fsnative_xfm",
+                "fsnative2t1w_xfm",
                 "surfaces",
                 "anat_aseg",
                 "anat_aparc",
@@ -364,49 +364,55 @@ def init_infant_anat_wf(
     if not freesurfer:
         return wf
 
-    # if running with precomputed aseg, or JLF, pass the aseg along to FreeSurfer
-    use_aseg = bool(precomp_aseg) or bool(segmentation_atlases)
-    # FreeSurfer surfaces
-    surface_recon_wf = init_infant_surface_recon_wf(
-        age_months=age_months,
-        use_aseg=use_aseg,
-    )
+    if config.workflow.force_reconall:
+        from smriprep.workflows.surfaces import init_surface_recon_wf
+
+        surface_recon_wf = init_surface_recon_wf(omp_nthreads=omp_nthreads, hires=hires)
+    else:
+        from .surfaces import init_infant_surface_recon_wf
+
+        # if running with precomputed aseg, or JLF, pass the aseg along to FreeSurfer
+        use_aseg = bool(precomp_aseg or segmentation_atlases)
+        surface_recon_wf = init_infant_surface_recon_wf(
+            age_months=age_months,
+            use_aseg=use_aseg,
+        )
 
     # fmt:off
     wf.connect([
-        (anat_seg_wf, surface_recon_wf, [
-            ("outputnode.anat_aseg", "inputnode.anat_aseg"),
-        ]),
         (inputnode, surface_recon_wf, [
             ("subject_id", "inputnode.subject_id"),
             ("subjects_dir", "inputnode.subjects_dir"),
             ("t2w", "inputnode.t2w"),
         ]),
+        (anat_seg_wf, surface_recon_wf, [
+            ("outputnode.anat_aseg", "inputnode.ants_segs"),
+        ]),
         (t1w_template_wf, surface_recon_wf, [
-            ("outputnode.out_file", "inputnode.anat_orig"),
+            ("outputnode.out_file", "inputnode.t1w"),
         ]),
         (t1w_preproc_wf, surface_recon_wf, [
-            ("outputnode.t1w_brain", "inputnode.anat_skullstripped"),
-            ("outputnode.t1w_preproc", "inputnode.anat_preproc"),
+            ("outputnode.t1w_brain", "inputnode.skullstripped_t1"),
+            ("outputnode.t1w_preproc", "inputnode.corrected_t1"),
         ]),
         (surface_recon_wf, outputnode, [
             ("outputnode.subjects_dir", "subjects_dir"),
             ("outputnode.subject_id", "subject_id"),
-            ("outputnode.anat2fsnative_xfm", "anat2fsnative_xfm"),
-            ("outputnode.fsnative2anat_xfm", "fsnative2anat_xfm"),
+            ("outputnode.t1w2fsnative_xfm", "t1w2fsnative_xfm"),
+            ("outputnode.fsnative2t1w_xfm", "fsnative2t1w_xfm"),
             ("outputnode.surfaces", "surfaces"),
-            ("outputnode.anat_aparc", "anat_aparc"),
-            ("outputnode.anat_aseg", "anat_aseg"),
+            ("outputnode.out_aparc", "anat_aparc"),
+            ("outputnode.out_aseg", "anat_aseg"),
         ]),
         (surface_recon_wf, anat_reports_wf, [
             ("outputnode.subject_id", "inputnode.subject_id"),
             ("outputnode.subjects_dir", "inputnode.subjects_dir"),
         ]),
         (surface_recon_wf, anat_derivatives_wf, [
-            ("outputnode.anat_aseg", "inputnode.t1w_fs_aseg"),
-            ("outputnode.anat_aparc", "inputnode.t1w_fs_aparc"),
-            ("outputnode.anat2fsnative_xfm", "inputnode.t1w2fsnative_xfm"),
-            ("outputnode.fsnative2anat_xfm", "inputnode.fsnative2t1w_xfm"),
+            ("outputnode.out_aseg", "inputnode.t1w_fs_aseg"),
+            ("outputnode.out_aparc", "inputnode.t1w_fs_aparc"),
+            ("outputnode.t1w2fsnative_xfm", "inputnode.t1w2fsnative_xfm"),
+            ("outputnode.fsnative2t1w_xfm", "inputnode.fsnative2t1w_xfm"),
             ("outputnode.surfaces", "inputnode.surfaces"),
         ]),
     ])

nibabies/workflows/anatomical/surfaces.py

@@ -15,17 +15,19 @@ def init_infant_surface_recon_wf(*, age_months, use_aseg=False, name="infant_sur
 
     from nibabies.interfaces.freesurfer import InfantReconAll
 
+    # Synchronized inputs to smriprep.workflows.surfaces.init_surface_recon_wf
     wf = LiterateWorkflow(name=name)
     inputnode = pe.Node(
         niu.IdentityInterface(
             fields=[
                 "subjects_dir",
                 "subject_id",
-                "anat_orig",
-                "anat_skullstripped",
-                "anat_preproc",
-                "anat_aseg",
+                "t1w",
                 "t2w",
+                "flair",
+                "skullstripped_t1",
+                "corrected_t1",
+                "ants_segs",
             ],
         ),
         name="inputnode",
@@ -35,11 +37,11 @@ def init_infant_surface_recon_wf(*, age_months, use_aseg=False, name="infant_sur
             fields=[
                 "subjects_dir",
                 "subject_id",
-                "anat2fsnative_xfm",
-                "fsnative2anat_xfm",
+                "t1w2fsnative_xfm",
+                "fsnative2t1w_xfm",
                 "surfaces",
-                "anat_aseg",
-                "anat_aparc",
+                "out_aseg",
+                "out_aparc",
             ]
         ),
         name="outputnode",
@@ -57,14 +59,14 @@ def init_infant_surface_recon_wf(*, age_months, use_aseg=False, name="infant_sur
     recon = pe.Node(InfantReconAll(age=age_months), name="reconall")
     fssource = pe.Node(nio.FreeSurferSource(), name='fssource', run_without_submitting=True)
 
-    fsnative2anat_xfm = pe.Node(
+    fsnative2t1w_xfm = pe.Node(
         RobustRegister(auto_sens=True, est_int_scale=True),
-        name='fsnative2anat_xfm',
+        name='fsnative2t1w_xfm',
     )
 
-    anat2fsnative_xfm = pe.Node(
+    t1w2fsnative_xfm = pe.Node(
         LTAConvert(out_lta=True, invert=True),
-        name="anat2fsnative_xfm",
+        name="t1w2fsnative_xfm",
     )
 
     # convert generated surfaces to GIFTIs
@@ -73,7 +75,7 @@ def init_infant_surface_recon_wf(*, age_months, use_aseg=False, name="infant_sur
     aparc2nii = pe.Node(fs.MRIConvert(out_type="niigz"), name="aparc2nii")
 
     if use_aseg:
-        wf.connect(inputnode, "anat_aseg", recon, "aseg_file")
+        wf.connect(inputnode, "ants_segs", recon, "aseg_file")
 
     # fmt: off
     wf.connect([
@@ -82,7 +84,7 @@ def init_infant_surface_recon_wf(*, age_months, use_aseg=False, name="infant_sur
             ('subject_id', 'subject_id'),
         ]),
         (inputnode, recon, [
-            ('anat_skullstripped', 'mask_file'),
+            ('skullstripped_t1', 'mask_file'),
             ('subject_id', 'subject_id'),
         ]),
         (gen_recon_outdir, recon, [
@@ -103,24 +105,27 @@ def init_infant_surface_recon_wf(*, age_months, use_aseg=False, name="infant_sur
         (fssource, outputnode, [
             (('aseg', _replace_mgz), 'anat_aseg'),
         ]),
-        (inputnode, fsnative2anat_xfm, [('anat_skullstripped', 'target_file')]),
-        (fssource, fsnative2anat_xfm, [
+        (inputnode, fsnative2t1w_xfm, [('skullstripped_t1', 'target_file')]),
+        (fssource, fsnative2t1w_xfm, [
             (('norm', _replace_mgz), 'source_file'),
         ]),
-        (fsnative2anat_xfm, anat2fsnative_xfm, [('out_reg_file', 'in_lta')]),
+        (fsnative2t1w_xfm, t1w2fsnative_xfm, [('out_reg_file', 'in_lta')]),
         (fssource, aparc2nii, [
             ('aparc_aseg', 'in_file'),
         ]),
         (aparc2nii, outputnode, [
-            ('out_file', 'anat_aparc'),
+            ('out_file', 'out_aparc'),
         ]),
-        (fsnative2anat_xfm, outputnode, [
-            ('out_reg_file', 'fsnative2anat_xfm'),
+        (fssource, outputnode, [
+            (('aseg', _replace_mgz), 'out_aseg'),
+        ]),
+        (fsnative2t1w_xfm, outputnode, [
+            ('out_reg_file', 'fsnative2t1w_xfm'),
         ]),
-        (anat2fsnative_xfm, outputnode, [
-            ('out_lta', 'anat2fsnative_xfm'),
+        (t1w2fsnative_xfm, outputnode, [
+            ('out_lta', 't1w2fsnative_xfm'),
         ]),
-        (fsnative2anat_xfm, gifti_surface_wf, [
+        (fsnative2t1w_xfm, gifti_surface_wf, [
             ('out_reg_file', 'inputnode.fsnative2t1w_xfm')]),
         (gifti_surface_wf, outputnode, [
             ('outputnode.surfaces', 'surfaces'),

nibabies/workflows/base.py

@@ -323,6 +323,7 @@ def init_single_subject_wf(subject_id, session_id=None):
         bids_root=config.execution.bids_dir,
         existing_derivatives=derivatives,
         freesurfer=config.workflow.run_reconall,
+        hires=config.workflow.hires,
         longitudinal=config.workflow.longitudinal,
         omp_nthreads=config.nipype.omp_nthreads,
         output_dir=nibabies_dir,
@@ -475,8 +476,8 @@ def init_single_subject_wf(subject_id, session_id=None):
                     # Undefined if --fs-no-reconall, but this is safe
                     ('outputnode.subjects_dir', 'inputnode.subjects_dir'),
                     ('outputnode.subject_id', 'inputnode.subject_id'),
-                    ('outputnode.anat2fsnative_xfm', 'inputnode.anat2fsnative_xfm'),
-                    ('outputnode.fsnative2anat_xfm', 'inputnode.fsnative2anat_xfm'),
+                    ('outputnode.t1w2fsnative_xfm', 'inputnode.t1w2fsnative_xfm'),
+                    ('outputnode.fsnative2t1w_xfm', 'inputnode.fsnative2t1w_xfm'),
                 ]),
             ])
             # fmt: on

nibabies/workflows/bold/base.py

@@ -123,9 +123,9 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False, existing_derivatives=Non
         FreeSurfer SUBJECTS_DIR
     subject_id
         FreeSurfer subject ID
-    anat2fsnative_xfm
+    t1w2fsnative_xfm
         LTA-style affine matrix translating from T1w to FreeSurfer-conformed subject space
-    fsnative2anat_xfm
+    fsnative2t1w_xfm
         LTA-style affine matrix translating from FreeSurfer-conformed subject space to T1w
     bold_ref
         BOLD reference file
@@ -333,8 +333,8 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False, existing_derivatives=Non
                 "fmap_id",
                 "sdc_method",
                 # if reconstructing with FreeSurfer (optional)
-                "anat2fsnative_xfm",
-                "fsnative2anat_xfm",
+                "t1w2fsnative_xfm",
+                "fsnative2t1w_xfm",
                 "subject_id",
                 "subjects_dir",
             ]
@@ -596,7 +596,7 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False, existing_derivatives=Non
             # Undefined if --fs-no-reconall, but this is safe
             ('subjects_dir', 'inputnode.subjects_dir'),
             ('subject_id', 'inputnode.subject_id'),
-            ('fsnative2anat_xfm', 'inputnode.fsnative2t1w_xfm'),
+            ('fsnative2t1w_xfm', 'inputnode.fsnative2t1w_xfm'),
         ]),
         (bold_final, bold_reg_wf, [
             ("boldref", "inputnode.ref_bold_brain")]),
@@ -858,7 +858,7 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False, existing_derivatives=Non
             (inputnode, bold_surf_wf, [
                 ('subjects_dir', 'inputnode.subjects_dir'),
                 ('subject_id', 'inputnode.subject_id'),
-                ('anat2fsnative_xfm', 'inputnode.t1w2fsnative_xfm')]),
+                ('t1w2fsnative_xfm', 'inputnode.t1w2fsnative_xfm')]),
             (bold_t1_trans_wf, bold_surf_wf, [('outputnode.bold_t1', 'inputnode.source_file')]),
             (bold_surf_wf, outputnode, [('outputnode.surfaces', 'surfaces')]),
             (bold_surf_wf, func_derivatives_wf, [