From 0688b555e5dbf6d78608f01ce96a77e4af398878 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Fri, 29 Sep 2023 16:23:17 -0400
Subject: [PATCH 01/14] FEAT: Allow single anatomical outputs

---
 nibabies/workflows/anatomical/outputs.py | 418 +++++++++++++----------
 1 file changed, 244 insertions(+), 174 deletions(-)

diff --git a/nibabies/workflows/anatomical/outputs.py b/nibabies/workflows/anatomical/outputs.py
index a934e013..e7ceb6a6 100644
--- a/nibabies/workflows/anatomical/outputs.py
+++ b/nibabies/workflows/anatomical/outputs.py
@@ -1,12 +1,20 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Writing outputs."""
+from __future__ import annotations
+
+import typing as ty
+from pathlib import Path
+
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
 from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 
 from ...interfaces import DerivativesDataSink
 
+if ty.TYPE_CHECKING:
+    from niworkflows.utils.spaces import SpatialReferences
+
 BIDS_TISSUE_ORDER = ("GM", "WM", "CSF")
 
 
@@ -74,13 +82,19 @@ def init_coreg_report_wf(*, output_dir, name="coreg_report_wf"):
     return workflow
 
 
-def init_anat_reports_wf(*, freesurfer, output_dir, sloppy, name="anat_reports_wf"):
+def init_anat_reports_wf(
+    *,
+    surface_recon: ty.Literal['freesurfer', 'infantfs', 'mcribs'] | None,
+    output_dir: str,
+    sloppy: bool,
+    name="anat_reports_wf",
+) -> Workflow:
     """
     Patched workflow for reports to allow no resolution for templates
     Set up a battery of datasinks to store reports in the right location.
     Parameters
     ----------
-    freesurfer : :obj:`bool`
+    recon_method : :obj:`bool`
         FreeSurfer was enabled
     output_dir : :obj:`str`
         Directory in which to save derivatives
@@ -127,10 +141,10 @@ def init_anat_reports_wf(*, freesurfer, output_dir, sloppy, name="anat_reports_w
 
     inputfields = [
         "source_file",
-        "t1w_conform_report",
-        "t1w_preproc",
-        "t1w_dseg",
-        "t1w_mask",
+        "anat_conform_report",
+        "anat_preproc",
+        "anat_dseg",
+        "anat_mask",
         "template",
         "std_t1w",
         "std_mask",
@@ -143,34 +157,34 @@ def init_anat_reports_wf(*, freesurfer, output_dir, sloppy, name="anat_reports_w
 
     seg_rpt = pe.Node(ROIsPlot(colors=["b", "magenta"], levels=[1.5, 2.5]), name="seg_rpt")
 
-    t1w_conform_check = pe.Node(
+    anat_conform_check = pe.Node(
         niu.Function(function=_empty_report),
-        name="t1w_conform_check",
+        name="anat_conform_check",
         run_without_submitting=True,
     )
 
-    ds_t1w_conform_report = pe.Node(
+    ds_anat_conform_report = pe.Node(
         DerivativesDataSink(base_directory=output_dir, desc="conform", datatype="figures"),
-        name="ds_t1w_conform_report",
+        name="ds_anat_conform_report",
         run_without_submitting=True,
     )
 
-    ds_t1w_dseg_mask_report = pe.Node(
+    ds_anat_dseg_mask_report = pe.Node(
         DerivativesDataSink(base_directory=output_dir, suffix="dseg", datatype="figures"),
-        name="ds_t1w_dseg_mask_report",
+        name="ds_anat_dseg_mask_report",
         run_without_submitting=True,
     )
 
     # fmt: off
     workflow.connect([
-        (inputnode, t1w_conform_check, [('t1w_conform_report', 'in_file')]),
-        (t1w_conform_check, ds_t1w_conform_report, [('out', 'in_file')]),
-        (inputnode, ds_t1w_conform_report, [('source_file', 'source_file')]),
-        (inputnode, ds_t1w_dseg_mask_report, [('source_file', 'source_file')]),
-        (inputnode, seg_rpt, [('t1w_preproc', 'in_file'),
-                              ('t1w_mask', 'in_mask'),
-                              ('t1w_dseg', 'in_rois')]),
-        (seg_rpt, ds_t1w_dseg_mask_report, [('out_report', 'in_file')]),
+        (inputnode, anat_conform_check, [('anat_conform_report', 'in_file')]),
+        (anat_conform_check, ds_anat_conform_report, [('out', 'in_file')]),
+        (inputnode, ds_anat_conform_report, [('source_file', 'source_file')]),
+        (inputnode, ds_anat_dseg_mask_report, [('source_file', 'source_file')]),
+        (inputnode, seg_rpt, [('anat_preproc', 'in_file'),
+                              ('anat_mask', 'in_mask'),
+                              ('anat_dseg', 'in_rois')]),
+        (seg_rpt, ds_anat_dseg_mask_report, [('out_report', 'in_file')]),
     ])
     # fmt: on
 
@@ -216,39 +230,43 @@ def init_anat_reports_wf(*, freesurfer, output_dir, sloppy, name="anat_reports_w
     ])
     # fmt: on
 
-    if freesurfer:
-        from smriprep.interfaces.reports import FSSurfaceReport
+    if not surface_recon:
+        return workflow
 
-        recon_report = pe.Node(FSSurfaceReport(), name="recon_report")
-        recon_report.interface._always_run = True
+    # TODO: Separate report for MCRIBS?
+    from smriprep.interfaces.reports import FSSurfaceReport
 
-        ds_recon_report = pe.Node(
-            DerivativesDataSink(base_directory=output_dir, desc="reconall", datatype="figures"),
-            name="ds_recon_report",
-            run_without_submitting=True,
-        )
-        # fmt: off
-        workflow.connect([
-            (inputnode, recon_report, [('subjects_dir', 'subjects_dir'),
-                                       ('subject_id', 'subject_id')]),
-            (recon_report, ds_recon_report, [('out_report', 'in_file')]),
-            (inputnode, ds_recon_report, [('source_file', 'source_file')])
-        ])
-        # fmt: on
+    recon_report = pe.Node(FSSurfaceReport(), name="recon_report")
+    recon_report.interface._always_run = True
+
+    ds_recon_report = pe.Node(
+        DerivativesDataSink(base_directory=output_dir, desc="reconall", datatype="figures"),
+        name="ds_recon_report",
+        run_without_submitting=True,
+    )
+    # fmt: off
+    workflow.connect([
+        (inputnode, recon_report, [('subjects_dir', 'subjects_dir'),
+                                    ('subject_id', 'subject_id')]),
+        (recon_report, ds_recon_report, [('out_report', 'in_file')]),
+        (inputnode, ds_recon_report, [('source_file', 'source_file')])
+    ])
+    # fmt: on
 
     return workflow
 
 
 def init_anat_derivatives_wf(
     *,
-    bids_root,
-    freesurfer,
-    num_t1w,
-    output_dir,
-    spaces,
-    cifti_output,
-    name="anat_derivatives_wf",
-    tpm_labels=BIDS_TISSUE_ORDER,
+    bids_root: Path | str,
+    output_dir: Path | str,
+    spaces: SpatialReferences,
+    cifti_output: bool,
+    num_t1w: int | None,
+    num_t2w: int | None,
+    surface_recon: ty.Literal['freesurfer', 'infantfs', 'mcribs'] | None,
+    tpm_labels: ty.Tuple[str, str, str] = BIDS_TISSUE_ORDER,
+    name: str = "anat_derivatives_wf",
 ):
     """
     Set up a battery of datasinks to store derivatives in the right location.
@@ -335,23 +353,29 @@ def init_anat_derivatives_wf(
         niu.IdentityInterface(
             fields=[
                 "template",
-                "source_files",
+                # T1w
+                "t1w_source_files",
                 "t1w_ref_xfms",
                 "t1w_preproc",
-                "t1w_mask",
-                "t1w_dseg",
-                "t1w_tpms",
+                # T2w
+                "t2w_source_files",
+                "t2w_ref_xfms",
+                "t2w_preproc",
+                # Can be in either T1w/T2w space
+                "anat_mask",
+                "anat_dseg",
+                "anat_tpms",
                 "anat2std_xfm",
                 "std2anat_xfm",
-                "t1w2fsnative_xfm",
-                "fsnative2t1w_xfm",
+                "anat2fsnative_xfm",
+                "fsnative2anat_xfm",
+                # FS
+                "anat_fs_aseg",
+                "anat_fs_aparc",
+                "anat_ribbon",
                 "surfaces",
                 "morphometrics",
-                "t1w_fs_aseg",
-                "t1w_fs_aparc",
-                "t2w_source_files",
-                "t2w_preproc",
-                "anat_ribbon",
+                # CIFTI
                 "cifti_metadata",
                 "cifti_density",
                 "cifti_morph",
@@ -361,16 +385,100 @@ def init_anat_derivatives_wf(
         ),
         name="inputnode",
     )
+    # The preferred space to use for to/from entities
+    source_files = "t1w_source_files" if num_t1w else "t2w_source_files"
+    space = "T1w" if num_t1w else "T2w"
+
+    if num_t1w:
+        raw_sources = pe.Node(niu.Function(function=_bids_relative), name="t1w_raw_sources")
+        raw_sources.inputs.bids_root = bids_root
+
+        ds_t1w_preproc = pe.Node(
+            DerivativesDataSink(base_directory=output_dir, desc="preproc", compress=True),
+            name="ds_t1w_preproc",
+            run_without_submitting=True,
+        )
+        ds_t1w_preproc.inputs.SkullStripped = False
+
+        if num_t1w > 1:
+            # Please note the dictionary unpacking to provide the from argument.
+            # It is necessary because from is a protected keyword (not allowed as argument name).
+            ds_t1w_ref_xfms = pe.MapNode(
+                DerivativesDataSink(
+                    base_directory=output_dir,
+                    to="T1w",
+                    mode="image",
+                    suffix="xfm",
+                    extension="txt",
+                    **{"from": "orig"},
+                ),
+                iterfield=["source_file", "in_file"],
+                name="ds_t1w_ref_xfms",
+                run_without_submitting=True,
+            )
+            # fmt:off
+            workflow.connect([
+                (inputnode, ds_t1w_ref_xfms, [('t1w_source_files', 'source_file'),
+                                              ('t1w_ref_xfms', 'in_file')]),
+            ])
+            # fmt:on
+
+    if num_t2w:
+
+        if not num_t1w:
+            raw_sources = pe.Node(niu.Function(function=_bids_relative), name="t2w_raw_sources")
+            raw_sources.inputs.bids_root = bids_root
+
+        ds_t2w_preproc = pe.Node(
+            DerivativesDataSink(base_directory=output_dir, desc="preproc", compress=True),
+            name="ds_t2w_preproc",
+            run_without_submitting=True,
+        )
+        if num_t1w:
+            ds_t2w_preproc.inputs.space = "T1w"
+
+        if num_t2w > 1:
+            # Please note the dictionary unpacking to provide the from argument.
+            # It is necessary because from is a protected keyword (not allowed as argument name).
+            ds_t2w_ref_xfms = pe.MapNode(
+                DerivativesDataSink(
+                    base_directory=output_dir,
+                    to="T1w",
+                    mode="image",
+                    suffix="xfm",
+                    extension="txt",
+                    **{"from": "orig"},
+                ),
+                iterfield=["source_file", "in_file"],
+                name="ds_t2w_ref_xfms",
+                run_without_submitting=True,
+            )
+            # fmt:off
+            workflow.connect([
+                (inputnode, ds_t2w_ref_xfms, [('t2w_source_files', 'source_file'),
+                                              ('t2w_ref_xfms', 'in_file')]),
+            ])
+            # fmt:on
+
+    ds_anat_mask = pe.Node(
+        DerivativesDataSink(base_directory=output_dir, desc="brain", suffix="mask", compress=True),
+        name="ds_anat_mask",
+        run_without_submitting=True,
+    )
+    ds_anat_mask.inputs.Type = "Brain"
 
-    raw_sources = pe.Node(niu.Function(function=_bids_relative), name="raw_sources")
-    raw_sources.inputs.bids_root = bids_root
+    ds_anat_dseg = pe.Node(
+        DerivativesDataSink(base_directory=output_dir, suffix="dseg", compress=True),
+        name="ds_anat_dseg",
+        run_without_submitting=True,
+    )
 
-    ds_t1w_preproc = pe.Node(
-        DerivativesDataSink(base_directory=output_dir, desc="preproc", compress=True),
-        name="ds_t1w_preproc",
+    ds_anat_tpms = pe.Node(
+        DerivativesDataSink(base_directory=output_dir, suffix="probseg", compress=True),
+        name="ds_anat_tpms",
         run_without_submitting=True,
     )
-    ds_t1w_preproc.inputs.SkullStripped = False
+    ds_anat_tpms.inputs.label = tpm_labels
 
     ds_anat_ribbon = pe.Node(
         DerivativesDataSink(
@@ -384,106 +492,67 @@ def init_anat_derivatives_wf(
         run_without_submitting=True,
     )
 
-    ds_t1w_mask = pe.Node(
-        DerivativesDataSink(base_directory=output_dir, desc="brain", suffix="mask", compress=True),
-        name="ds_t1w_mask",
-        run_without_submitting=True,
-    )
-    ds_t1w_mask.inputs.Type = "Brain"
-
-    ds_t1w_dseg = pe.Node(
-        DerivativesDataSink(base_directory=output_dir, suffix="dseg", compress=True),
-        name="ds_t1w_dseg",
-        run_without_submitting=True,
-    )
-
-    ds_t2w_preproc = pe.Node(
-        DerivativesDataSink(
-            data_dtype="i2", base_directory=output_dir, space="T1w", desc="preproc", compress=True
-        ),
-        name="ds_t2w_preproc",
-        run_without_submitting=True,
-    )
+    if num_t1w:
+        # fmt:off
+        workflow.connect([
+            (inputnode, ds_t1w_preproc, [('t1w_preproc', 'in_file'),
+                                         ('t1w_source_files', 'source_file')]),
+        ])
+        # fmt:on
 
-    ds_t1w_tpms = pe.Node(
-        DerivativesDataSink(base_directory=output_dir, suffix="probseg", compress=True),
-        name="ds_t1w_tpms",
-        run_without_submitting=True,
-    )
-    ds_t1w_tpms.inputs.label = tpm_labels
+    if num_t2w:
+        # fmt:off
+        workflow.connect([
+            (inputnode, ds_t2w_preproc, [('t2w_preproc', 'in_file'),
+                                         ('t2w_source_files', 'source_file')]),
+        ])
+        # fmt:on
 
-    # fmt: off
+    # fmt:off
     workflow.connect([
-        (inputnode, raw_sources, [('source_files', 'in_files')]),
-        (inputnode, ds_t1w_preproc, [('t1w_preproc', 'in_file'),
-                                     ('source_files', 'source_file')]),
-        (inputnode, ds_t2w_preproc, [('t2w_preproc', 'in_file'),
-                                     ('t2w_source_files', 'source_file')]),
-        (inputnode, ds_t1w_mask, [('t1w_mask', 'in_file'),
-                                  ('source_files', 'source_file')]),
-        (inputnode, ds_t1w_tpms, [('t1w_tpms', 'in_file'),
-                                  ('source_files', 'source_file')]),
-        (inputnode, ds_t1w_dseg, [('t1w_dseg', 'in_file'),
-                                  ('source_files', 'source_file')]),
+        (inputnode, raw_sources, [(source_files, 'in_files')]),
+        (inputnode, ds_anat_mask, [('anat_mask', 'in_file'),
+                                   (source_files, 'source_file')]),
+        (inputnode, ds_anat_tpms, [('anat_tpms', 'in_file'),
+                                   (source_files, 'source_file')]),
+        (inputnode, ds_anat_dseg, [('anat_dseg', 'in_file'),
+                                   (source_files, 'source_file')]),
         (inputnode, ds_anat_ribbon, [('anat_ribbon', 'in_file'),
-                                     ('source_files', 'source_file')]),
-        (raw_sources, ds_t1w_mask, [('out', 'RawSources')]),
+                                     (source_files, 'source_file')]),
+        (raw_sources, ds_anat_mask, [('out', 'RawSources')]),
     ])
-    # fmt: on
+    # fmt:on
 
     # Transforms
     if spaces.get_spaces(nonstandard=False, dim=(3,)):
-        ds_std2t1w_xfm = pe.MapNode(
-            DerivativesDataSink(base_directory=output_dir, to="T1w", mode="image", suffix="xfm"),
+        ds_std2anat_xfm = pe.MapNode(
+            DerivativesDataSink(base_directory=output_dir, to=space, mode="image", suffix="xfm"),
             iterfield=("in_file", "from"),
-            name="ds_std2t1w_xfm",
+            name="ds_std2anat_xfm",
             run_without_submitting=True,
         )
 
-        ds_t1w2std_xfm = pe.MapNode(
+        ds_anat2std_xfm = pe.MapNode(
             DerivativesDataSink(
-                base_directory=output_dir, mode="image", suffix="xfm", **{"from": "T1w"}
+                base_directory=output_dir, mode="image", suffix="xfm", **{"from": space}
             ),
             iterfield=("in_file", "to"),
-            name="ds_t1w2std_xfm",
+            name="ds_anat2std_xfm",
             run_without_submitting=True,
         )
 
-        # fmt: off
+        # fmt:off
         workflow.connect([
-            (inputnode, ds_t1w2std_xfm, [
+            (inputnode, ds_anat2std_xfm, [
                 ('anat2std_xfm', 'in_file'),
                 (('template', _combine_cohort), 'to'),
-                ('source_files', 'source_file')]),
-            (inputnode, ds_std2t1w_xfm, [
+                (source_files, 'source_file')]),
+            (inputnode, ds_std2anat_xfm, [
                 ('std2anat_xfm', 'in_file'),
                 (('template', _combine_cohort), 'from'),
-                ('source_files', 'source_file')]),
+                (source_files, 'source_file')]),
         ])
-        # fmt: on
-
-    if num_t1w > 1:
-        # Please note the dictionary unpacking to provide the from argument.
-        # It is necessary because from is a protected keyword (not allowed as argument name).
-        ds_t1w_ref_xfms = pe.MapNode(
-            DerivativesDataSink(
-                base_directory=output_dir,
-                to="T1w",
-                mode="image",
-                suffix="xfm",
-                extension="txt",
-                **{"from": "orig"},
-            ),
-            iterfield=["source_file", "in_file"],
-            name="ds_t1w_ref_xfms",
-            run_without_submitting=True,
-        )
-        # fmt: off
-        workflow.connect([
-            (inputnode, ds_t1w_ref_xfms, [('source_files', 'source_file'),
-                                          ('t1w_ref_xfms', 'in_file')]),
-        ])
-        # fmt: on
+        # fmt:on
 
     # Write derivatives in standard spaces specified by --output-spaces
     if getattr(spaces, "_cached") is not None and spaces.cached.references:
@@ -515,8 +584,7 @@ def init_anat_derivatives_wf(
 
         gen_ref = pe.Node(GenerateSamplingReference(), name="gen_ref", mem_gb=0.01)
 
-        # Mask T1w preproc images
-        mask_t1w = pe.Node(ApplyMask(), name="mask_t1w")
+        mask_anat = pe.Node(ApplyMask(), name="mask_anat")
 
         # Resample T1w-space inputs
         anat2std_t1w = pe.Node(
@@ -581,15 +649,17 @@ def init_anat_derivatives_wf(
         #           output in the data/io_spec.json file.
         ds_std_tpms.inputs.label = tpm_labels
 
+        preproc_file = 't1w_preproc' if num_t1w else 't2w_preproc'
+
         # fmt: off
         workflow.connect([
-            (inputnode, mask_t1w, [('t1w_preproc', 'in_file'),
-                                   ('t1w_mask', 'in_mask')]),
-            (mask_t1w, anat2std_t1w, [('out_file', 'input_image')]),
-            (inputnode, anat2std_mask, [('t1w_mask', 'input_image')]),
-            (inputnode, anat2std_dseg, [('t1w_dseg', 'input_image')]),
-            (inputnode, anat2std_tpms, [('t1w_tpms', 'input_image')]),
-            (inputnode, gen_ref, [('t1w_preproc', 'moving_image')]),
+            (inputnode, mask_anat, [(preproc_file, 'in_file'),
+                                   ('anat_mask', 'in_mask')]),
+            (mask_anat, anat2std_t1w, [('out_file', 'input_image')]),
+            (inputnode, anat2std_mask, [('anat_mask', 'input_image')]),
+            (inputnode, anat2std_dseg, [('anat_dseg', 'input_image')]),
+            (inputnode, anat2std_tpms, [('anat_tpms', 'input_image')]),
+            (inputnode, gen_ref, [(preproc_file, 'moving_image')]),
             (inputnode, select_xfm, [
                 ('anat2std_xfm', 'anat2std_xfm'),
                 ('template', 'keys')]),
@@ -622,7 +692,7 @@ def init_anat_derivatives_wf(
             ]
             # Connect the source_file input of these datasinks
             + [
-                (inputnode, n, [("source_files", "source_file")])
+                (inputnode, n, [(source_files, "source_file")])
                 for n in (ds_std_t1w, ds_std_mask, ds_std_dseg, ds_std_tpms)
             ]
             # Connect the space input of these datasinks
@@ -636,7 +706,7 @@ def init_anat_derivatives_wf(
             ]
         )
 
-    if not freesurfer:
+    if not surface_recon:
         return workflow
 
     from niworkflows.interfaces.nitransforms import ConcatenateXFMs
@@ -645,28 +715,28 @@ def init_anat_derivatives_wf(
     # FS native space transforms
     lta2itk_fwd = pe.Node(ConcatenateXFMs(), name="lta2itk_fwd", run_without_submitting=True)
     lta2itk_inv = pe.Node(ConcatenateXFMs(), name="lta2itk_inv", run_without_submitting=True)
-    ds_t1w_fsnative = pe.Node(
+    ds_anat_fsnative = pe.Node(
         DerivativesDataSink(
             base_directory=output_dir,
             mode="image",
             to="fsnative",
             suffix="xfm",
             extension="txt",
-            **{"from": "T1w"},
+            **{"from": space},
         ),
-        name="ds_t1w_fsnative",
+        name="ds_anat_fsnative",
         run_without_submitting=True,
     )
-    ds_fsnative_t1w = pe.Node(
+    ds_fsnative_anat = pe.Node(
         DerivativesDataSink(
             base_directory=output_dir,
             mode="image",
-            to="T1w",
+            to=space,
             suffix="xfm",
             extension="txt",
             **{"from": "fsnative"},
         ),
-        name="ds_fsnative_t1w",
+        name="ds_fsnative_anat",
         run_without_submitting=True,
     )
     # Surfaces
@@ -722,49 +792,49 @@ def init_anat_derivatives_wf(
         run_without_submitting=True,
     )
     # Parcellations
-    ds_t1w_fsaseg = pe.Node(
+    ds_anat_fsaseg = pe.Node(
         DerivativesDataSink(base_directory=output_dir, desc="aseg", suffix="dseg", compress=True),
-        name="ds_t1w_fsaseg",
+        name="ds_anat_fsaseg",
         run_without_submitting=True,
     )
-    ds_t1w_fsparc = pe.Node(
+    ds_anat_fsparc = pe.Node(
         DerivativesDataSink(
             base_directory=output_dir, desc="aparcaseg", suffix="dseg", compress=True
         ),
-        name="ds_t1w_fsparc",
+        name="ds_anat_fsparc",
         run_without_submitting=True,
     )
 
     # fmt: off
     workflow.connect([
-        (inputnode, lta2itk_fwd, [('t1w2fsnative_xfm', 'in_xfms')]),
-        (inputnode, lta2itk_inv, [('fsnative2t1w_xfm', 'in_xfms')]),
-        (inputnode, ds_t1w_fsnative, [('source_files', 'source_file')]),
-        (lta2itk_fwd, ds_t1w_fsnative, [('out_xfm', 'in_file')]),
-        (inputnode, ds_fsnative_t1w, [('source_files', 'source_file')]),
-        (lta2itk_inv, ds_fsnative_t1w, [('out_xfm', 'in_file')]),
+        (inputnode, lta2itk_fwd, [('anat2fsnative_xfm', 'in_xfms')]),
+        (inputnode, lta2itk_inv, [('fsnative2anat_xfm', 'in_xfms')]),
+        (inputnode, ds_anat_fsnative, [(source_files, 'source_file')]),
+        (lta2itk_fwd, ds_anat_fsnative, [('out_xfm', 'in_file')]),
+        (inputnode, ds_fsnative_anat, [(source_files, 'source_file')]),
+        (lta2itk_inv, ds_fsnative_anat, [('out_xfm', 'in_file')]),
         (inputnode, name_surfs, [('surfaces', 'in_file')]),
         (inputnode, ds_surfs, [('surfaces', 'in_file'),
-                               ('source_files', 'source_file')]),
+                               (source_files, 'source_file')]),
         (name_surfs, ds_surfs, [('hemi', 'hemi'),
                                 ('suffix', 'suffix')]),
         (inputnode, name_regs, [('sphere_reg', 'in_file')]),
         (inputnode, ds_regs, [('sphere_reg', 'in_file'),
-                              ('source_files', 'source_file')]),
+                              (source_files, 'source_file')]),
         (name_regs, ds_regs, [('hemi', 'hemi')]),
         (inputnode, name_reg_fsLR, [('sphere_reg_fsLR', 'in_file')]),
         (inputnode, ds_reg_fsLR, [('sphere_reg_fsLR', 'in_file'),
-                                  ('source_files', 'source_file')]),
+                                  (source_files, 'source_file')]),
         (name_reg_fsLR, ds_reg_fsLR, [('hemi', 'hemi')]),
         (inputnode, name_morphs, [('morphometrics', 'in_file')]),
         (inputnode, ds_morphs, [('morphometrics', 'in_file'),
-                                ('source_files', 'source_file')]),
+                                (source_files, 'source_file')]),
         (name_morphs, ds_morphs, [('hemi', 'hemi'),
                                   ('suffix', 'suffix')]),
-        (inputnode, ds_t1w_fsaseg, [('t1w_fs_aseg', 'in_file'),
-                                    ('source_files', 'source_file')]),
-        (inputnode, ds_t1w_fsparc, [('t1w_fs_aparc', 'in_file'),
-                                    ('source_files', 'source_file')]),
+        (inputnode, ds_anat_fsaseg, [('anat_fs_aseg', 'in_file'),
+                                    (source_files, 'source_file')]),
+        (inputnode, ds_anat_fsparc, [('anat_fs_aparc', 'in_file'),
+                                    (source_files, 'source_file')]),
     ])
     # fmt: on
     if cifti_output:
@@ -782,7 +852,7 @@ def init_anat_derivatives_wf(
         # fmt:off
         workflow.connect([
             (inputnode, ds_cifti_morph, [('cifti_morph', 'in_file'),
-                                         ('source_files', 'source_file'),
+                                         (source_files, 'source_file'),
                                          ('cifti_density', 'density'),
                                          (('cifti_metadata', _read_jsons), 'meta_dict')])
         ])

From 23471097c1a581437ca07be6415c195c92c8aeea Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Mon, 2 Oct 2023 17:05:03 -0400
Subject: [PATCH 02/14] FEAT: Remove T1w only check, reflect modality used on
 wf desc

---
 nibabies/workflows/anatomical/segmentation.py | 10 +++-------
 1 file changed, 3 insertions(+), 7 deletions(-)

diff --git a/nibabies/workflows/anatomical/segmentation.py b/nibabies/workflows/anatomical/segmentation.py
index 38a92e41..ce903749 100644
--- a/nibabies/workflows/anatomical/segmentation.py
+++ b/nibabies/workflows/anatomical/segmentation.py
@@ -37,11 +37,6 @@ def init_anat_segmentations_wf(
     from niworkflows.engine.workflows import LiterateWorkflow as Workflow
     from niworkflows.utils.connections import listify
 
-    if anat_modality != "T1w":
-        raise NotImplementedError(
-            "Only T1w images are currently accepted for the segmentation workflow."
-        )
-
     if precomp_aseg and template_dir:
         print("Found precomputed aseg; skipping JointLabelFusion", file=sys.stderr)
         template_dir = None
@@ -67,7 +62,8 @@ def init_anat_segmentations_wf(
         from nipype.interfaces.fsl.base import Info as FSLInfo
 
         wf.__desc__ += (
-            f"the brain-extracted T1w using FSL FAST {FSLInfo.version() or '(version unknown)'}."
+            f"the brain-extracted {anat_modality} using FSL FAST "
+            f"{FSLInfo.version() or '(version unknown)'}."
         )
 
         # Use FSL FAST for segmentations
@@ -99,7 +95,7 @@ def init_anat_segmentations_wf(
         from nipype.interfaces.ants.base import Info as ANTsInfo
 
         wf.__desc__ += (
-            "the brain-extracted T1w using ANTs JointFusion, distributed with ANTs "
+            f"the brain-extracted {anat_modality} using ANTs JointFusion, distributed with ANTs "
             f"{ANTsInfo.version() or '(version unknown)'}."
         )
         tmpl_anats, tmpl_segs = _parse_segmentation_atlases(anat_modality, template_dir)

From eee58b54871c75a7d9f77882757631631851b44b Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Mon, 2 Oct 2023 17:07:21 -0400
Subject: [PATCH 03/14] FEAT: Add separate workflow for single modality
 anatomical processing

---
 nibabies/workflows/anatomical/base.py | 534 ++++++++++++++++++++------
 1 file changed, 421 insertions(+), 113 deletions(-)

diff --git a/nibabies/workflows/anatomical/base.py b/nibabies/workflows/anatomical/base.py
index dc475b43..1a226e59 100644
--- a/nibabies/workflows/anatomical/base.py
+++ b/nibabies/workflows/anatomical/base.py
@@ -5,16 +5,63 @@
 from pathlib import Path
 
 from nipype.interfaces import utility as niu
+from nipype.interfaces.ants.base import Info as ANTsInfo
 from nipype.pipeline import engine as pe
 from niworkflows.engine.workflows import LiterateWorkflow
 from niworkflows.utils.spaces import Reference, SpatialReferences
-
-from ... import config
+from smriprep.workflows.norm import init_anat_norm_wf
+
+from nibabies import config
+from nibabies.utils.misc import fix_multi_source_name
+
+# Relative imports to avoid verbosity
+from .brain_extraction import init_infant_brain_extraction_wf
+from .outputs import (
+    init_anat_derivatives_wf,
+    init_anat_reports_wf,
+    init_coreg_report_wf,
+)
+from .preproc import init_anat_preproc_wf
+from .registration import init_coregister_derivatives_wf, init_coregistration_wf
+from .segmentation import init_anat_segmentations_wf
+from .surfaces import init_anat_ribbon_wf
+from .template import init_anat_template_wf
 
 if ty.TYPE_CHECKING:
     from nibabies.utils.bids import Derivatives
 
 
+ANAT_OUT_FIELDS = [
+    "anat_preproc",
+    "anat_brain",
+    "anat_mask",
+    "anat_dseg",
+    "anat_tpms",
+    "anat_ref_xfms",
+    "std_preproc",
+    "std_brain",
+    "std_dseg",
+    "std_tpms",
+    "subjects_dir",
+    "subject_id",
+    "anat2std_xfm",
+    "std2anat_xfm",
+    "t1w2fsnative_xfm",
+    "fsnative2t1w_xfm",
+    "surfaces",
+    "morphometrics",
+    "anat_aseg",
+    "anat_mcrib",
+    "anat_aparc",
+    "anat_ribbon",
+    "template",
+    # registration sphere space is dependent on surface recon method
+    "sphere_reg",
+    "sphere_reg_fsLR",
+    "midthickness_fsLR",
+]
+
+
 def init_infant_anat_wf(
     *,
     age_months: int,
@@ -33,7 +80,7 @@ def init_infant_anat_wf(
     skull_strip_mode: str,
     skull_strip_template: Reference,
     sloppy: bool,
-    spaces: SpatialReferences | None,
+    spaces: SpatialReferences,
     cifti_output: ty.Literal['91k', '170k'] | None,
     name: str = "infant_anat_wf",
 ) -> LiterateWorkflow:
@@ -86,118 +133,13 @@ def init_infant_anat_wf(
     surfaces
         GIFTI surfaces (gray/white boundary, midthickness, pial, inflated)
     """
-    from nipype.interfaces.ants.base import Info as ANTsInfo
-    from smriprep.workflows.norm import init_anat_norm_wf
-
-    from ...utils.misc import fix_multi_source_name
-    from .brain_extraction import init_infant_brain_extraction_wf
-    from .outputs import (
-        init_anat_derivatives_wf,
-        init_anat_reports_wf,
-        init_coreg_report_wf,
-    )
-    from .preproc import init_anat_preproc_wf
-    from .registration import init_coregister_derivatives_wf, init_coregistration_wf
-    from .segmentation import init_anat_segmentations_wf
-    from .surfaces import init_anat_ribbon_wf
-    from .template import init_anat_template_wf
-
-    # for now, T1w only
-    num_t1w = len(t1w) if t1w else 0
-    num_t2w = len(t2w) if t2w else 0
-
-    # Expected derivatives: Prioritize T1w space if available, otherwise fall back to T2w
-    deriv_mask = derivatives.mask
-    deriv_aseg = derivatives.aseg
+    if not t1w or not t2w:
+        # Error type?
+        raise RuntimeError("Both T1w and T2w images are required to run this workflow.")
 
+    num_t1w = len(t1w)
+    num_t2w = len(t2w)
     wf = LiterateWorkflow(name=name)
-    desc = f"""\n
-Anatomical data preprocessing
-
-: A total of {num_t1w} T1w and {num_t2w} T2w images were found within the input
-BIDS dataset."""
-
-    inputnode = pe.Node(
-        niu.IdentityInterface(fields=["t1w", "t2w", "subject_id", "subjects_dir"]),  # FLAIR / ROI?
-        name="inputnode",
-    )
-    outputnode = pe.Node(
-        niu.IdentityInterface(
-            fields=[
-                "anat_preproc",
-                "anat_brain",
-                "anat_mask",
-                "anat_dseg",
-                "anat_tpms",
-                "anat_ref_xfms",
-                "std_preproc",
-                "std_brain",
-                "std_dseg",
-                "std_tpms",
-                "subjects_dir",
-                "subject_id",
-                "anat2std_xfm",
-                "std2anat_xfm",
-                "t1w2fsnative_xfm",
-                "fsnative2t1w_xfm",
-                "surfaces",
-                "morphometrics",
-                "anat_aseg",
-                "anat_mcrib",
-                "anat_aparc",
-                "anat_ribbon",
-                "template",
-                # registration sphere space is dependent on surface recon method
-                "sphere_reg",
-                "sphere_reg_fsLR",
-                "midthickness_fsLR",
-            ]
-        ),
-        name="outputnode",
-    )
-
-    desc += (
-        """\
-All of the T1-weighted images were denoised and corrected for intensity non-uniformity (INU)"""
-        if num_t1w > 1
-        else """\
-The T1-weighted (T1w) image was denoised and corrected for intensity non-uniformity (INU)"""
-    )
-
-    desc += """\
-with `N4BiasFieldCorrection` [@n4], distributed with ANTs {ants_ver} \
-[@ants, RRID:SCR_004757]"""
-    desc += ".\n" if num_t1w > 1 else ", and used as T1w-reference throughout the workflow.\n"
-
-    desc += (
-        "A previously computed mask was used to skull-strip the anatomical image."
-        if deriv_mask
-        else """\
-The T1w-reference was then skull-stripped with a modified implementation of
-the `antsBrainExtraction.sh` workflow (from ANTs), using {skullstrip_tpl}
-as target template.
-"""
-    )
-
-    wf.__desc__ = desc.format(
-        ants_ver=ANTsInfo.version() or "(version unknown)",
-        skullstrip_tpl=skull_strip_template.fullname,
-    )
-    wf.__postdesc__ = ""
-
-    # Define output workflows
-    anat_reports_wf = init_anat_reports_wf(
-        freesurfer=freesurfer, output_dir=output_dir, sloppy=sloppy
-    )
-
-    anat_derivatives_wf = init_anat_derivatives_wf(
-        bids_root=bids_root,
-        freesurfer=freesurfer,
-        num_t1w=num_t1w,
-        output_dir=output_dir,
-        spaces=spaces,
-        cifti_output=cifti_output,
-    )
 
     # Derivatives used based on the following truth table:
     # |--------|--------|---------------------------------|------------------|
@@ -234,6 +176,39 @@ def init_infant_anat_wf(
         t2w_aseg,
     )
 
+    desc = _gen_anat_wf_desc(
+        t1w=t1w,
+        t2w=t2w,
+        mask=t1w_mask or t2w_mask,
+        aseg=t1w_aseg or t2w_aseg,
+    )
+
+    wf.__desc__ = desc.format(
+        ants_ver=ANTsInfo.version() or "(version unknown)",
+        skullstrip_tpl=skull_strip_template.fullname,
+    )
+    wf.__postdesc__ = ""
+
+    inputnode = pe.Node(
+        niu.IdentityInterface(fields=["t1w", "t2w", "subject_id", "subjects_dir"]),  # FLAIR / ROI?
+        name="inputnode",
+    )
+    outputnode = pe.Node(niu.IdentityInterface(fields=ANAT_OUT_FIELDS), name="outputnode")
+
+    # Define output workflows
+    anat_reports_wf = init_anat_reports_wf(
+        freesurfer=freesurfer, output_dir=output_dir, sloppy=sloppy
+    )
+
+    anat_derivatives_wf = init_anat_derivatives_wf(
+        bids_root=bids_root,
+        freesurfer=freesurfer,
+        num_t1w=num_t1w,
+        output_dir=output_dir,
+        spaces=spaces,
+        cifti_output=cifti_output,
+    )
+
     t1w_template_wf = init_anat_template_wf(
         contrast="T1w",
         num_files=num_t1w,
@@ -606,3 +581,336 @@ def init_infant_anat_wf(
         # fmt:on
 
     return wf
+
+
+def init_infant_single_anat_wf(
+    *,
+    age_months: int,
+    ants_affine_init: bool,
+    t1w: list | None,
+    t2w: list | None,
+    contrast: ty.Literal['T1w', 'T2w'],
+    bids_root: str | Path,
+    derivatives: Derivatives,
+    freesurfer: bool,
+    hires: bool | None,
+    longitudinal: bool,
+    omp_nthreads: int,
+    output_dir: str | Path,
+    segmentation_atlases: str | Path | None,
+    skull_strip_mode: str,
+    skull_strip_template: Reference,
+    sloppy: bool,
+    spaces: SpatialReferences,
+    cifti_output: ty.Literal['91k', '170k'] | None,
+    name: str = "infant_single_anat_wf",
+) -> LiterateWorkflow:
+    """"""
+    if t1w and t2w:
+        # Error type?
+        raise RuntimeError(
+            "This workflow uses only T1w or T2w inputs, but both contrasts are available."
+        )
+
+    anat_files = t1w or t2w
+    num_files = len(anat_files)
+    workflow = LiterateWorkflow(name=name)
+
+    # Precomputed derivatives
+    if contrast == 'T1w':
+        mask = derivatives.t1w_mask
+        aseg = derivatives.t1w_aseg
+    elif contrast == 'T2w':
+        mask = derivatives.t2w_mask
+        aseg = derivatives.t2w_aseg
+
+    config.loggers.workflow.info(
+        f"Derivatives used (%s):\n\t<mask - %s>\n\t<aseg %s>\n\t", contrast, bool(mask), bool(aseg)
+    )
+
+    inputnode = pe.Node(
+        niu.IdentityInterface(fields=["t1w", "t2w", "subject_id", "subjects_dir"]),  # FLAIR / ROI?
+        name="inputnode",
+    )
+    outputnode = pe.Node(niu.IdentityInterface(fields=ANAT_OUT_FIELDS), name="outputnode")
+
+    desc = _gen_anat_wf_desc(
+        t1w=anat_files if contrast == 'T1w' else None,
+        t2w=anat_files if contrast == 'T2w' else None,
+        mask=bool(mask),
+    )
+    workflow.__desc__ = desc.format(
+        ants_ver=ANTsInfo.version() or "(version unknown)",
+        skullstrip_tpl=skull_strip_template.fullname,
+    )
+    workflow.__postdesc__ = ""
+
+    # outputs
+    recon_method = config.workflow.surface_recon_method  # TODO: Make workflow parameter
+    anat_reports_wf = init_anat_reports_wf(
+        surface_recon=recon_method, output_dir=output_dir, sloppy=sloppy
+    )
+
+    # TODO: Update transforms TO-FROM to reflect contrast
+    anat_derivatives_wf = init_anat_derivatives_wf(
+        bids_root=bids_root,
+        output_dir=output_dir,
+        surface_recon=recon_method,
+        num_t1w=num_files if contrast == 'T1w' else None,
+        num_t2w=num_files if contrast == 'T2w' else None,
+        spaces=spaces,
+        cifti_output=bool(cifti_output),
+    )
+
+    # template
+    anat_template_wf = init_anat_template_wf(
+        contrast=contrast,
+        num_files=num_files,
+        longitudinal=longitudinal,
+        omp_nthreads=omp_nthreads,
+        sloppy=sloppy,
+        has_mask=bool(mask),
+        has_aseg=bool(aseg),
+        name=f"{contrast.lower()}_template_wf",
+    )
+    # preproc
+    anat_preproc_wf = init_anat_preproc_wf(name=f"{contrast.lower()}_preproc_wf")
+    # T2-only brain extraction
+    anat_seg_wf = init_anat_segmentations_wf(
+        anat_modality=contrast,
+        template_dir=segmentation_atlases,
+        sloppy=sloppy,
+        omp_nthreads=omp_nthreads,
+        precomp_aseg=bool(aseg),
+    )
+    # T2-only segmentation
+    anat_norm_wf = init_anat_norm_wf(
+        sloppy=sloppy,
+        omp_ntheads=omp_nthreads,
+        templates=spaces.get_spaces(nonstandard=False, dim=(3,)),
+    )
+
+    if mask:
+        from niworkflows.interfaces.nibabel import ApplyMask
+
+        mask_ref = derivatives.references[f'{contrast.lower()}_mask']
+        anat_preproc_wf.inputnode.inputs.mask_reference = mask_ref
+
+        apply_deriv_mask = pe.Node(ApplyMask(), name='apply_deriv_mask')
+        # fmt:off
+        workflow.connect([
+            (anat_preproc_wf, anat_norm_wf, [
+                ('outputnode.anat_mask', 'inputnode.moving_mask')]),
+            (anat_preproc_wf, apply_deriv_mask, [
+                ('outputnode.anat_preproc', 'in_file')]),
+            (anat_template_wf, apply_deriv_mask, [
+                ('outputnode.anat_mask', 'in_mask')]),
+            (apply_deriv_mask, anat_seg_wf, [
+                ("out_mask", "inputnode.anat_brain")]),
+            (anat_template_wf, anat_derivatives_wf, [
+                ('outputnode.anat_mask', 'inputnode.anat_mask')]),
+            (anat_template_wf, outputnode, [
+                ('outputnode.anat_mask', 'anat_mask')]),
+        ])
+        # fmt:on
+
+    else:
+        brain_extraction_wf = init_infant_brain_extraction_wf(
+            age_months=age_months,
+            ants_affine_init=ants_affine_init,
+            skull_strip_template=skull_strip_template.space,
+            template_specs=skull_strip_template.spec,
+            omp_nthreads=omp_nthreads,
+            sloppy=sloppy,
+            debug="registration" in config.execution.debug,
+        )
+        # fmt:off
+        workflow.connect([
+            (anat_preproc_wf, brain_extraction_wf, [('outputnode.anat_preproc', 'inputnode.t2w_preproc')]),
+            (brain_extraction_wf, anat_seg_wf, [('outputnode.t2w_brain', 'inputnode.anat_brain')]),
+            (brain_extraction_wf, anat_norm_wf, [('outputnode.out_mask', 'inputnode.moving_mask')]),
+            (brain_extraction_wf, anat_derivatives_wf, [('outputnode.out_mask', 'inputnode.anat_mask')]),
+        ])
+        # fmt:on
+
+    # fmt:off
+    workflow.connect([
+        (inputnode, anat_template_wf, [("anat_file", "inputnode.anat_files")]),
+        (inputnode, anat_reports_wf, [("anat_file", "inputnode.source_file")]),
+        (inputnode, anat_norm_wf, [(("anat_file", fix_multi_source_name), "inputnode.orig_t1w")]),
+
+        (anat_template_wf, outputnode, [
+            ("outputnode.anat_realign_xfm", "anat_ref_xfms")]),
+        (anat_template_wf, anat_preproc_wf, [
+            ("outputnode.anat_ref", "inputnode.in_anat")]),
+        (anat_template_wf, anat_derivatives_wf, [
+            ("outputnode.anat_valid_list", f"inputnode.{contrast.lower()}_source_files"),
+            ("outputnode.anat_realign_xfm", f"inputnode.{contrast.lower()}_ref_xfms")]),
+        (anat_template_wf, anat_reports_wf, [
+            ("outputnode.out_report", "inputnode.anat_conform_report")]),
+        (anat_preproc_wf, anat_norm_wf, [
+            ('outputnode.anat_preproc', 'inputnode.moving_image')]),
+        (anat_preproc_wf, anat_derivatives_wf, [
+            ('outputnode.anat_preproc', f'inputnode.{contrast.lower()}_preproc')]),
+        (anat_seg_wf, outputnode, [
+            ("outputnode.anat_dseg", "anat_dseg"),
+            ("outputnode.anat_tpms", "anat_tpms")]),
+        (anat_seg_wf, anat_derivatives_wf, [
+            ("outputnode.anat_dseg", "inputnode.anat_dseg"),
+            ("outputnode.anat_tpms", "inputnode.anat_tpms"),
+        ]),
+        (anat_seg_wf, anat_norm_wf, [
+            ("outputnode.anat_dseg", "inputnode.moving_segmentation"),
+            ("outputnode.anat_tpms", "inputnode.moving_tpms")]),
+
+        (anat_norm_wf, anat_reports_wf, [("poutputnode.template", "inputnode.template")]),
+        (anat_norm_wf, outputnode, [
+            ("poutputnode.standardized", "std_preproc"),
+            ("poutputnode.std_mask", "std_mask"),
+            ("poutputnode.std_dseg", "std_dseg"),
+            ("poutputnode.std_tpms", "std_tpms"),
+            ("outputnode.template", "template"),
+            ("outputnode.anat2std_xfm", "anat2std_xfm"),
+            ("outputnode.std2anat_xfm", "std2anat_xfm")]),
+        (anat_norm_wf, anat_derivatives_wf, [
+            ("outputnode.template", "inputnode.template"),
+            ("outputnode.anat2std_xfm", "inputnode.anat2std_xfm"),
+            ("outputnode.std2anat_xfm", "inputnode.std2anat_xfm")]),
+        (outputnode, anat_reports_wf, [
+            ("anat_preproc", "inputnode.t1w_preproc"),
+            ("anat_mask", "inputnode.anat_mask"),
+            ("anat_dseg", "inputnode.anat_dseg"),
+            ("std_preproc", "inputnode.std_t1w"),
+            ("std_mask", "inputnode.std_mask"),
+        ]),
+    ])
+    # fmt:on
+    # TODO: Remove `freesurfer` option
+    if not recon_method:
+        return workflow
+
+    elif recon_method == 'freesurfer':
+        from smriprep.workflows.surfaces import init_surface_recon_wf
+
+        surface_recon_wf = init_surface_recon_wf(omp_nthreads=omp_nthreads, hires=hires)
+    elif recon_method == 'infantfs':
+        from .surfaces import init_infantfs_surface_recon_wf
+
+        # if running with precomputed aseg, or JLF, pass the aseg along to FreeSurfer
+        use_aseg = bool(derivatives.aseg or segmentation_atlases)
+        surface_recon_wf = init_infantfs_surface_recon_wf(
+            age_months=age_months,
+            use_aseg=use_aseg,
+        )
+
+    elif recon_method == 'mcribs':
+        from .surfaces import init_mcribs_sphere_reg_wf, init_mcribs_surface_recon_wf
+
+        # t2w mask, t2w aseg
+        surface_recon_wf = init_mcribs_surface_recon_wf(
+            omp_nthreads=omp_nthreads,
+            use_aseg=bool(aseg),  # TODO: Incorporate mcribs segmentation
+            use_mask=bool(mask),  # TODO: Pass in mask regardless of derivatives
+            mcribs_dir=str(config.execution.mcribs_dir),  # Needed to preserve runs
+        )
+        # M-CRIB-S to dHCP42week (32k)
+        sphere_reg_wf = init_mcribs_sphere_reg_wf()
+
+        # fmt:off
+        workflow.connect([
+            (anat_preproc_wf, surface_recon_wf, [('outputnode.anat_preproc', 'inputnode.t2w')]),
+        ])
+        # fmt:on
+        if aseg:
+            workflow.connect(
+                anat_template_wf, 'outputnode.anat_aseg', surface_recon_wf, 'inputnode.ants_segs'
+            )
+        else:
+            # TODO: Use MCRIBS segmentation
+            ...
+        if mask:
+            workflow.connect(
+                anat_template_wf, 'outputnode.anat_mask', surface_recon_wf, 'inputnode.anat_mask'
+            )
+        else:
+            workflow.connect(
+                brain_extraction_wf, 'outputnode.out_mask', surface_recon_wf, 'inputnode.anat_mask'
+            )
+    else:
+        raise NotImplementedError
+
+    return workflow
+
+
+def _gen_anat_wf_desc(t1w: list | None, t2w: list | None, mask: bool) -> str:
+    """Generate the anatomical workflow description."""
+    if not t1w and not t2w:
+        return ''
+
+    # If only a single anatomical modality is provided
+    modality = None
+    anat = None
+    if not t1w or not t2w:
+        anat = t1w or t2w
+        modality = 'T1w' if t1w else 'T2w'
+
+    desc = """\n\nAnatomical data preprocessing\n:"""
+
+    # Anatomicals found
+    if anat is not None:
+        desc += (
+            f"A total of {len(anat)} {modality} images were found "
+            "within the input BIDS dataset.\n"
+        )
+    else:
+        desc += (
+            f"A total of {len(t1w)} T1w and {len(t2w)} T2w images "
+            "were found within the input BIDS dataset.\n"
+        )
+
+    # Template + Preproc workflows
+    if t1w:
+        if len(t1w) == 1:
+            desc += (
+                f"The T1-weighted (T1w) image was denoised "
+                "and corrected for intensity non-uniformity (INU)"
+            )
+        else:
+            desc += (
+                "All of the T1-weighted images were corrected for intensity "
+                "non-uniformity (INU)"
+            )
+        desc += (
+            "with `N4BiasFieldCorrection` [@n4], distributed with ANTs {ants_ver} "
+            "[@ants, RRID:SCR_004757]"
+        )
+        desc += ".\n" if len(t1w) > 1 else ", and used as T1w-reference throughout the workflow.\n"
+    if t2w:
+        if len(t2w) == 1:
+            desc += (
+                "The T2-weighted (T2w) image was denoised and corrected for intensity "
+                "non-uniformity (INU)"
+            )
+        else:
+            desc += (
+                "All of the T2-weighted images were corrected for intensity "
+                "non-uniformity (INU)"
+            )
+        desc += (
+            "with `N4BiasFieldCorrection` [@n4], distributed with ANTs {ants_ver} "
+            "[@ants, RRID:SCR_004757]"
+        )
+        desc += ".\n" if len(t2w) > 1 else ", and used as T2w-reference throughout the workflow.\n"
+
+    # Precomputed derivatives
+    if mask:
+        desc += "A previously computed mask was used to skull-strip the anatomical image."
+
+    else:
+        desc += (
+            f"The {modality or 'T2w'}-reference was then skull-stripped with a modified "
+            "implementation of the `antsBrainExtraction.sh` workflow (from ANTs), using "
+            "{skullstrip_tpl} as target template."
+        )
+
+    return desc

From 95ab5eef694ce136cc87174b3c6508528bcde586 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Mon, 2 Oct 2023 22:25:09 -0400
Subject: [PATCH 04/14] RF: Call alternative workflow if missing anatomicals

---
 nibabies/workflows/base.py | 29 ++++++++++++++++++++++++++++-
 1 file changed, 28 insertions(+), 1 deletion(-)

diff --git a/nibabies/workflows/base.py b/nibabies/workflows/base.py
index eecfc5af..10b39499 100644
--- a/nibabies/workflows/base.py
+++ b/nibabies/workflows/base.py
@@ -206,7 +206,7 @@ def init_single_subject_wf(
 
     from ..utils.bids import Derivatives
     from ..utils.misc import fix_multi_source_name
-    from .anatomical import init_infant_anat_wf
+    from .anatomical import init_infant_anat_wf, init_infant_single_anat_wf
 
     name = (
         f"single_subject_{subject_id}_{session_id}_wf"
@@ -344,6 +344,33 @@ def init_single_subject_wf(
         run_without_submitting=True,
     )
 
+    wf_args = dict(
+        ants_affine_init=True,
+        age_months=age,
+        anat_modality=anat_modality,
+        t1w=subject_data["t1w"],
+        t2w=subject_data["t2w"],
+        bids_root=config.execution.bids_dir,
+        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,
+        segmentation_atlases=config.execution.segmentation_atlases_dir,
+        skull_strip_mode=config.workflow.skull_strip_t1w,
+        skull_strip_template=Reference.from_string(config.workflow.skull_strip_template)[0],
+        sloppy=config.execution.sloppy,
+        spaces=spaces,
+        cifti_output=config.workflow.cifti_output,
+    )
+
+    if subject_data['t1w'] and subject_data['t2w']:
+        anat_preproc_wf = init_infant_anat_wf(**wf_args)
+    else:
+        anat_preproc_wf = init_infant_single_anat_wf(
+            contrast='T1w' if subject_data['t1w'] else 'T2w', **wf_args
+        )
     # Preprocessing of anatomical (includes registration to UNCInfant)
     anat_preproc_wf = init_infant_anat_wf(
         ants_affine_init=True,

From d0d938739a73c96502af4372b3c9caa16ed1c608 Mon Sep 17 00:00:00 2001
From: Mathias Goncalves <goncalves.mathias@gmail.com>
Date: Tue, 3 Oct 2023 14:44:59 -0400
Subject: [PATCH 05/14] FIX: Missing connections, surfaces, syntax

---
 nibabies/workflows/anatomical/__init__.py |   2 +-
 nibabies/workflows/anatomical/base.py     | 175 +++++++++++++++++-----
 nibabies/workflows/base.py                |  42 ++----
 3 files changed, 150 insertions(+), 69 deletions(-)

diff --git a/nibabies/workflows/anatomical/__init__.py b/nibabies/workflows/anatomical/__init__.py
index 33d993b2..021d133d 100644
--- a/nibabies/workflows/anatomical/__init__.py
+++ b/nibabies/workflows/anatomical/__init__.py
@@ -1 +1 @@
-from .base import init_infant_anat_wf
+from .base import init_infant_anat_wf, init_infant_single_anat_wf
diff --git a/nibabies/workflows/anatomical/base.py b/nibabies/workflows/anatomical/base.py
index 1a226e59..ca3d71df 100644
--- a/nibabies/workflows/anatomical/base.py
+++ b/nibabies/workflows/anatomical/base.py
@@ -46,8 +46,8 @@
     "subject_id",
     "anat2std_xfm",
     "std2anat_xfm",
-    "t1w2fsnative_xfm",
-    "fsnative2t1w_xfm",
+    "anat2fsnative_xfm",
+    "fsnative2anat_xfm",
     "surfaces",
     "morphometrics",
     "anat_aseg",
@@ -68,7 +68,7 @@ def init_infant_anat_wf(
     ants_affine_init: bool,
     t1w: list,
     t2w: list,
-    anat_modality: str,
+    contrast: ty.Literal['T1w', 'T2w'],
     bids_root: str | Path,
     derivatives: Derivatives,
     freesurfer: bool,
@@ -252,7 +252,7 @@ def init_infant_anat_wf(
 
     # Segmentation - initial implementation should be simple: JLF
     anat_seg_wf = init_anat_segmentations_wf(
-        anat_modality=anat_modality.capitalize(),  # TODO: Revisit this option
+        anat_modality=contrast.capitalize(),  # TODO: Revisit this option
         template_dir=segmentation_atlases,
         sloppy=sloppy,
         omp_nthreads=omp_nthreads,
@@ -625,7 +625,10 @@ def init_infant_single_anat_wf(
         aseg = derivatives.t2w_aseg
 
     config.loggers.workflow.info(
-        f"Derivatives used (%s):\n\t<mask - %s>\n\t<aseg %s>\n\t", contrast, bool(mask), bool(aseg)
+        f"Derivatives used (%s):\n\t\t<Mask: %s>\n\t\t<Aseg: %s>\n",
+        contrast,
+        bool(mask),
+        bool(aseg),
     )
 
     inputnode = pe.Node(
@@ -635,8 +638,8 @@ def init_infant_single_anat_wf(
     outputnode = pe.Node(niu.IdentityInterface(fields=ANAT_OUT_FIELDS), name="outputnode")
 
     desc = _gen_anat_wf_desc(
-        t1w=anat_files if contrast == 'T1w' else None,
-        t2w=anat_files if contrast == 'T2w' else None,
+        t1w=t1w or None,
+        t2w=t2w or None,
         mask=bool(mask),
     )
     workflow.__desc__ = desc.format(
@@ -686,31 +689,33 @@ def init_infant_single_anat_wf(
     # T2-only segmentation
     anat_norm_wf = init_anat_norm_wf(
         sloppy=sloppy,
-        omp_ntheads=omp_nthreads,
+        omp_nthreads=omp_nthreads,
         templates=spaces.get_spaces(nonstandard=False, dim=(3,)),
     )
+    # Aggregate mask, applied mask
+    mask_buffer = pe.Node(
+        niu.IdentityInterface(fields=['anat_mask', 'anat_brain']),
+        name='mask_buffer',
+    )
 
     if mask:
         from niworkflows.interfaces.nibabel import ApplyMask
 
+        anat_template_wf.inputs.inputnode.anat_mask = mask
         mask_ref = derivatives.references[f'{contrast.lower()}_mask']
-        anat_preproc_wf.inputnode.inputs.mask_reference = mask_ref
+        anat_template_wf.inputs.inputnode.mask_reference = mask_ref
 
         apply_deriv_mask = pe.Node(ApplyMask(), name='apply_deriv_mask')
         # fmt:off
         workflow.connect([
-            (anat_preproc_wf, anat_norm_wf, [
-                ('outputnode.anat_mask', 'inputnode.moving_mask')]),
+            (anat_template_wf, mask_buffer, [
+                ('outputnode.anat_mask', 'anat_mask')]),
             (anat_preproc_wf, apply_deriv_mask, [
                 ('outputnode.anat_preproc', 'in_file')]),
             (anat_template_wf, apply_deriv_mask, [
                 ('outputnode.anat_mask', 'in_mask')]),
-            (apply_deriv_mask, anat_seg_wf, [
-                ("out_mask", "inputnode.anat_brain")]),
-            (anat_template_wf, anat_derivatives_wf, [
-                ('outputnode.anat_mask', 'inputnode.anat_mask')]),
-            (anat_template_wf, outputnode, [
-                ('outputnode.anat_mask', 'anat_mask')]),
+            (apply_deriv_mask, mask_buffer, [
+                ('out_file', 'anat_brain')]),
         ])
         # fmt:on
 
@@ -726,18 +731,28 @@ def init_infant_single_anat_wf(
         )
         # fmt:off
         workflow.connect([
-            (anat_preproc_wf, brain_extraction_wf, [('outputnode.anat_preproc', 'inputnode.t2w_preproc')]),
-            (brain_extraction_wf, anat_seg_wf, [('outputnode.t2w_brain', 'inputnode.anat_brain')]),
-            (brain_extraction_wf, anat_norm_wf, [('outputnode.out_mask', 'inputnode.moving_mask')]),
-            (brain_extraction_wf, anat_derivatives_wf, [('outputnode.out_mask', 'inputnode.anat_mask')]),
+            (anat_preproc_wf, brain_extraction_wf, [
+                ('outputnode.anat_preproc', 'inputnode.t2w_preproc')]),
+            (brain_extraction_wf, mask_buffer, [
+                ('outputnode.t2w_brain', 'anat_brain'),
+                ('outputnode.out_mask', 'anat_mask')]),
         ])
         # fmt:on
 
+    if aseg:
+        anat_template_wf.inputs.inputnode.anat_aseg = aseg
+        aseg_ref = derivatives.references[f'{contrast.lower()}_aseg']
+        anat_template_wf.inputs.inputnode.aseg_reference = aseg_ref
+
+        workflow.connect(
+            anat_template_wf, 'outputnode.anat_aseg', anat_seg_wf, 'inputnode.anat_aseg'
+        )
+
     # fmt:off
     workflow.connect([
-        (inputnode, anat_template_wf, [("anat_file", "inputnode.anat_files")]),
-        (inputnode, anat_reports_wf, [("anat_file", "inputnode.source_file")]),
-        (inputnode, anat_norm_wf, [(("anat_file", fix_multi_source_name), "inputnode.orig_t1w")]),
+        (inputnode, anat_template_wf, [(contrast.lower(), "inputnode.anat_files")]),
+        (inputnode, anat_reports_wf, [(contrast.lower(), "inputnode.source_file")]),
+        (inputnode, anat_norm_wf, [((contrast.lower(), fix_multi_source_name), "inputnode.orig_t1w")]),
 
         (anat_template_wf, outputnode, [
             ("outputnode.anat_realign_xfm", "anat_ref_xfms")]),
@@ -750,19 +765,26 @@ def init_infant_single_anat_wf(
             ("outputnode.out_report", "inputnode.anat_conform_report")]),
         (anat_preproc_wf, anat_norm_wf, [
             ('outputnode.anat_preproc', 'inputnode.moving_image')]),
+        (anat_preproc_wf, outputnode, [
+            ('outputnode.anat_preproc', 'anat_preproc')]),
         (anat_preproc_wf, anat_derivatives_wf, [
             ('outputnode.anat_preproc', f'inputnode.{contrast.lower()}_preproc')]),
+        (mask_buffer, anat_derivatives_wf, [
+            ('anat_mask', 'inputnode.anat_mask')]),
+        (mask_buffer, outputnode, [
+            ('anat_mask', 'anat_mask')]),
+        (mask_buffer, anat_seg_wf, [('anat_brain', 'inputnode.anat_brain')]),
         (anat_seg_wf, outputnode, [
             ("outputnode.anat_dseg", "anat_dseg"),
             ("outputnode.anat_tpms", "anat_tpms")]),
         (anat_seg_wf, anat_derivatives_wf, [
             ("outputnode.anat_dseg", "inputnode.anat_dseg"),
-            ("outputnode.anat_tpms", "inputnode.anat_tpms"),
-        ]),
+            ("outputnode.anat_tpms", "inputnode.anat_tpms")]),
+        (mask_buffer, anat_norm_wf, [
+            ('anat_mask', 'inputnode.moving_mask')]),
         (anat_seg_wf, anat_norm_wf, [
             ("outputnode.anat_dseg", "inputnode.moving_segmentation"),
             ("outputnode.anat_tpms", "inputnode.moving_tpms")]),
-
         (anat_norm_wf, anat_reports_wf, [("poutputnode.template", "inputnode.template")]),
         (anat_norm_wf, outputnode, [
             ("poutputnode.standardized", "std_preproc"),
@@ -777,7 +799,7 @@ def init_infant_single_anat_wf(
             ("outputnode.anat2std_xfm", "inputnode.anat2std_xfm"),
             ("outputnode.std2anat_xfm", "inputnode.std2anat_xfm")]),
         (outputnode, anat_reports_wf, [
-            ("anat_preproc", "inputnode.t1w_preproc"),
+            ("anat_preproc", "inputnode.anat_preproc"),
             ("anat_mask", "inputnode.anat_mask"),
             ("anat_dseg", "inputnode.anat_dseg"),
             ("std_preproc", "inputnode.std_t1w"),
@@ -828,17 +850,98 @@ def init_infant_single_anat_wf(
         else:
             # TODO: Use MCRIBS segmentation
             ...
-        if mask:
-            workflow.connect(
-                anat_template_wf, 'outputnode.anat_mask', surface_recon_wf, 'inputnode.anat_mask'
-            )
-        else:
-            workflow.connect(
-                brain_extraction_wf, 'outputnode.out_mask', surface_recon_wf, 'inputnode.anat_mask'
-            )
     else:
         raise NotImplementedError
 
+    # Anatomical ribbon file using HCP signed-distance volume method
+    anat_ribbon_wf = init_anat_ribbon_wf()
+
+    # fmt:off
+    workflow.connect([
+        (inputnode, surface_recon_wf, [
+            ("subject_id", "inputnode.subject_id"),
+            ("subjects_dir", "inputnode.subjects_dir")]),
+        (anat_template_wf, surface_recon_wf, [
+            ("outputnode.anat_ref", "inputnode.t1w"),
+        ]),
+        (mask_buffer, surface_recon_wf, [
+            ("anat_brain", "inputnode.skullstripped_t1"),
+            ("anat_mask", "inputnode.anat_mask")]),
+        (anat_preproc_wf, surface_recon_wf, [
+            ("outputnode.anat_preproc", "inputnode.corrected_t1")]),
+        (surface_recon_wf, outputnode, [
+            ("outputnode.subjects_dir", "subjects_dir"),
+            ("outputnode.subject_id", "subject_id"),
+            ("outputnode.t1w2fsnative_xfm", "anat2fsnative_xfm"),
+            ("outputnode.fsnative2t1w_xfm", "fsnative2anat_xfm"),
+            ("outputnode.surfaces", "surfaces"),
+            ("outputnode.morphometrics", "morphometrics"),
+            ("outputnode.out_aparc", "anat_aparc"),
+            ("outputnode.out_aseg", "anat_aseg"),
+        ]),
+        (mask_buffer, anat_ribbon_wf, [
+            ("anat_mask", "inputnode.t1w_mask"),
+        ]),
+        (surface_recon_wf, anat_ribbon_wf, [
+            ("outputnode.surfaces", "inputnode.surfaces"),
+        ]),
+        (anat_ribbon_wf, outputnode, [
+            ("outputnode.anat_ribbon", "anat_ribbon")
+        ]),
+        (anat_ribbon_wf, anat_derivatives_wf, [
+            ("outputnode.anat_ribbon", "inputnode.anat_ribbon"),
+        ]),
+        (surface_recon_wf, sphere_reg_wf, [
+            ('outputnode.subject_id', 'inputnode.subject_id'),
+            ('outputnode.subjects_dir', 'inputnode.subjects_dir'),
+        ]),
+        (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.out_aseg", "inputnode.anat_fs_aseg"),
+            ("outputnode.out_aparc", "inputnode.anat_fs_aparc"),
+            ("outputnode.t1w2fsnative_xfm", "inputnode.anat2fsnative_xfm"),
+            ("outputnode.fsnative2t1w_xfm", "inputnode.fsnative2anat_xfm"),
+            ("outputnode.surfaces", "inputnode.surfaces"),
+            ("outputnode.morphometrics", "inputnode.morphometrics"),
+        ]),
+        (sphere_reg_wf, outputnode, [
+            ('outputnode.sphere_reg', 'sphere_reg'),
+            ('outputnode.sphere_reg_fsLR', 'sphere_reg_fsLR')]),
+        (sphere_reg_wf, anat_derivatives_wf, [
+            ('outputnode.sphere_reg', 'inputnode.sphere_reg'),
+            ('outputnode.sphere_reg_fsLR', 'inputnode.sphere_reg_fsLR')]),
+    ])
+    # fmt: on
+
+    if cifti_output:
+        from nibabies.workflows.anatomical.resampling import (
+            init_anat_fsLR_resampling_wf,
+        )
+
+        is_mcribs = recon_method == "mcribs"
+        # handles morph_grayords_wf
+        anat_fsLR_resampling_wf = init_anat_fsLR_resampling_wf(cifti_output, mcribs=is_mcribs)
+        anat_derivatives_wf.get_node('inputnode').inputs.cifti_density = cifti_output
+        # fmt:off
+        workflow.connect([
+            (sphere_reg_wf, anat_fsLR_resampling_wf, [
+                ('outputnode.sphere_reg', 'inputnode.sphere_reg'),
+                ('outputnode.sphere_reg_fsLR', 'inputnode.sphere_reg_fsLR')]),
+            (surface_recon_wf, anat_fsLR_resampling_wf, [
+                ('outputnode.subject_id', 'inputnode.subject_id'),
+                ('outputnode.subjects_dir', 'inputnode.subjects_dir'),
+                ('outputnode.surfaces', 'inputnode.surfaces'),
+                ('outputnode.morphometrics', 'inputnode.morphometrics')]),
+            (anat_fsLR_resampling_wf, anat_derivatives_wf, [
+                ("outputnode.cifti_morph", "inputnode.cifti_morph"),
+                ("outputnode.cifti_metadata", "inputnode.cifti_metadata")]),
+            (anat_fsLR_resampling_wf, outputnode, [
+                ("outputnode.midthickness_fsLR", "midthickness_fsLR")])
+        ])
+        # fmt:on
     return workflow
 
 
diff --git a/nibabies/workflows/base.py b/nibabies/workflows/base.py
index 10b39499..9f5758ab 100644
--- a/nibabies/workflows/base.py
+++ b/nibabies/workflows/base.py
@@ -229,7 +229,8 @@ def init_single_subject_wf(
 
     anat_only = config.workflow.anat_only
     derivatives = Derivatives(bids_root=config.execution.layout.root)
-    anat_modality = "t1w" if subject_data["t1w"] else "t2w"
+    contrast = "T1w" if subject_data["t1w"] else "T2w"
+    single_modality = not (subject_data['t1w'] and subject_data['t2w'])
     # Make sure we always go through these two checks
     if not anat_only and not subject_data["bold"]:
         task_id = config.execution.task_id
@@ -347,7 +348,7 @@ def init_single_subject_wf(
     wf_args = dict(
         ants_affine_init=True,
         age_months=age,
-        anat_modality=anat_modality,
+        contrast=contrast,
         t1w=subject_data["t1w"],
         t2w=subject_data["t2w"],
         bids_root=config.execution.bids_dir,
@@ -364,33 +365,10 @@ def init_single_subject_wf(
         spaces=spaces,
         cifti_output=config.workflow.cifti_output,
     )
-
-    if subject_data['t1w'] and subject_data['t2w']:
-        anat_preproc_wf = init_infant_anat_wf(**wf_args)
-    else:
-        anat_preproc_wf = init_infant_single_anat_wf(
-            contrast='T1w' if subject_data['t1w'] else 'T2w', **wf_args
-        )
-    # Preprocessing of anatomical (includes registration to UNCInfant)
-    anat_preproc_wf = init_infant_anat_wf(
-        ants_affine_init=True,
-        age_months=age,
-        anat_modality=anat_modality,
-        t1w=subject_data["t1w"],
-        t2w=subject_data["t2w"],
-        bids_root=config.execution.bids_dir,
-        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,
-        segmentation_atlases=config.execution.segmentation_atlases_dir,
-        skull_strip_mode=config.workflow.skull_strip_t1w,
-        skull_strip_template=Reference.from_string(config.workflow.skull_strip_template)[0],
-        sloppy=config.execution.sloppy,
-        spaces=spaces,
-        cifti_output=config.workflow.cifti_output,
+    anat_preproc_wf = (
+        init_infant_anat_wf(**wf_args)
+        if not single_modality
+        else init_infant_single_anat_wf(**wf_args)
     )
 
     # fmt: off
@@ -424,17 +402,17 @@ def init_single_subject_wf(
 
     workflow.connect([
         (bidssrc, bids_info, [
-            (('t1w', fix_multi_source_name), 'in_file'),
+            ((contrast.lower(), fix_multi_source_name), 'in_file'),
         ]),
         (bidssrc, summary, [
             ('t1w', 't1w'),
             ('t2w', 't2w'),
         ]),
         (bidssrc, ds_report_summary, [
-            (('t1w', fix_multi_source_name), 'source_file'),
+            ((contrast.lower(), fix_multi_source_name), 'source_file'),
         ]),
         (bidssrc, ds_report_about, [
-            (('t1w', fix_multi_source_name), 'source_file'),
+            ((contrast.lower(), fix_multi_source_name), 'source_file'),
         ]),
     ])
     # fmt: on

From 7edad3184f9808ca4415479d90e2619b00272310 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Tue, 3 Oct 2023 21:07:27 -0400
Subject: [PATCH 06/14] RF: Reflect new changes to dual modality workflow

---
 nibabies/workflows/anatomical/base.py | 38 +++++++++++++--------------
 nibabies/workflows/base.py            |  4 +--
 2 files changed, 21 insertions(+), 21 deletions(-)

diff --git a/nibabies/workflows/anatomical/base.py b/nibabies/workflows/anatomical/base.py
index ca3d71df..262c37df 100644
--- a/nibabies/workflows/anatomical/base.py
+++ b/nibabies/workflows/anatomical/base.py
@@ -124,10 +124,10 @@ def init_infant_anat_wf(
         Inverse transform of the above.
     subject_id
         FreeSurfer subject ID
-    t1w2fsnative_xfm
+    anat2fsnative_xfm
         LTA-style affine matrix translating from T1w to
         FreeSurfer-conformed subject space
-    fsnative2t1w_xfm
+    fsnative2anat_xfm
         LTA-style affine matrix translating from FreeSurfer-conformed
         subject space to T1w
     surfaces
@@ -180,7 +180,6 @@ def init_infant_anat_wf(
         t1w=t1w,
         t2w=t2w,
         mask=t1w_mask or t2w_mask,
-        aseg=t1w_aseg or t2w_aseg,
     )
 
     wf.__desc__ = desc.format(
@@ -197,13 +196,14 @@ def init_infant_anat_wf(
 
     # Define output workflows
     anat_reports_wf = init_anat_reports_wf(
-        freesurfer=freesurfer, output_dir=output_dir, sloppy=sloppy
+        surface_recon=freesurfer, output_dir=output_dir, sloppy=sloppy
     )
 
     anat_derivatives_wf = init_anat_derivatives_wf(
         bids_root=bids_root,
-        freesurfer=freesurfer,
+        surface_recon=freesurfer,
         num_t1w=num_t1w,
+        num_t2w=num_t2w,
         output_dir=output_dir,
         spaces=spaces,
         cifti_output=cifti_output,
@@ -278,10 +278,10 @@ def init_infant_anat_wf(
             ("outputnode.anat_realign_xfm", "anat_ref_xfms")]),
         (t1w_template_wf, t1w_preproc_wf, [("outputnode.anat_ref", "inputnode.in_anat")]),
         (t1w_template_wf, anat_derivatives_wf, [
-            ("outputnode.anat_valid_list", "inputnode.source_files"),
+            ("outputnode.anat_valid_list", "inputnode.t1w_source_files"),
             ("outputnode.anat_realign_xfm", "inputnode.t1w_ref_xfms")]),
         (t1w_template_wf, anat_reports_wf, [
-            ("outputnode.out_report", "inputnode.t1w_conform_report")]),
+            ("outputnode.out_report", "inputnode.anat_conform_report")]),
 
         (t2w_template_wf, t2w_preproc_wf, [("outputnode.anat_ref", "inputnode.in_anat")]),
         (t2w_template_wf, anat_derivatives_wf, [
@@ -298,7 +298,7 @@ def init_infant_anat_wf(
             ("outputnode.t1w_mask", "inputnode.moving_mask")]),
         (coregistration_wf, anat_seg_wf, [("outputnode.t1w_brain", "inputnode.anat_brain")]),
         (coregistration_wf, anat_derivatives_wf, [
-            ("outputnode.t1w_mask", "inputnode.t1w_mask"),
+            ("outputnode.t1w_mask", "inputnode.anat_mask"),
             ("outputnode.t1w_preproc", "inputnode.t1w_preproc"),
             ("outputnode.t2w_preproc", "inputnode.t2w_preproc"),
          ]),
@@ -312,8 +312,8 @@ def init_infant_anat_wf(
             ("outputnode.anat_dseg", "anat_dseg"),
             ("outputnode.anat_tpms", "anat_tpms")]),
         (anat_seg_wf, anat_derivatives_wf, [
-            ("outputnode.anat_dseg", "inputnode.t1w_dseg"),
-            ("outputnode.anat_tpms", "inputnode.t1w_tpms"),
+            ("outputnode.anat_dseg", "inputnode.anat_dseg"),
+            ("outputnode.anat_tpms", "inputnode.anat_tpms"),
         ]),
         (anat_seg_wf, anat_norm_wf, [
             ("outputnode.anat_dseg", "inputnode.moving_segmentation"),
@@ -334,9 +334,9 @@ def init_infant_anat_wf(
             ("outputnode.std2anat_xfm", "inputnode.std2anat_xfm")]),
 
         (outputnode, anat_reports_wf, [
-            ("anat_preproc", "inputnode.t1w_preproc"),
-            ("anat_mask", "inputnode.t1w_mask"),
-            ("anat_dseg", "inputnode.t1w_dseg"),
+            ("anat_preproc", "inputnode.anat_preproc"),
+            ("anat_mask", "inputnode.anat_mask"),
+            ("anat_dseg", "inputnode.anat_dseg"),
             ("std_preproc", "inputnode.std_t1w"),
             ("std_mask", "inputnode.std_mask"),
         ]),
@@ -509,8 +509,8 @@ def init_infant_anat_wf(
         (surface_recon_wf, outputnode, [
             ("outputnode.subjects_dir", "subjects_dir"),
             ("outputnode.subject_id", "subject_id"),
-            ("outputnode.t1w2fsnative_xfm", "t1w2fsnative_xfm"),
-            ("outputnode.fsnative2t1w_xfm", "fsnative2t1w_xfm"),
+            ("outputnode.t1w2fsnative_xfm", "anat2fsnative_xfm"),
+            ("outputnode.fsnative2t1w_xfm", "fsnative2anat_xfm"),
             ("outputnode.surfaces", "surfaces"),
             ("outputnode.morphometrics", "morphometrics"),
             ("outputnode.out_aparc", "anat_aparc"),
@@ -537,10 +537,10 @@ def init_infant_anat_wf(
             ("outputnode.subjects_dir", "inputnode.subjects_dir"),
         ]),
         (surface_recon_wf, anat_derivatives_wf, [
-            ("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.out_aseg", "inputnode.anat_fs_aseg"),
+            ("outputnode.out_aparc", "inputnode.anat_fs_aparc"),
+            ("outputnode.t1w2fsnative_xfm", "inputnode.anat2fsnative_xfm"),
+            ("outputnode.fsnative2t1w_xfm", "inputnode.fsnative2anat_xfm"),
             ("outputnode.surfaces", "inputnode.surfaces"),
             ("outputnode.morphometrics", "inputnode.morphometrics"),
         ]),
diff --git a/nibabies/workflows/base.py b/nibabies/workflows/base.py
index 9f5758ab..b47bac04 100644
--- a/nibabies/workflows/base.py
+++ b/nibabies/workflows/base.py
@@ -477,8 +477,8 @@ def init_single_subject_wf(
                 # Undefined if --fs-no-reconall, but this is safe
                 ('outputnode.subjects_dir', 'inputnode.subjects_dir'),
                 ('outputnode.subject_id', 'inputnode.subject_id'),
-                ('outputnode.t1w2fsnative_xfm', 'inputnode.t1w2fsnative_xfm'),
-                ('outputnode.fsnative2t1w_xfm', 'inputnode.fsnative2t1w_xfm'),
+                ('outputnode.anat2fsnative_xfm', 'inputnode.t1w2fsnative_xfm'),
+                ('outputnode.fsnative2anat_xfm', 'inputnode.fsnative2t1w_xfm'),
                 ('outputnode.surfaces', 'inputnode.surfaces'),
                 ('outputnode.morphometrics', 'inputnode.morphometrics'),
                 ('outputnode.anat_ribbon', 'inputnode.anat_ribbon'),

From 4b715c96f64ce9e1f8af994f0a9c344fed28af69 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Wed, 4 Oct 2023 11:49:15 -0400
Subject: [PATCH 07/14] STY: Fix indentations, add pep8 config

---
 .pep8speaks.yml                          | 6 ++++++
 nibabies/workflows/anatomical/outputs.py | 8 ++++----
 2 files changed, 10 insertions(+), 4 deletions(-)
 create mode 100644 .pep8speaks.yml

diff --git a/.pep8speaks.yml b/.pep8speaks.yml
new file mode 100644
index 00000000..eecf4012
--- /dev/null
+++ b/.pep8speaks.yml
@@ -0,0 +1,6 @@
+scanner:
+    diff_only: True
+    linter: pycodestyle
+
+pycodestyle:
+    max-line-length: 100
diff --git a/nibabies/workflows/anatomical/outputs.py b/nibabies/workflows/anatomical/outputs.py
index e7ceb6a6..bf62340a 100644
--- a/nibabies/workflows/anatomical/outputs.py
+++ b/nibabies/workflows/anatomical/outputs.py
@@ -247,7 +247,7 @@ def init_anat_reports_wf(
     # fmt: off
     workflow.connect([
         (inputnode, recon_report, [('subjects_dir', 'subjects_dir'),
-                                    ('subject_id', 'subject_id')]),
+                                   ('subject_id', 'subject_id')]),
         (recon_report, ds_recon_report, [('out_report', 'in_file')]),
         (inputnode, ds_recon_report, [('source_file', 'source_file')])
     ])
@@ -654,7 +654,7 @@ def init_anat_derivatives_wf(
         # fmt: off
         workflow.connect([
             (inputnode, mask_anat, [(preproc_file, 'in_file'),
-                                   ('anat_mask', 'in_mask')]),
+                                    ('anat_mask', 'in_mask')]),
             (mask_anat, anat2std_t1w, [('out_file', 'input_image')]),
             (inputnode, anat2std_mask, [('anat_mask', 'input_image')]),
             (inputnode, anat2std_dseg, [('anat_dseg', 'input_image')]),
@@ -832,9 +832,9 @@ def init_anat_derivatives_wf(
         (name_morphs, ds_morphs, [('hemi', 'hemi'),
                                   ('suffix', 'suffix')]),
         (inputnode, ds_anat_fsaseg, [('anat_fs_aseg', 'in_file'),
-                                    (source_files, 'source_file')]),
+                                     (source_files, 'source_file')]),
         (inputnode, ds_anat_fsparc, [('anat_fs_aparc', 'in_file'),
-                                    (source_files, 'source_file')]),
+                                     (source_files, 'source_file')]),
     ])
     # fmt: on
     if cifti_output:

From 6c38c073db5ef7dbec3238339715da880cc777aa Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Wed, 8 Nov 2023 17:02:12 -0500
Subject: [PATCH 08/14] FIX: Connections for T1-only

---
 nibabies/workflows/anatomical/base.py    | 15 +++++++++------
 nibabies/workflows/anatomical/outputs.py |  1 -
 2 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/nibabies/workflows/anatomical/base.py b/nibabies/workflows/anatomical/base.py
index 262c37df..d004080c 100644
--- a/nibabies/workflows/anatomical/base.py
+++ b/nibabies/workflows/anatomical/base.py
@@ -463,12 +463,10 @@ def init_infant_anat_wf(
         # M-CRIB-S to dHCP42week (32k)
         sphere_reg_wf = init_mcribs_sphere_reg_wf()
 
-        # fmt:off
         wf.connect([
             (t2w_template_wf, denoise_t2w, [('outputnode.anat_ref', 'input_image')]),
             (denoise_t2w, surface_recon_wf, [('output_image', 'inputnode.t2w')]),
-        ])
-        # fmt:on
+        ])  # fmt:skip
         if derivatives.aseg:
             wf.connect(deriv_buffer, 't2w_aseg', surface_recon_wf, 'inputnode.ants_segs')
         if derivatives.mask:
@@ -811,7 +809,7 @@ def init_infant_single_anat_wf(
     if not recon_method:
         return workflow
 
-    elif recon_method == 'freesurfer':
+    if recon_method == 'freesurfer':
         from smriprep.workflows.surfaces import init_surface_recon_wf
 
         surface_recon_wf = init_surface_recon_wf(omp_nthreads=omp_nthreads, hires=hires)
@@ -853,6 +851,12 @@ def init_infant_single_anat_wf(
     else:
         raise NotImplementedError
 
+    if recon_method in ('freesurfer', 'infantfs'):
+        from smriprep.workflows.surfaces import init_sphere_reg_wf
+
+        # fsaverage to fsLR
+        sphere_reg_wf = init_sphere_reg_wf()
+
     # Anatomical ribbon file using HCP signed-distance volume method
     anat_ribbon_wf = init_anat_ribbon_wf()
 
@@ -865,8 +869,7 @@ def init_infant_single_anat_wf(
             ("outputnode.anat_ref", "inputnode.t1w"),
         ]),
         (mask_buffer, surface_recon_wf, [
-            ("anat_brain", "inputnode.skullstripped_t1"),
-            ("anat_mask", "inputnode.anat_mask")]),
+            ("anat_brain", "inputnode.skullstripped_t1")]),
         (anat_preproc_wf, surface_recon_wf, [
             ("outputnode.anat_preproc", "inputnode.corrected_t1")]),
         (surface_recon_wf, outputnode, [
diff --git a/nibabies/workflows/anatomical/outputs.py b/nibabies/workflows/anatomical/outputs.py
index bf62340a..3c511f93 100644
--- a/nibabies/workflows/anatomical/outputs.py
+++ b/nibabies/workflows/anatomical/outputs.py
@@ -424,7 +424,6 @@ def init_anat_derivatives_wf(
             # fmt:on
 
     if num_t2w:
-
         if not num_t1w:
             raw_sources = pe.Node(niu.Function(function=_bids_relative), name="t2w_raw_sources")
             raw_sources.inputs.bids_root = bids_root

From 853d7b2119417e91ee49c894928feef3b582a378 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Thu, 9 Nov 2023 12:02:44 -0500
Subject: [PATCH 09/14] CI: Test single anatomical workflow

---
 .circleci/bcp_anat_t2only_outputs.txt | 55 +++++++++++++++++++++++++++
 .circleci/config.yml                  | 35 +++++++++++++++++
 2 files changed, 90 insertions(+)
 create mode 100644 .circleci/bcp_anat_t2only_outputs.txt

diff --git a/.circleci/bcp_anat_t2only_outputs.txt b/.circleci/bcp_anat_t2only_outputs.txt
new file mode 100644
index 00000000..fa30fa14
--- /dev/null
+++ b/.circleci/bcp_anat_t2only_outputs.txt
@@ -0,0 +1,55 @@
+.bidsignore
+dataset_description.json
+desc-aparcaseg_dseg.tsv
+desc-aseg_dseg.tsv
+logs
+logs/CITATION.bib
+logs/CITATION.html
+logs/CITATION.md
+logs/CITATION.tex
+sub-01
+sub-01/ses-1mo
+sub-01/ses-1mo/anat
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_desc-aparcaseg_dseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_desc-aseg_dseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_desc-brain_mask.json
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_desc-brain_mask.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_desc-preproc_T2w.json
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_desc-preproc_T2w.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_desc-ribbon_mask.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_dseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-MNIInfant+1_to-T2w_mode-image_xfm.h5
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-T2w_to-MNIInfant+1_mode-image_xfm.h5
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-T2w_to-fsnative_mode-image_xfm.txt
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-fsnative_to-T2w_mode-image_xfm.txt
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_curv.shape.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_desc-reg_sphere.surf.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_inflated.surf.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_midthickness.surf.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_pial.surf.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_space-fsLR_desc-reg_sphere.surf.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_sulc.shape.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_thickness.shape.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_white.surf.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_curv.shape.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_desc-reg_sphere.surf.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_inflated.surf.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_midthickness.surf.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_pial.surf.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_space-fsLR_desc-reg_sphere.surf.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_sulc.shape.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_thickness.shape.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_white.surf.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_label-CSF_probseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_label-GM_probseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_label-WM_probseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_desc-brain_mask.json
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_desc-brain_mask.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_desc-preproc_T1w.json
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_desc-preproc_T1w.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_dseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-CSF_probseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-GM_probseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-WM_probseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_desc-preproc_T2w.nii.gz
+sub-01_ses-1mo.html
diff --git a/.circleci/config.yml b/.circleci/config.yml
index 9755d783..079b9760 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -397,6 +397,41 @@ jobs:
             pip install nibabel numpy nitransforms
             python /tmp/src/nibabies/scripts/check_outputs.py /tmp/${DATASET}/derivatives/nibabies
             exit $?
+      - run:
+          name: Create copy with only T2w data
+          command: |
+            mkdir -p /tmp/data/${DATASET}-t2only
+            cp /tmp/data/${DATASET}/dataset_description.json /tmp/data/${DATASET}-t2only
+            cp -r /tmp/data/${DATASET}/sub-01 /tmp/data/${DATASET}-t2only/sub-01
+            rm -f /tmp/data/${DATASET}-t2only/sub-01/ses-1mo/anat/*_T1w.*
+      - run:
+          name: Run nibabies single anatomical workflow
+          no_output_timeout: 1h
+          command: |
+            mkdir -p /tmp/data/${DATASET}-t2only /tmp/${DATASET}/derivatives/nibabies-t2only
+            nibabies-wrapper docker /tmp/data/${DATASET}-t2only /tmp/${DATASET}/derivatives/nibabies-t2only participant \
+                -i nipreps/nibabies:dev \
+                -e NIBABIES_DEV 1 --user $(id -u):$(id -g) \
+                --network none --notrack \
+                --config $PWD/nipype.cfg -w /tmp/${DATASET}/work \
+                --fs-subjects-dir /tmp/data/${DATASET}/derivatives/infant-freesurfer \
+                --skull-strip-template UNCInfant:cohort-1 \
+                --output-spaces MNIInfant:cohort-1 func \
+                --sloppy --write-graph --mem-mb 14000 \
+                --nthreads 4 -vv --age-months 2 --sloppy \
+                --derivatives /tmp/data/${DATASET}/derivatives/precomputed \
+                --output-layout bids --anat-only
+      - run:
+          name: Checking outputs of T2-only nibabies anat
+          command: |
+            mkdir -p /tmp/${DATASET}/test
+            CHECK_OUTPUTS_FILE="${DATASET}_anat_t2only_outputs.txt"
+            cd /tmp/${DATASET}/derivatives/nibabies-t2only && tree -I 'figures|log' -lifa --noreport | sed s+^\./++ | sed '1d' | sort > /tmp/${DATASET}/test/outputs.out
+            cat /tmp/${DATASET}/test/outputs.out
+            sort -o /tmp/${DATASET}/test/expected.out /tmp/src/nibabies/.circleci/${CHECK_OUTPUTS_FILE}
+            diff /tmp/${DATASET}/test/expected.out /tmp/${DATASET}/test/outputs.out
+            rm -rf /tmp/${DATASET}/test
+            exit $?
       - store_artifacts:
           path: /tmp/bcp/derivatives
 

From 3455784eafe33a3306ea359c24044f74a4ff8288 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Thu, 9 Nov 2023 12:42:25 -0500
Subject: [PATCH 10/14] FIX: Do not raise validation error if no T1

---
 nibabies/utils/bids.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nibabies/utils/bids.py b/nibabies/utils/bids.py
index 765ca47e..bfd63e76 100644
--- a/nibabies/utils/bids.py
+++ b/nibabies/utils/bids.py
@@ -281,7 +281,7 @@ def validate_input_dir(exec_env, bids_dir, participant_label):
             "MISSING_TSV_COLUMN_EEG_ELECTRODES",
             "MISSING_SESSION",
         ],
-        "error": ["NO_T1W"],
+        "error": [],
         "ignoredFiles": ["/dataset_description.json", "/participants.tsv"],
     }
     # Limit validation only to data from requested participants

From 1533815c1feb2bdedbc4d5ac236d4e7ef4fb3962 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Thu, 9 Nov 2023 13:23:42 -0500
Subject: [PATCH 11/14] CI: Use separate workdir, show tree

---
 .circleci/config.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 079b9760..b9260f23 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -404,16 +404,17 @@ jobs:
             cp /tmp/data/${DATASET}/dataset_description.json /tmp/data/${DATASET}-t2only
             cp -r /tmp/data/${DATASET}/sub-01 /tmp/data/${DATASET}-t2only/sub-01
             rm -f /tmp/data/${DATASET}-t2only/sub-01/ses-1mo/anat/*_T1w.*
+            tree /tmp/data/${DATASET}-t2only
       - run:
           name: Run nibabies single anatomical workflow
           no_output_timeout: 1h
           command: |
-            mkdir -p /tmp/data/${DATASET}-t2only /tmp/${DATASET}/derivatives/nibabies-t2only
+            mkdir -p /tmp/data/${DATASET}-t2only /tmp/${DATASET}/derivatives/nibabies-t2only /tmp/${DATASET}/work-t2only
             nibabies-wrapper docker /tmp/data/${DATASET}-t2only /tmp/${DATASET}/derivatives/nibabies-t2only participant \
                 -i nipreps/nibabies:dev \
                 -e NIBABIES_DEV 1 --user $(id -u):$(id -g) \
                 --network none --notrack \
-                --config $PWD/nipype.cfg -w /tmp/${DATASET}/work \
+                --config $PWD/nipype.cfg -w /tmp/${DATASET}/work-t2only \
                 --fs-subjects-dir /tmp/data/${DATASET}/derivatives/infant-freesurfer \
                 --skull-strip-template UNCInfant:cohort-1 \
                 --output-spaces MNIInfant:cohort-1 func \

From 7d1447bcb4166ab2fcd3febbb19ff9005fc81f22 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Thu, 9 Nov 2023 17:06:41 -0500
Subject: [PATCH 12/14] CI: Rename derivatives to T2w space

---
 .circleci/config.yml | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index b9260f23..4a921f02 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -405,6 +405,14 @@ jobs:
             cp -r /tmp/data/${DATASET}/sub-01 /tmp/data/${DATASET}-t2only/sub-01
             rm -f /tmp/data/${DATASET}-t2only/sub-01/ses-1mo/anat/*_T1w.*
             tree /tmp/data/${DATASET}-t2only
+            mkdir -p /tmp/data/${DATASET}-t2only/derivatives
+            cp -r /tmp/data/${DATASET}/derivatives/precomputed /tmp/data/${DATASET}-t2only/derivatives
+            # rename the derivatives for now - this is only possible since they share the same space
+            sudo apt install rename
+            rename 's/space-T1w/space-T2w/' /tmp/data/${DATASET}-t2only/derivatives/precomputed/sub-01/ses-1mo/anat/*
+            sed -i 's/_T1w./_T2w./g' /tmp/data/${DATASET}-t2only/derivatives/precomputed/sub-01/ses-1mo/anat/*json
+            tree /tmp/data/${DATASET}-t2only/derivatives/precomputed
+
       - run:
           name: Run nibabies single anatomical workflow
           no_output_timeout: 1h
@@ -420,7 +428,7 @@ jobs:
                 --output-spaces MNIInfant:cohort-1 func \
                 --sloppy --write-graph --mem-mb 14000 \
                 --nthreads 4 -vv --age-months 2 --sloppy \
-                --derivatives /tmp/data/${DATASET}/derivatives/precomputed \
+                --derivatives /tmp/data/${DATASET}-t2only/derivatives/precomputed \
                 --output-layout bids --anat-only
       - run:
           name: Checking outputs of T2-only nibabies anat

From b00fbd7efd947457c021a66b60f4e0a9d41cf08d Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Fri, 10 Nov 2023 08:47:06 -0500
Subject: [PATCH 13/14] FIX: Add metadata to T2w preproc

---
 nibabies/workflows/anatomical/outputs.py | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/nibabies/workflows/anatomical/outputs.py b/nibabies/workflows/anatomical/outputs.py
index 3c511f93..37892249 100644
--- a/nibabies/workflows/anatomical/outputs.py
+++ b/nibabies/workflows/anatomical/outputs.py
@@ -433,6 +433,8 @@ def init_anat_derivatives_wf(
             name="ds_t2w_preproc",
             run_without_submitting=True,
         )
+        ds_t2w_preproc.inputs.SkullStripped = False
+
         if num_t1w:
             ds_t2w_preproc.inputs.space = "T1w"
 
@@ -492,20 +494,16 @@ def init_anat_derivatives_wf(
     )
 
     if num_t1w:
-        # fmt:off
         workflow.connect([
             (inputnode, ds_t1w_preproc, [('t1w_preproc', 'in_file'),
                                          ('t1w_source_files', 'source_file')]),
-        ])
-        # fmt:on
+        ])  # fmt:skip
 
     if num_t2w:
-        # fmt:off
         workflow.connect([
             (inputnode, ds_t2w_preproc, [('t2w_preproc', 'in_file'),
                                          ('t2w_source_files', 'source_file')]),
-        ])
-        # fmt:on
+        ])  # fmt:skip
 
     # fmt:off
     workflow.connect([

From bc7ee38b2e7ee0b2579e23deb6377a772aa6e438 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Fri, 10 Nov 2023 09:27:48 -0500
Subject: [PATCH 14/14] CI: Adjust expected outputs

---
 .circleci/bcp_anat_outputs.txt        | 1 +
 .circleci/bcp_anat_t2only_outputs.txt | 5 ++---
 .circleci/bcp_full_outputs.txt        | 1 +
 3 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/.circleci/bcp_anat_outputs.txt b/.circleci/bcp_anat_outputs.txt
index fcd4c3ee..b32939d3 100644
--- a/.circleci/bcp_anat_outputs.txt
+++ b/.circleci/bcp_anat_outputs.txt
@@ -51,5 +51,6 @@ sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_dseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-CSF_probseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-GM_probseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-WM_probseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T1w_desc-preproc_T2w.json
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T1w_desc-preproc_T2w.nii.gz
 sub-01_ses-1mo.html
diff --git a/.circleci/bcp_anat_t2only_outputs.txt b/.circleci/bcp_anat_t2only_outputs.txt
index fa30fa14..21824e2b 100644
--- a/.circleci/bcp_anat_t2only_outputs.txt
+++ b/.circleci/bcp_anat_t2only_outputs.txt
@@ -45,11 +45,10 @@ sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_label-GM_probseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_label-WM_probseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_desc-brain_mask.json
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_desc-brain_mask.nii.gz
-sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_desc-preproc_T1w.json
-sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_desc-preproc_T1w.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_desc-preproc_T2w.json
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_desc-preproc_T2w.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_dseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-CSF_probseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-GM_probseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-WM_probseg.nii.gz
-sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_desc-preproc_T2w.nii.gz
 sub-01_ses-1mo.html
diff --git a/.circleci/bcp_full_outputs.txt b/.circleci/bcp_full_outputs.txt
index a8ceb3aa..fff15bb7 100644
--- a/.circleci/bcp_full_outputs.txt
+++ b/.circleci/bcp_full_outputs.txt
@@ -51,6 +51,7 @@ sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_dseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-CSF_probseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-GM_probseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-WM_probseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T1w_desc-preproc_T2w.json
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T1w_desc-preproc_T2w.nii.gz
 sub-01/ses-1mo/fmap
 sub-01/ses-1mo/fmap/sub-01_ses-1mo_run-001_fmapid-auto00000_desc-coeff_fieldmap.nii.gz