ENH: Merge T2w images and coregister to T1w template (#2941)

## Changes proposed in this pull request

Integrates and connects up nipreps/smriprep#319.

## Documentation that should be reviewed

* [x] Mention in docs

docs/outputs.rst

@@ -82,6 +82,7 @@ Anatomical derivatives are placed in each subject's ``anat`` subfolder::
   sub-<subject_label>/
     anat/
       sub-<subject_label>[_space-<space_label>]_desc-preproc_T1w.nii.gz
+      sub-<subject_label>[_space-<space_label>]_desc-preproc_T2w.nii.gz
       sub-<subject_label>[_space-<space_label>]_desc-brain_mask.nii.gz
       sub-<subject_label>[_space-<space_label>]_dseg.nii.gz
       sub-<subject_label>[_space-<space_label>]_label-CSF_probseg.nii.gz
@@ -92,6 +93,12 @@ Spatially-standardized derivatives are denoted with a space label,
 such as ``MNI152NLin2009cAsym``, while derivatives in
 the original ``T1w`` space omit the ``space-`` keyword.
 
+T2w images are aligned to the anatomical (``T1w``) space, if found.
+
+.. note::
+
+   T2w derivatives are only generated if FreeSurfer processing is enabled.
+
 Additionally, the following transforms are saved::
 
   sub-<subject_label>/

fmriprep/__about__.py

@@ -25,7 +25,7 @@
 try:
     from ._version import __version__
 except ImportError:
-    __version__ == "0+unknown"
+    __version__ = "0+unknown"
 
 __packagename__ = 'fmriprep'
 __copyright__ = 'Copyright 2023, The NiPreps Developers'

fmriprep/workflows/base.py

@@ -308,6 +308,7 @@ def init_single_subject_wf(subject_id: str):
         skull_strip_template=Reference.from_string(config.workflow.skull_strip_template)[0],
         spaces=spaces,
         t1w=subject_data['t1w'],
+        t2w=subject_data['t2w'],
     )
     # fmt:off
     workflow.connect([

pyproject.toml

@@ -33,7 +33,7 @@ dependencies = [
     "pybids >= 0.15.0",
     "requests",
     "sdcflows ~= 2.2.2",
-    "smriprep ~= 0.10.0",
+    "smriprep @ git+https://github.com/nipreps/smriprep.git@master",
     "tedana ~= 0.0.9",
     "templateflow >= 0.6",
     "toml",
@@ -91,6 +91,9 @@ fmriprep = "fmriprep.cli.run:main"
 # Hatch configurations
 #
 
+[tool.hatch.metadata]
+allow-direct-references = true
+
 [tool.hatch.build.targets.sdist]
 exclude = [".git_archival.txt"]  # No longer needed in sdist