Add templateflow to DatasetLinks.

nipreps · Apr 1, 2024 · 258791c · 258791c
1 parent 123c3f8
commit 258791c
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Showing 3 changed files with 10 additions and 2 deletions.
diff --git a/fmriprep/config.py b/fmriprep/config.py
@@ -91,6 +91,8 @@
 import os
 from multiprocessing import set_start_method
 
+from templateflow.conf import TF_LAYOUT
+
 # Disable NiPype etelemetry always
 _disable_et = bool(os.getenv('NO_ET') is not None or os.getenv('NIPYPE_NO_ET') is not None)
 os.environ['NIPYPE_NO_ET'] = '1'
@@ -525,7 +527,10 @@ def _process_value(value):
                 for k, v in filters.items():
                     cls.bids_filters[acq][k] = _process_value(v)
 
-        dataset_links = {'raw': cls.bids_dir}
+        dataset_links = {
+            'raw': cls.bids_dir,
+            'templateflow': Path(TF_LAYOUT.root),
+        }
         for deriv_name, deriv_path in cls.derivatives.items():
             dataset_links[deriv_name] = deriv_path
         cls.dataset_links = dataset_links

diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py
@@ -474,6 +474,7 @@ def init_bold_wf(
             ]),
             (inputnode, ds_bold_std_wf, [
                 ('anat2std_xfm', 'inputnode.anat2std_xfm'),
+                ('std_t1w', 'inputnode.template'),
                 ('std_space', 'inputnode.space'),
                 ('std_resolution', 'inputnode.resolution'),
                 ('std_cohort', 'inputnode.cohort'),

diff --git a/fmriprep/workflows/bold/outputs.py b/fmriprep/workflows/bold/outputs.py
@@ -734,6 +734,7 @@ def init_ds_volumes_wf(
                 'bold_mask',  # boldref space
                 'bold_ref',  # boldref space
                 't2star',  # boldref space
+                'template',  # target reference image from original transform
                 # Anatomical
                 'boldref2anat_xfm',
                 # Template
@@ -749,7 +750,7 @@ def init_ds_volumes_wf(
 
     sources = pe.Node(
         BIDSURI(
-            numinputs=3,
+            numinputs=4,
             dataset_links=config.execution.dataset_links,
             out_dir=str(config.execution.fmriprep_dir.absolute()),
         ),
@@ -776,6 +777,7 @@ def init_ds_volumes_wf(
             ('source_files', 'in1'),
             ('boldref2anat_xfm', 'in2'),
             ('anat2std_xfm', 'in3'),
+            ('template', 'in4'),
         ]),
         (inputnode, boldref2target, [
             # Note that ANTs expects transforms in target-to-source order