Add templateflow to DatasetLinks (#3267)

References #3261.

## Changes proposed in this pull request

- Add the TemplateFlow base directory to the DatasetLinks.
- Add the template used for normalization to the Sources for
standard-space volumetric outputs.

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

fmriprep/utils/bids.py

@@ -148,6 +148,8 @@ def write_derivative_description(bids_dir, deriv_dir, dataset_links=None):
     # Add DatasetLinks
     if dataset_links:
         desc['DatasetLinks'] = {k: str(v) for k, v in dataset_links.items()}
+        if 'templateflow' in dataset_links:
+            desc['DatasetLinks']['templateflow'] = 'https://github.com/templateflow/templateflow'
 
     Path.write_text(deriv_dir / 'dataset_description.json', json.dumps(desc, indent=4))
 

fmriprep/workflows/bold/base.py

@@ -424,6 +424,8 @@ def init_bold_wf(
                 ('outputnode.bold_mask', 'inputnode.bold_mask'),
                 ('outputnode.coreg_boldref', 'inputnode.bold_ref'),
                 ('outputnode.boldref2anat_xfm', 'inputnode.boldref2anat_xfm'),
+                ('outputnode.motion_xfm', 'inputnode.motion_xfm'),
+                ('outputnode.boldref2fmap_xfm', 'inputnode.boldref2fmap_xfm'),
             ]),
             (bold_native_wf, ds_bold_t1_wf, [('outputnode.t2star_map', 'inputnode.t2star')]),
             (bold_anat_wf, ds_bold_t1_wf, [
@@ -474,6 +476,7 @@ 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'),
@@ -482,6 +485,8 @@ def init_bold_wf(
                 ('outputnode.bold_mask', 'inputnode.bold_mask'),
                 ('outputnode.coreg_boldref', 'inputnode.bold_ref'),
                 ('outputnode.boldref2anat_xfm', 'inputnode.boldref2anat_xfm'),
+                ('outputnode.motion_xfm', 'inputnode.motion_xfm'),
+                ('outputnode.boldref2fmap_xfm', 'inputnode.boldref2fmap_xfm'),
             ]),
             (bold_native_wf, ds_bold_std_wf, [('outputnode.t2star_map', 'inputnode.t2star')]),
             (bold_std_wf, ds_bold_std_wf, [

fmriprep/workflows/bold/outputs.py

@@ -659,6 +659,7 @@ def init_ds_bold_native_wf(
                 ('source_files', 'source_file'),
                 ('bold', 'in_file'),
             ]),
+            (sources, ds_bold, [('out', 'Sources')]),
         ])  # fmt:skip
 
     if bold_output and multiecho:
@@ -734,6 +735,7 @@ 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
@@ -742,14 +744,17 @@ def init_ds_volumes_wf(
                 'space',
                 'cohort',
                 'resolution',
+                # Transforms previously used to generate the outputs
+                'motion_xfm',
+                'boldref2fmap_xfm',
             ]
         ),
         name='inputnode',
     )
 
     sources = pe.Node(
         BIDSURI(
-            numinputs=3,
+            numinputs=6,
             dataset_links=config.execution.dataset_links,
             out_dir=str(config.execution.fmriprep_dir.absolute()),
         ),
@@ -774,8 +779,11 @@ def init_ds_volumes_wf(
     workflow.connect([
         (inputnode, sources, [
             ('source_files', 'in1'),
-            ('boldref2anat_xfm', 'in2'),
-            ('anat2std_xfm', 'in3'),
+            ('motion_xfm', 'in2'),
+            ('boldref2fmap_xfm', 'in3'),
+            ('boldref2anat_xfm', 'in4'),
+            ('anat2std_xfm', 'in5'),
+            ('template', 'in6'),
         ]),
         (inputnode, boldref2target, [
             # Note that ANTs expects transforms in target-to-source order