Fix CBF CIFTI generation when --project-goodvoxels is enabled (#460)

* Fix CBF CIFTI generation.

* Revert "Fix CBF CIFTI generation."

This reverts commit f56aabf.

* Update test to raise error.

* Reapply "Fix CBF CIFTI generation."

This reverts commit f7583b5.

* Add comments.

Author: tsalo

aslprep/tests/test_cli.py

@@ -355,7 +355,7 @@ def test_test_003_full(data_dir, output_dir, working_dir):
         output_dir,
         working_dir,
         level='full',
-        extra_params=['--cifti-output', '91k'],
+        extra_params=['--cifti-output', '91k', '--project-goodvoxels'],
     )
 
 

aslprep/workflows/asl/base.py

@@ -770,7 +770,6 @@ def init_asl_wf(
         ds_asl_cifti_wf.inputs.inputnode.source_files = [asl_file]
         workflow.connect([
             (inputnode, ds_asl_cifti_wf, [
-                ('t1w_preproc', 'inputnode.anat'),
                 ('mni6_mask', 'inputnode.mni6_mask'),
                 ('anat2mni6_xfm', 'inputnode.anat2mni6_xfm'),
                 ('white', 'inputnode.white'),
@@ -780,6 +779,10 @@ def init_asl_wf(
                 ('sphere_reg_fsLR', 'inputnode.sphere_reg_fsLR'),
                 ('cortex_mask', 'inputnode.cortex_mask'),
             ]),
+            (asl_anat_wf, ds_asl_cifti_wf, [
+                # Used for affine/resolution reference only
+                ('outputnode.resampling_reference', 'inputnode.anat_ref_file'),
+            ]),
             (asl_fit_wf, ds_asl_cifti_wf, [
                 ('outputnode.aslref2anat_xfm', 'inputnode.aslref2anat_xfm'),
             ]),

aslprep/workflows/asl/outputs.py

@@ -837,11 +837,12 @@ def init_ds_ciftis_wf(
     inputnode_fields = [
         'asl_cifti',
         'source_files',
-        # Anatomical
-        'anat',
+        # ASL-resolution, anatomical-space reference image
+        'anat_ref_file',
         'aslref2anat_xfm',
         # Template
         'anat2mni6_xfm',
+        # Template reference image. Resolution depends on CIFTI output resolution
         'mni6_mask',
         # Pre-computed goodvoxels mask. May be Undefined.
         'goodvoxels_mask',
@@ -927,7 +928,7 @@ def init_ds_ciftis_wf(
         workflow.connect([
             (inputnode, warp_cbf_to_anat, [
                 (cbf_deriv, 'input_image'),
-                ('anat', 'reference_image'),
+                ('anat_ref_file', 'reference_image'),
                 ('aslref2anat_xfm', 'transforms'),
             ]),
         ])  # fmt:skip