Fix some things.

PennLINC · Nov 21, 2023 · 560e052 · 560e052
1 parent dd7ce51
commit 560e052
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Showing 3 changed files with 4 additions and 7 deletions.
diff --git a/aslprep/workflows/asl/base.py b/aslprep/workflows/asl/base.py
@@ -695,6 +695,7 @@ def init_asl_preproc_wf(
             ("asl_file", "inputnode.name_source"),
             ("t1w_tpms", "inputnode.t1w_tpms"),
             ("t1w_mask", "inputnode.t1w_mask"),
+            ("mni2009c2anat_xfm", "inputnode.mni2009c2anat_xfm"),
         ]),
         (asl_fit_wf, cbf_qc_wf, [
             ("outputnode.asl_mask", "inputnode.asl_mask"),

diff --git a/aslprep/workflows/asl/fit.py b/aslprep/workflows/asl/fit.py
@@ -26,7 +26,6 @@
 import bids
 import nibabel as nb
 import numpy as np
-from fmriprep.interfaces.reports import FunctionalSummary
 from fmriprep.workflows.bold.registration import init_bold_reg_wf
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
@@ -39,6 +38,7 @@
 # ASL workflows
 # TODO: Replace with fMRIPrep imports once new release is made
 from aslprep import config
+from aslprep.interfaces.reports import FunctionalSummary
 from aslprep.interfaces.resampling import (
     DistortionParameters,
     ReconstructFieldmap,
@@ -193,7 +193,6 @@ def init_asl_fit_wf(
     )
 
     # Get metadata from ASL file(s)
-    entities = extract_entities(asl_file)
     metadata = layout.get_metadata(asl_file)
     # Patch RepetitionTimePreparation into RepetitionTime,
     # for the sake of BOLD-based interfaces and workflows.
@@ -279,16 +278,14 @@ def init_asl_fit_wf(
             registration_dof=config.workflow.asl2t1w_dof,
             registration_init=config.workflow.asl2t1w_init,
             pe_direction=metadata.get("PhaseEncodingDirection"),
-            echo_idx=entities.get("echo", []),
             tr=metadata["RepetitionTime"],
             orientation=orientation,
-            algo_dummy_scans=0,
         ),
         name="summary",
         mem_gb=config.DEFAULT_MEMORY_MIN_GB,
         run_without_submitting=True,
     )
-    workflow.connect([(inputnode, summary, [("dummy_scans", "dummy_scans")])])
+    # workflow.connect([(inputnode, summary, [("dummy_scans", "dummy_scans")])])
 
     asl_fit_reports_wf = init_asl_fit_reports_wf(
         sdc_correction=not (fieldmap_id is None),

diff --git a/aslprep/workflows/asl/qc.py b/aslprep/workflows/asl/qc.py
@@ -2,7 +2,6 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Workflows for calculating CBF QC metrics."""
 from nipype.interfaces import utility as niu
-from nipype.interfaces.afni import Resample
 from nipype.pipeline import engine as pe
 from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 from templateflow.api import get as get_template
@@ -11,7 +10,6 @@
 from aslprep.interfaces.ants import ApplyTransforms
 from aslprep.interfaces.bids import DerivativesDataSink
 from aslprep.interfaces.qc import ComputeCBFQC
-from aslprep.utils.misc import _select_last_in_list
 
 
 def init_cbf_qc_wf(
@@ -80,6 +78,7 @@ def init_cbf_qc_wf(
                 "t1w_mask",
                 "t1w_tpms",
                 "aslref2anat_xfm",
+                "mni2009c2anat_xfm",
                 # CBF inputs
                 "mean_cbf",
                 # SCORE/SCRUB inputs