Try patching connection.

PennLINC · Oct 10, 2023 · e6395c3 · e6395c3
1 parent a54afa9
commit e6395c3
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Showing 6 changed files with 32 additions and 2 deletions.
diff --git a/xcp_d/tests/data/test_ds001419_cifti_outputs.txt b/xcp_d/tests/data/test_ds001419_cifti_outputs.txt
@@ -165,6 +165,7 @@ xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-fsLR_den-91k_desc-interpolate
 xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-fsLR_den-91k_desc-interpolated_bold.json
 xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-fsLR_den-91k_desc-linc_qc.csv
 xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-fsLR_den-91k_reho.dscalar.nii
+xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-fsLR_den-91k_reho.json
 xcp_d/sub-01/func/sub-01_task-imagery_run-02_desc-dcan_qc.hdf5
 xcp_d/sub-01/func/sub-01_task-imagery_run-02_desc-filtered_motion.json
 xcp_d/sub-01/func/sub-01_task-imagery_run-02_desc-filtered_motion.tsv
@@ -277,6 +278,7 @@ xcp_d/sub-01/func/sub-01_task-imagery_run-02_space-fsLR_den-91k_desc-interpolate
 xcp_d/sub-01/func/sub-01_task-imagery_run-02_space-fsLR_den-91k_desc-interpolated_bold.json
 xcp_d/sub-01/func/sub-01_task-imagery_run-02_space-fsLR_den-91k_desc-linc_qc.csv
 xcp_d/sub-01/func/sub-01_task-imagery_run-02_space-fsLR_den-91k_reho.dscalar.nii
+xcp_d/sub-01/func/sub-01_task-imagery_run-02_space-fsLR_den-91k_reho.json
 xcp_d/sub-01/func/sub-01_task-imagery_space-fsLR_atlas-4S1052Parcels_den-91k_timeseries.ptseries.nii
 xcp_d/sub-01/func/sub-01_task-imagery_space-fsLR_atlas-4S1052Parcels_timeseries.tsv
 xcp_d/sub-01/func/sub-01_task-imagery_space-fsLR_atlas-4S152Parcels_den-91k_timeseries.ptseries.nii

diff --git a/xcp_d/tests/data/test_pnc_cifti_outputs.txt b/xcp_d/tests/data/test_pnc_cifti_outputs.txt
@@ -212,4 +212,5 @@ xcp_d/sub-1648798153/ses-PNC1/func/sub-1648798153_ses-PNC1_task-rest_acq-singleb
 xcp_d/sub-1648798153/ses-PNC1/func/sub-1648798153_ses-PNC1_task-rest_acq-singleband_space-fsLR_den-91k_desc-interpolated_bold.json
 xcp_d/sub-1648798153/ses-PNC1/func/sub-1648798153_ses-PNC1_task-rest_acq-singleband_space-fsLR_den-91k_desc-linc_qc.csv
 xcp_d/sub-1648798153/ses-PNC1/func/sub-1648798153_ses-PNC1_task-rest_acq-singleband_space-fsLR_den-91k_reho.dscalar.nii
+xcp_d/sub-1648798153/ses-PNC1/func/sub-1648798153_ses-PNC1_task-rest_acq-singleband_space-fsLR_den-91k_reho.json
 xcp_d/sub-1648798153_ses-PNC1_executive_summary.html
diff --git a/xcp_d/tests/data/test_pnc_cifti_t2wonly_outputs.txt b/xcp_d/tests/data/test_pnc_cifti_t2wonly_outputs.txt
@@ -211,4 +211,5 @@ xcp_d/sub-1648798153/ses-PNC1/func/sub-1648798153_ses-PNC1_task-idemo_space-fsLR
 xcp_d/sub-1648798153/ses-PNC1/func/sub-1648798153_ses-PNC1_task-idemo_space-fsLR_den-91k_desc-interpolated_bold.json
 xcp_d/sub-1648798153/ses-PNC1/func/sub-1648798153_ses-PNC1_task-idemo_space-fsLR_den-91k_desc-linc_qc.csv
 xcp_d/sub-1648798153/ses-PNC1/func/sub-1648798153_ses-PNC1_task-idemo_space-fsLR_den-91k_reho.dscalar.nii
+xcp_d/sub-1648798153/ses-PNC1/func/sub-1648798153_ses-PNC1_task-idemo_space-fsLR_den-91k_reho.json
 xcp_d/sub-1648798153_ses-PNC1_executive_summary.html
diff --git a/xcp_d/workflows/bold.py b/xcp_d/workflows/bold.py
@@ -528,7 +528,10 @@ def init_postprocess_nifti_wf(
 
     # fmt:off
     workflow.connect([
-        (inputnode, postproc_derivatives_wf, [("atlas_names", "inputnode.atlas_names")]),
+        (inputnode, postproc_derivatives_wf, [
+            ("fmriprep_confounds_file", "inputnode.fmriprep_confounds_file"),
+            ("atlas_names", "inputnode.atlas_names"),
+        ]),
         (prepare_confounds_wf, postproc_derivatives_wf, [
             ("outputnode.confounds_file", "inputnode.confounds_file"),
             ("outputnode.filtered_motion", "inputnode.filtered_motion"),

diff --git a/xcp_d/workflows/cifti.py b/xcp_d/workflows/cifti.py
@@ -497,7 +497,10 @@ def init_postprocess_cifti_wf(
 
     # fmt:off
     workflow.connect([
-        (inputnode, postproc_derivatives_wf, [("atlas_names", "inputnode.atlas_names")]),
+        (inputnode, postproc_derivatives_wf, [
+            ("fmriprep_confounds_file", "fmriprep_confounds_file"),
+            ("atlas_names", "inputnode.atlas_names"),
+        ]),
         (denoise_bold_wf, postproc_derivatives_wf, [
             ("outputnode.interpolated_filtered_bold", "inputnode.interpolated_filtered_bold"),
             ("outputnode.censored_denoised_bold", "inputnode.censored_denoised_bold"),

diff --git a/xcp_d/workflows/outputs.py b/xcp_d/workflows/outputs.py
@@ -302,6 +302,18 @@ def init_postproc_derivatives_wf(
     )
     preprocessed_bold_sources.inputs.in1 = name_source
 
+    preprocessed_confounds_sources = pe.Node(
+        InferBIDSURIs(
+            numinputs=1,
+            dataset_name="preprocessed",
+            dataset_path=fmri_dir,
+        ),
+        name="preprocessed_confounds_sources",
+        run_without_submitting=True,
+        mem_gb=1,
+    )
+    preprocessed_confounds_sources.inputs.in1 = name_source
+
     ds_temporal_mask = pe.Node(
         DerivativesDataSink(
             base_directory=output_dir,
@@ -828,6 +840,14 @@ def init_postproc_derivatives_wf(
             ]),
         ])
         # fmt:on
+    else:
+        # fmt:off
+        workflow.connect([
+            (inputnode, outputnode, [
+                ("interpolated_filtered_bold", "interpolated_filtered_bold"),
+            ]),
+        ])
+        # fmt:on
 
     if bandpass_filter and (fd_thresh <= 0):
         # fmt:off