Merge branch 'main' into peraf

Author: tsalo

xcp_d/workflows/anatomical/parcellation.py

@@ -139,7 +139,7 @@ def init_parcellate_surfaces_wf(files_to_parcellate, name='parcellate_surfaces_w
         ])  # fmt:skip
 
         parcellate_surface_wf = init_parcellate_cifti_wf(
-            mem_gb={'bold': 2},
+            mem_gb={'bold': 2, 'volume': 1},
             compute_mask=True,
             name=f'parcellate_{file_to_parcellate}_wf',
         )

xcp_d/workflows/bold/cifti.py

@@ -213,12 +213,10 @@ def init_postprocess_cifti_wf(
         name='outputnode',
     )
 
-    mem_gbx = mem_gb
-
     downcast_data = pe.Node(
         ConvertTo32(),
         name='downcast_data',
-        mem_gb=mem_gbx['bold'],
+        mem_gb=mem_gb['bold'],
     )
 
     workflow.connect([
@@ -233,7 +231,7 @@ def init_postprocess_cifti_wf(
         TR=TR,
         exact_scans=exact_scans,
         head_radius=head_radius,
-        mem_gb=mem_gbx,
+        mem_gb=mem_gb,
     )
 
     workflow.connect([
@@ -249,7 +247,7 @@ def init_postprocess_cifti_wf(
         ]),
     ])  # fmt:skip
 
-    denoise_bold_wf = init_denoise_bold_wf(TR=TR, mem_gb=mem_gbx)
+    denoise_bold_wf = init_denoise_bold_wf(TR=TR, mem_gb=mem_gb)
 
     workflow.connect([
         (prepare_confounds_wf, denoise_bold_wf, [
@@ -264,7 +262,7 @@ def init_postprocess_cifti_wf(
     ])  # fmt:skip
 
     if despike:
-        despike_wf = init_despike_wf(TR=TR, mem_gb=mem_gbx)
+        despike_wf = init_despike_wf(TR=TR, mem_gb=mem_gb)
 
         workflow.connect([
             (prepare_confounds_wf, despike_wf, [
@@ -288,7 +286,7 @@ def init_postprocess_cifti_wf(
     skip_alff = (not bandpass_filter) or ('alff' in config.workflow.skip_outputs)
 
     if not skip_alff:
-        alff_wf = init_alff_wf(name_source=bold_file, TR=TR, mem_gb=mem_gbx)
+        alff_wf = init_alff_wf(name_source=bold_file, TR=TR, mem_gb=mem_gb)
 
         workflow.connect([
             (inputnode, alff_wf, [
@@ -306,7 +304,7 @@ def init_postprocess_cifti_wf(
     # Skip ReHo calculation if requested
     skip_reho = 'reho' in config.workflow.skip_outputs
     if not skip_reho:
-        reho_wf = init_reho_cifti_wf(name_source=bold_file, mem_gb=mem_gbx)
+        reho_wf = init_reho_cifti_wf(name_source=bold_file, mem_gb=mem_gb)
 
         workflow.connect([
             (inputnode, reho_wf, [
@@ -341,7 +339,7 @@ def init_postprocess_cifti_wf(
     qc_report_wf = init_qc_report_wf(
         TR=TR,
         head_radius=head_radius,
-        mem_gb=mem_gbx,
+        mem_gb=mem_gb,
         name='qc_report_wf',
     )
 
@@ -421,7 +419,7 @@ def init_postprocess_cifti_wf(
 
     if config.execution.atlases:
         connectivity_wf = init_functional_connectivity_cifti_wf(
-            mem_gb=mem_gbx,
+            mem_gb=mem_gb,
             exact_scans=exact_scans,
             has_multiple_runs=has_multiple_runs,
             skip_reho=skip_reho,
@@ -488,7 +486,7 @@ def init_postprocess_cifti_wf(
             preproc_nifti=run_data['nifti_file'],
             t1w_available=t1w_available,
             t2w_available=t2w_available,
-            mem_gb=mem_gbx,
+            mem_gb=mem_gb,
         )
         workflow.connect([
             (inputnode, execsummary_functional_plots_wf, [

xcp_d/workflows/bold/nifti.py

@@ -221,12 +221,10 @@ def init_postprocess_nifti_wf(
         name='outputnode',
     )
 
-    mem_gbx = mem_gb
-
     downcast_data = pe.Node(
         ConvertTo32(),
         name='downcast_data',
-        mem_gb=mem_gbx['bold'],
+        mem_gb=mem_gb['bold'],
     )
 
     workflow.connect([
@@ -246,7 +244,7 @@ def init_postprocess_nifti_wf(
         TR=TR,
         exact_scans=exact_scans,
         head_radius=head_radius,
-        mem_gb=mem_gbx,
+        mem_gb=mem_gb,
     )
 
     workflow.connect([
@@ -262,7 +260,7 @@ def init_postprocess_nifti_wf(
         ]),
     ])  # fmt:skip
 
-    denoise_bold_wf = init_denoise_bold_wf(TR=TR, mem_gb=mem_gbx)
+    denoise_bold_wf = init_denoise_bold_wf(TR=TR, mem_gb=mem_gb)
 
     workflow.connect([
         (downcast_data, denoise_bold_wf, [('bold_mask', 'inputnode.mask')]),
@@ -278,7 +276,7 @@ def init_postprocess_nifti_wf(
     ])  # fmt:skip
 
     if despike:
-        despike_wf = init_despike_wf(TR=TR, mem_gb=mem_gbx)
+        despike_wf = init_despike_wf(TR=TR, mem_gb=mem_gb)
 
         workflow.connect([
             (prepare_confounds_wf, despike_wf, [
@@ -302,7 +300,7 @@ def init_postprocess_nifti_wf(
     skip_alff = (not bandpass_filter) or ('alff' in config.workflow.skip_outputs)
 
     if not skip_alff:
-        alff_wf = init_alff_wf(name_source=bold_file, TR=TR, mem_gb=mem_gbx)
+        alff_wf = init_alff_wf(name_source=bold_file, TR=TR, mem_gb=mem_gb)
 
         workflow.connect([
             (downcast_data, alff_wf, [('bold_mask', 'inputnode.bold_mask')]),
@@ -317,7 +315,7 @@ def init_postprocess_nifti_wf(
     # Skip ReHo calculation if requested
     skip_reho = 'reho' in config.workflow.skip_outputs
     if not skip_reho:
-        reho_wf = init_reho_nifti_wf(name_source=bold_file, mem_gb=mem_gbx)
+        reho_wf = init_reho_nifti_wf(name_source=bold_file, mem_gb=mem_gb)
 
         workflow.connect([
             (downcast_data, reho_wf, [('bold_mask', 'inputnode.bold_mask')]),
@@ -346,7 +344,7 @@ def init_postprocess_nifti_wf(
     qc_report_wf = init_qc_report_wf(
         TR=TR,
         head_radius=head_radius,
-        mem_gb=mem_gbx,
+        mem_gb=mem_gb,
         name='qc_report_wf',
     )
 
@@ -433,7 +431,7 @@ def init_postprocess_nifti_wf(
     if config.execution.atlases:
         connectivity_wf = init_functional_connectivity_nifti_wf(
             has_multiple_runs=has_multiple_runs,
-            mem_gb=mem_gbx,
+            mem_gb=mem_gb,
             skip_reho=skip_reho,
             skip_alff=skip_alff,
         )
@@ -493,7 +491,7 @@ def init_postprocess_nifti_wf(
             preproc_nifti=bold_file,
             t1w_available=t1w_available,
             t2w_available=t2w_available,
-            mem_gb=mem_gbx,
+            mem_gb=mem_gb,
         )
         workflow.connect([
             # Use inputnode for executive summary instead of downcast_data

xcp_d/workflows/parcellation.py

@@ -272,7 +272,7 @@ def init_parcellate_cifti_wf(
             from xcp_d.workflows.parcellation import init_parcellate_cifti_wf
 
             with mock_config():
-                wf = init_parcellate_cifti_wf(mem_gb={"bold": 2})
+                wf = init_parcellate_cifti_wf(mem_gb={"bold": 2, "volume": 1})
 
     Parameters
     ----------
@@ -431,7 +431,7 @@ def init_parcellate_cifti_wf(
         ),
         name='threshold_coverage',
         iterfield=['data'],
-        mem_gb=config.DEFAULT_MEMORY_MIN_GB,
+        mem_gb=2 * mem_gb['volume'],
     )
     workflow.connect([(coverage_buffer, threshold_coverage, [('coverage_cifti', 'data')])])
 
@@ -440,7 +440,7 @@ def init_parcellate_cifti_wf(
         CiftiMask(),
         name='mask_parcellated_data',
         iterfield=['in_file', 'mask'],
-        mem_gb=config.DEFAULT_MEMORY_MIN_GB,
+        mem_gb=2 * mem_gb['volume'],
     )
     workflow.connect([
         (parcellate_data, mask_parcellated_data, [('out_file', 'in_file')]),