Split EPI pipeline in two, improve names, add docs....

aramis-lab · Mar 31, 2023 · cb4ce9e · cb4ce9e
1 parent abb12cb
commit cb4ce9e
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Showing 2 changed files with 259 additions and 96 deletions.
diff --git a/clinica/pipelines/dwi_preprocessing_using_t1/dwi_preprocessing_using_t1_pipeline.py b/clinica/pipelines/dwi_preprocessing_using_t1/dwi_preprocessing_using_t1_pipeline.py
@@ -366,9 +366,9 @@ def build_core_nodes(self):
                                         ("out_reference_b0", "inputnode.ref_b0")]),  # TODO: check if really needed...
                 (mask_b0_pre, eddy_fsl, [("mask_file", "inputnode.in_mask")]),
                 # Magnetic susceptibility correction
-                (init_node, sdc, [("t1w", "inputnode.T1")]),
-                (eddy_fsl, sdc, [("outputnode.out_corrected", "inputnode.DWI")]),
-                (eddy_fsl, sdc, [("outputnode.out_rotated_bvecs", "inputnode.bvec")]),
+                (init_node, sdc, [("t1w", "inputnode.t1_filename")]),
+                (eddy_fsl, sdc, [("outputnode.out_corrected", "inputnode.dwi_filename")]),
+                (eddy_fsl, sdc, [("outputnode.out_rotated_bvecs", "inputnode.b_vectors_filename")]),
                 # Bias correction
                 (prepare_b0, bias, [("out_updated_bval", "in_bval")]),
                 (sdc, bias, [("outputnode.DWIs_epicorrected", "in_file"),