with pre-config

Author: birajstha

CHANGELOG.md

@@ -29,6 +29,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - New switch `mask_sbref` under `func_input_prep` in functional registration and set to default `on`.
 - New resource `desc-head_bold` as non skull-stripped bold from nodeblock `bold_masking`.
 - `censor_file_path` from `offending_timepoints_connector` in the `build_nuisance_regressor` node.
+- `deoblique` field in pipeline config with `warp` and `refit` options to apply `3dWarp` or `3drefit` during data initialization.
 
 ### Changed
 

CPAC/func_preproc/func_preproc.py

@@ -708,6 +708,7 @@ def fsl_afni_subworkflow(cfg, pipe_num, opt=None):
 )
 def func_reorient(wf, cfg, strat_pool, pipe_num, opt=None):
     """Deoblique and Reorient functional timeseries."""
+    outputs = {}
     if opt not in func_reorient.option_val:
         raise ValueError(
             f"\n[!] Error: Invalid option {opt} for func_reorient. \n"
@@ -726,7 +727,7 @@ def func_reorient(wf, cfg, strat_pool, pipe_num, opt=None):
 
         interpolate_node = pe.Node(
             Function(
-                input_names=["timing_file", "target_slices", "out_file"],
+                input_names=["timing_file", "target_slices", "00000000000000000"],
                 output_names=["out_file"],
                 function=interpolate_slice_timing,
             ),
@@ -747,6 +748,8 @@ def func_reorient(wf, cfg, strat_pool, pipe_num, opt=None):
         tpattern_node, tpattern = strat_pool.get_data("tpattern")
         wf.connect(tpattern_node, tpattern, interpolate_node, "timing_file")
 
+        outputs = {"tpattern": (interpolate_node, "out_file")}
+
     elif opt == "refit":
         func_deoblique = pe.Node(
             interface=afni_utils.Refit(),
@@ -770,11 +773,12 @@ def func_reorient(wf, cfg, strat_pool, pipe_num, opt=None):
     func_reorient_node.inputs.orientation = cfg.pipeline_setup["desired_orientation"]
     func_reorient_node.inputs.outputtype = "NIFTI_GZ"
 
-    outputs = {
-        "desc-preproc_bold": (func_reorient_node, "out_file"),
-        "desc-reorient_bold": (func_reorient_node, "out_file"),
-        "tpattern": (interpolate_node, "out_file"),
-    }
+    outputs.update(
+        {
+            "desc-preproc_bold": (func_reorient_node, "out_file"),
+            "desc-reorient_bold": (func_reorient_node, "out_file"),
+        }
+    )
 
     return (wf, outputs)
 

CPAC/resources/configs/pipeline_config_blank.yml

@@ -251,6 +251,12 @@ surface_analysis:
 
 anatomical_preproc:
   run: Off
+
+  # [warp] - Deoblique the input image using AFNI 3dWarp. Changes header and the image data.
+  # [refit] - Clear the header of the input image using AFNI 3drefit. Changes only the header.
+  # applies for both T1w and T2w images
+  deoblique: ["refit"]
+
   acpc_alignment:
     T1w_brain_ACPC_template:
 
@@ -953,6 +959,10 @@ functional_preproc:
     # Convert raw data from LPI to RPI
     run: On
 
+    # [warp] - Deoblique the input image using AFNI 3dWarp. Changes header and the image data. Applies interpolation to the slice-timing metadata.
+    # [refit] - Clear the header of the input image using AFNI 3drefit. Changes only the header.
+    deoblique: ["refit"]
+
   slice_timing_correction:
 
     # Interpolate voxel time courses so they are sampled at the same time points.

CPAC/resources/configs/pipeline_config_default.yml

@@ -291,7 +291,7 @@ anatomical_preproc:
   # [warp] - Deoblique the input image using AFNI 3dWarp. Changes header and the image data.
   # [refit] - Clear the header of the input image using AFNI 3drefit. Changes only the header.
   # applies for both T1w and T2w images
-  deoblique: ["warp"]
+  deoblique: ["refit"]
 
   # Non-local means filtering via ANTs DenoiseImage
   non_local_means_filtering:
@@ -1027,7 +1027,7 @@ functional_preproc:
     # Convert raw data from LPI to RPI
     run: On
 
-    # [warp] - Deoblique the input image using AFNI 3dWarp. Changes header and the image data.
+    # [warp] - Deoblique the input image using AFNI 3dWarp. Changes header and the image data. Applies interpolation to the slice-timing metadata.
     # [refit] - Clear the header of the input image using AFNI 3drefit. Changes only the header.
     deoblique: ["refit"]