Freesurfer ingress reorient

CPAC/anat_preproc/utils.py

@@ -502,6 +502,38 @@ def mri_convert(in_file, reslice_like=None, out_file=None, args=None):
     return out_file
 
 
+def mri_convert_reorient(in_file, orientation, out_file=None):
+    """
+    Reorient the mgz files using mri_orient.
+
+    Parameters
+    ----------
+    in_file : string
+        A path of mgz input file.
+    orientation : string
+        Orientation of the output file.
+    out_file : string
+        A path of mgz output file.
+    args : string
+        Arguments of mri_convert.
+
+    Returns
+    -------
+    out_file : string
+        A path of reoriented mgz output file.
+    """
+    import os
+
+    if out_file is None:
+        out_file = in_file.split(".")[0] + "_reoriented.mgz"
+
+    cmd = "mri_convert %s %s --out_orientation %s" % (in_file, out_file, orientation)
+
+    os.system(cmd)
+
+    return out_file
+
+
 def wb_command(in_file):
     import os
 

CPAC/pipeline/engine.py

@@ -30,6 +30,7 @@
 from nipype.interfaces import afni
 from nipype.interfaces.utility import Rename
 
+from CPAC.anat_preproc.utils import mri_convert_reorient
 from CPAC.image_utils.spatial_smoothing import spatial_smoothing
 from CPAC.image_utils.statistical_transforms import (
     fisher_z_score_standardize,
@@ -66,6 +67,7 @@
 from CPAC.utils.utils import (
     check_prov_for_regtool,
     create_id_string,
+    flip_orientation_code,
     get_last_prov_entry,
     read_json,
     write_output_json,
@@ -2043,9 +2045,30 @@ def ingress_freesurfer(wf, rpool, cfg, data_paths, unique_id, part_id, ses_id):
                 creds_path=data_paths["creds_path"],
                 dl_dir=cfg.pipeline_setup["working_directory"]["path"],
             )
-            rpool.set_data(
-                key, fs_ingress, "outputspec.data", {}, "", f"fs_{key}_ingress"
-            )
+            # if .mgz reorient to RPI
+            if outfile.endswith(".mgz"):
+                reorient_mgz = pe.Node(
+                    Function(
+                        input_names=["in_file", "orientation", "out_file"],
+                        output_names=["out_file"],
+                        function=mri_convert_reorient,
+                    ),
+                    name=f"reorient_mgz_{key}",
+                )
+                # Flip orientation before reorient because mri_convert's orientation is opposite that of AFNI
+                reorient_mgz.inputs.orientation = flip_orientation_code(
+                    cfg.pipeline_setup["desired_orientation"]
+                )
+                reorient_mgz.inputs.out_file = None
+                wf.connect(fs_ingress, "outputspec.data", reorient_mgz, "in_file")
+
+                rpool.set_data(
+                    key, reorient_mgz, "out_file", {}, "", f"fs_{key}_ingress"
+                )
+            else:
+                rpool.set_data(
+                    key, fs_ingress, "outputspec.data", {}, "", f"fs_{key}_ingress"
+                )
         else:
             warnings.warn(
                 str(LookupError(f"\n[!] Path does not exist for {fullpath}.\n"))

CPAC/utils/utils.py

@@ -2631,3 +2631,11 @@ def _replace_in_value_list(current_value, replacement_tuple):
         for v in current_value
         if bool(v) and v not in {"None", "Off", ""}
     ]
+
+
+def flip_orientation_code(code):
+    """
+    Reverts an orientation code by flipping R↔L, A↔P, and I↔S.
+    """
+    flip_dict = {"R": "L", "L": "R", "A": "P", "P": "A", "I": "S", "S": "I"}
+    return "".join(flip_dict[c] for c in code)