reverting adding reorient node at the very begining and passing orien…

…tation set in config in the existing nodes for reorientations

CPAC/anat_preproc/anat_preproc.py

@@ -1233,7 +1233,7 @@ def freesurfer_fsl_brain_connector(wf, cfg, strat_pool, pipe_num, opt):
         mem_gb=0,
         mem_x=(0.0115, "in_file", "t"),
     )
-    reorient_fs_brainmask.inputs.orientation = "RPI"
+    reorient_fs_brainmask.inputs.orientation = cfg.pipeline_setup["desired_orientation"]
     reorient_fs_brainmask.inputs.outputtype = "NIFTI_GZ"
 
     wf.connect(
@@ -1255,7 +1255,7 @@ def freesurfer_fsl_brain_connector(wf, cfg, strat_pool, pipe_num, opt):
         mem_gb=0,
         mem_x=(0.0115, "in_file", "t"),
     )
-    reorient_fs_T1.inputs.orientation = "RPI"
+    reorient_fs_T1.inputs.orientation = cfg.pipeline_setup["desired_orientation"]
     reorient_fs_T1.inputs.outputtype = "NIFTI_GZ"
 
     wf.connect(convert_fs_T1_to_nifti, "out_file", reorient_fs_T1, "in_file")
@@ -1454,10 +1454,21 @@ def anatomical_init(wf, cfg, strat_pool, pipe_num, opt=None):
     node, out = strat_pool.get_data("T1w")
     wf.connect(node, out, anat_deoblique, "in_file")
 
+    anat_reorient = pe.Node(
+        interface=afni.Resample(),
+        name=f"anat_reorient_{pipe_num}",
+        mem_gb=0,
+        mem_x=(0.0115, "in_file", "t"),
+    )
+    anat_reorient.inputs.orientation = cfg.pipeline_setup["desired_orientation"]
+    anat_reorient.inputs.outputtype = "NIFTI_GZ"
+
+    wf.connect(anat_deoblique, "out_file", anat_reorient, "in_file")
+
     outputs = {
-        "desc-preproc_T1w": (anat_deoblique, "out_file"),
-        "desc-reorient_T1w": (anat_deoblique, "out_file"),
-        "desc-head_T1w": (anat_deoblique, "out_file"),
+        "desc-preproc_T1w": (anat_reorient, "out_file"),
+        "desc-reorient_T1w": (anat_reorient, "out_file"),
+        "desc-head_T1w": (anat_reorient, "out_file"),
     }
 
     return (wf, outputs)
@@ -2251,10 +2262,21 @@ def anatomical_init_T2(wf, cfg, strat_pool, pipe_num, opt=None):
     node, out = strat_pool.get_data("T2w")
     wf.connect(node, out, T2_deoblique, "in_file")
 
+    T2_reorient = pe.Node(
+        interface=afni.Resample(),
+        name=f"T2_reorient_{pipe_num}",
+        mem_gb=0,
+        mem_x=(0.0115, "in_file", "t"),
+    )
+    T2_reorient.inputs.orientation = cfg.pipeline_setup["desired_orientation"]
+    T2_reorient.inputs.outputtype = "NIFTI_GZ"
+
+    wf.connect(T2_deoblique, "out_file", T2_reorient, "in_file")
+
     outputs = {
-        "desc-preproc_T2w": (T2_deoblique, "out_file"),
-        "desc-reorient_T2w": (T2_deoblique, "out_file"),
-        "desc-head_T2w": (T2_deoblique, "out_file"),
+        "desc-preproc_T2w": (T2_reorient, "out_file"),
+        "desc-reorient_T2w": (T2_reorient, "out_file"),
+        "desc-head_T2w": (T2_reorient, "out_file"),
     }
 
     return (wf, outputs)

CPAC/func_preproc/func_preproc.py

@@ -521,9 +521,21 @@ def func_reorient(wf, cfg, strat_pool, pipe_num, opt=None):
     node, out = strat_pool.get_data("bold")
     wf.connect(node, out, func_deoblique, "in_file")
 
+    func_reorient = pe.Node(
+        interface=afni_utils.Resample(),
+        name=f"func_reorient_{pipe_num}",
+        mem_gb=0,
+        mem_x=(0.0115, "in_file", "t"),
+    )
+
+    func_reorient.inputs.orientation = cfg.pipeline_setup["desired_orientation"]
+    func_reorient.inputs.outputtype = "NIFTI_GZ"
+
+    wf.connect(func_deoblique, "out_file", func_reorient, "in_file")
+
     outputs = {
-        "desc-preproc_bold": (func_deoblique, "out_file"),
-        "desc-reorient_bold": (func_deoblique, "out_file"),
+        "desc-preproc_bold": (func_reorient, "out_file"),
+        "desc-reorient_bold": (func_reorient, "out_file"),
     }
 
     return (wf, outputs)

CPAC/pipeline/engine.py

@@ -1932,17 +1932,7 @@ def ingress_raw_anat_data(wf, rpool, cfg, data_paths, unique_id, part_id, ses_id
             dl_dir=cfg.pipeline_setup["working_directory"]["path"],
             img_type="anat",
         )
-        reorient = pe.Node(
-            interface=afni.Resample(),
-            name=f"reorient_T1w_{part_id}_{ses_id}",
-        )
-
-        reorient.inputs.orientation = desired_orientation
-        reorient.inputs.outputtype = "NIFTI_GZ"
-
-        wf.connect(anat_flow, "outputspec.anat", reorient, "in_file")
-
-        rpool.set_data("T1w", reorient, "out_file", {}, "", "anat_ingress")
+        rpool.set_data("T1w", anat_flow, "outputspec.anat", {}, "", "anat_ingress")
 
     if "T2w" in data_paths["anat"]:
         anat_flow_T2 = create_anat_datasource(f"anat_T2w_gather_{part_id}_{ses_id}")
@@ -1953,17 +1943,7 @@ def ingress_raw_anat_data(wf, rpool, cfg, data_paths, unique_id, part_id, ses_id
             dl_dir=cfg.pipeline_setup["working_directory"]["path"],
             img_type="anat",
         )
-        reorient = pe.Node(
-            interface=afni.Resample(),
-            name=f"reorient_T1w_{part_id}_{ses_id}",
-        )
-
-        reorient.inputs.orientation = desired_orientation
-        reorient.inputs.outputtype = "NIFTI_GZ"
-
-        wf.connect(anat_flow_T2, "outputspec.anat", reorient, "in_file")
-
-        rpool.set_data("T2w", reorient, "out_file", {}, "", "anat_ingress")
+        rpool.set_data("T2w", anat_flow_T2, "outputspec.anat", {}, "", "anat_ingress")
 
     if cfg.surface_analysis["freesurfer"]["ingress_reconall"]:
         rpool = ingress_freesurfer(
@@ -2010,28 +1990,13 @@ 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"],
     )
-    node = fs_ingress
-    out = "outputspec.data"
-    node_name = "freesurfer_config_ingress"
-
-    if fs_path.endswith(".nii.gz" or ".nii"):
-        reorient = pe.Node(
-            interface=afni.Resample(),
-            name=f"reorient_fs_{part_id}_{ses_id}",
-        )
-        reorient.inputs.orientation = cfg.pipeline_setup["desired_orientation"]
-        reorient.inputs.outputtype = "NIFTI_GZ"
-        wf.connect(fs_ingress, "outputspec.data", reorient, "in_file")
-        node = reorient
-        out = "out_file"
-        node_name = "reorient_fs"
     rpool.set_data(
         "freesurfer-subject-dir",
-        node,
-        out,
+        fs_ingress,
+        "outputspec.data",
         {},
         "",
-        node_name,
+        "freesurfer_config_ingress",
     )
 
     recon_outs = {
@@ -2094,15 +2059,8 @@ def ingress_raw_func_data(wf, rpool, cfg, data_paths, unique_id, part_id, ses_id
     func_wf.get_node("inputnode").iterables = ("scan", list(func_paths_dct.keys()))
 
     rpool.set_data("subject", func_wf, "outputspec.subject", {}, "", "func_ingress")
-    reorient = pe.Node(
-        interface=afni.Resample(),
-        name=f"reorient_func_{part_id}_{ses_id}",
-    )
-    reorient.inputs.orientation = cfg.pipeline_setup["desired_orientation"]
-    reorient.inputs.outputtype = "NIFTI_GZ"
-    wf.connect(func_wf, "outputspec.rest", reorient, "in_file")
-    rpool.set_data("bold", reorient, "out_file", {}, "", "func_ingress")
-    # rpool.set_data("bold", func_wf, "outputspec.rest", {}, "", "func_ingress")
+
+    rpool.set_data("bold", func_wf, "outputspec.rest", {}, "", "func_ingress")
 
     rpool.set_data("scan", func_wf, "outputspec.scan", {}, "", "func_ingress")