Merge pull request #2140 from FCP-INDI/feature/check_orientations

➕ Reorient resources to set orientation in config

CHANGELOG.md

@@ -20,11 +20,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - `pyproject.toml` file with `[build-system]` defined.
 - [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/FCP-INDI/C-PAC/main.svg)](https://results.pre-commit.ci/latest/github/FCP-INDI/C-PAC/main) badge to [`README`](./README.md).
+- `desired_orientation` key in participant-level pipeline config under `pipeline_setup`.
+- Required positional parameter "wf" in input and output of `ingress_pipeconfig_paths` function, where a node to reorient templates is added to the `wf`.
+- Required positional parameter "orientation" to `resolve_resolution`.
+- Optional positional argument "cfg" to `create_lesion_preproc`.
 
 ### Changed
 
 - Moved `pygraphviz` from requirements to `graphviz` optional dependencies group.
 - Automatically tag untagged `subject_id` and `unique_id` as `!!str` when loading data config files.
+- Made orientation configurable (was hard-coded as "RPI").
 
 ### Fixed
 

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")
@@ -1460,7 +1460,7 @@ def anatomical_init(wf, cfg, strat_pool, pipe_num, opt=None):
         mem_gb=0,
         mem_x=(0.0115, "in_file", "t"),
     )
-    anat_reorient.inputs.orientation = "RPI"
+    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")
@@ -2268,7 +2268,7 @@ def anatomical_init_T2(wf, cfg, strat_pool, pipe_num, opt=None):
         mem_gb=0,
         mem_x=(0.0115, "in_file", "t"),
     )
-    T2_reorient.inputs.orientation = "RPI"
+    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")

CPAC/anat_preproc/lesion_preproc.py

@@ -58,7 +58,7 @@ def inverse_lesion(lesion_path):
     return lesion_out
 
 
-def create_lesion_preproc(wf_name="lesion_preproc"):
+def create_lesion_preproc(cfg=None, wf_name="lesion_preproc"):
     """Process lesions masks.
 
     Lesion mask file is deobliqued and reoriented in the same way as the T1 in
@@ -133,7 +133,9 @@ def create_lesion_preproc(wf_name="lesion_preproc"):
         mem_x=(0.0115, "in_file", "t"),
     )
 
-    lesion_reorient.inputs.orientation = "RPI"
+    lesion_reorient.inputs.orientation = (
+        cfg.pipeline_setup["desired_orientation"] if cfg else "RPI"
+    )
     lesion_reorient.inputs.outputtype = "NIFTI_GZ"
 
     preproc.connect(lesion_deoblique, "out_file", lesion_reorient, "in_file")

CPAC/func_preproc/func_preproc.py

@@ -528,7 +528,7 @@ def func_reorient(wf, cfg, strat_pool, pipe_num, opt=None):
         mem_x=(0.0115, "in_file", "t"),
     )
 
-    func_reorient.inputs.orientation = "RPI"
+    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")
@@ -1290,7 +1290,7 @@ def bold_mask_anatomical_refined(wf, cfg, strat_pool, pipe_num, opt=None):
         mem_x=(0.0115, "in_file", "t"),
     )
 
-    func_reorient.inputs.orientation = "RPI"
+    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")

CPAC/longitudinal_pipeline/longitudinal_workflow.py

@@ -1204,6 +1204,7 @@ def func_longitudinal_template_wf(subject_id, strat_list, config):
         resampled_template.inputs.template = template
         resampled_template.inputs.template_name = template_name
         resampled_template.inputs.tag = tag
+        resampled_template.inputs.orientation = config["desired_orientation"]
 
         strat_init.update_resource_pool(
             {template_name: (resampled_template, "resampled_template")}

CPAC/pipeline/engine.py

@@ -25,6 +25,7 @@
 import warnings
 
 from nipype import config, logging
+from nipype.interfaces import afni
 from nipype.interfaces.utility import Rename
 
 from CPAC.image_utils.spatial_smoothing import spatial_smoothing
@@ -35,7 +36,11 @@
 from CPAC.pipeline import nipype_pipeline_engine as pe
 from CPAC.pipeline.check_outputs import ExpectedOutputs
 from CPAC.pipeline.nodeblock import NodeBlockFunction
-from CPAC.pipeline.utils import MOVEMENT_FILTER_KEYS, name_fork, source_set
+from CPAC.pipeline.utils import (
+    MOVEMENT_FILTER_KEYS,
+    name_fork,
+    source_set,
+)
 from CPAC.registration.registration import transform_derivative
 from CPAC.resources.templates.lookup_table import lookup_identifier
 from CPAC.utils.bids_utils import res_in_filename
@@ -2403,7 +2408,7 @@ def strip_template(data_label, dir_path, filename):
     return data_label, json
 
 
-def ingress_pipeconfig_paths(cfg, rpool, unique_id, creds_path=None):
+def ingress_pipeconfig_paths(wf, cfg, rpool, unique_id, creds_path=None):
     # ingress config file paths
     # TODO: may want to change the resource keys for each to include one level up in the YAML as well
 
@@ -2412,6 +2417,7 @@ def ingress_pipeconfig_paths(cfg, rpool, unique_id, creds_path=None):
 
     template_csv = p.resource_filename("CPAC", "resources/cpac_templates.csv")
     template_df = pd.read_csv(template_csv, keep_default_na=False)
+    desired_orientation = cfg.pipeline_setup["desired_orientation"]
 
     for row in template_df.itertuples():
         key = row.Key
@@ -2468,32 +2474,29 @@ def ingress_pipeconfig_paths(cfg, rpool, unique_id, creds_path=None):
 
             resampled_template = pe.Node(
                 Function(
-                    input_names=["resolution", "template", "template_name", "tag"],
+                    input_names=[
+                        "orientation",
+                        "resolution",
+                        "template",
+                        "template_name",
+                        "tag",
+                    ],
                     output_names=["resampled_template"],
                     function=resolve_resolution,
                     as_module=True,
                 ),
                 name="resampled_" + key,
             )
 
+            resampled_template.inputs.orientation = desired_orientation
             resampled_template.inputs.resolution = resolution
             resampled_template.inputs.template = val
             resampled_template.inputs.template_name = key
             resampled_template.inputs.tag = tag
 
-            # the set_data below is set up a little differently, because we are
-            # injecting and also over-writing already-existing entries
-            # other alternative would have been to ingress into the
-            # resampled_template node from the already existing entries, but we
-            # didn't do that here
-            rpool.set_data(
-                key,
-                resampled_template,
-                "resampled_template",
-                json_info,
-                "",
-                "template_resample",
-            )  # pipe_idx (after the blank json {}) should be the previous strat that you want deleted! because you're not connecting this the regular way, you have to do it manually
+            node = resampled_template
+            output = "resampled_template"
+            node_name = "template_resample"
 
         elif val:
             config_ingress = create_general_datasource(f"gather_{key}")
@@ -2503,14 +2506,33 @@ def ingress_pipeconfig_paths(cfg, rpool, unique_id, creds_path=None):
                 creds_path=creds_path,
                 dl_dir=cfg.pipeline_setup["working_directory"]["path"],
             )
-            rpool.set_data(
-                key,
-                config_ingress,
-                "outputspec.data",
-                json_info,
-                "",
-                f"{key}_config_ingress",
-            )
+            node = config_ingress
+            output = "outputspec.data"
+            node_name = f"{key}_config_ingress"
+
+            if val.endswith(".nii" or ".nii.gz"):
+                check_reorient = pe.Node(
+                    interface=afni.Resample(),
+                    name=f"reorient_{key}",
+                )
+
+                check_reorient.inputs.orientation = desired_orientation
+                check_reorient.inputs.outputtype = "NIFTI_GZ"
+
+                wf.connect(node, output, check_reorient, "in_file")
+                node = check_reorient
+                output = "out_file"
+                node_name = f"{key}_reorient"
+
+        rpool.set_data(
+            key,
+            node,
+            output,
+            json_info,
+            "",
+            node_name,
+        )
+
     # templates, resampling from config
     """
     template_keys = [
@@ -2596,8 +2618,7 @@ def _set_nested(attr, keys):
         )
         cfg.set_nested(cfg, key, node)
     """
-
-    return rpool
+    return wf, rpool
 
 
 def initiate_rpool(wf, cfg, data_paths=None, part_id=None):
@@ -2668,7 +2689,7 @@ def initiate_rpool(wf, cfg, data_paths=None, part_id=None):
                 )
 
     # grab any file paths from the pipeline config YAML
-    rpool = ingress_pipeconfig_paths(cfg, rpool, unique_id, creds_path)
+    wf, rpool = ingress_pipeconfig_paths(wf, cfg, rpool, unique_id, creds_path)
 
     # output files with 4 different scans
 

CPAC/pipeline/schema.py

@@ -423,6 +423,9 @@ def sanitize(filename):
         "skip env check": Maybe(bool),  # flag for skipping an environment check
         "pipeline_setup": {
             "pipeline_name": All(str, Length(min=1), sanitize),
+            "desired_orientation": In(
+                {"RPI", "LPI", "RAI", "LAI", "RAS", "LAS", "RPS", "LPS"}
+            ),
             "output_directory": {
                 "path": str,
                 "source_outputs_dir": Maybe(str),

CPAC/pipeline/test/test_engine.py

@@ -90,7 +90,7 @@ def test_ingress_pipeconfig_data(pipe_config, bids_dir, test_dir):
 
     rpool = ResourcePool(name=unique_id, cfg=cfg)
 
-    rpool = ingress_pipeconfig_paths(cfg, rpool, sub_data_dct, unique_id)
+    wf, rpool = ingress_pipeconfig_paths(wf, cfg, rpool, sub_data_dct, unique_id)
 
     rpool.gather_pipes(wf, cfg, all=True)
 

CPAC/registration/registration.py

@@ -1736,7 +1736,7 @@ def ANTs_registration_connector(
             "ANTs"
         ]["use_lesion_mask"]:
             # Create lesion preproc node to apply afni Refit and Resample
-            lesion_preproc = create_lesion_preproc(wf_name=f"lesion_preproc{symm}")
+            lesion_preproc = create_lesion_preproc(cfg, wf_name=f"lesion_preproc{symm}")
             wf.connect(inputNode, "lesion_mask", lesion_preproc, "inputspec.lesion")
             wf.connect(
                 lesion_preproc,

CPAC/registration/tests/mocks.py

@@ -151,6 +151,7 @@ def configuration_strategy_mock(method="FSL"):
         resampled_template.inputs.template = template
         resampled_template.inputs.template_name = template_name
         resampled_template.inputs.tag = tag
+        resampled_template.inputs.orientation = "RPI"
 
         strat.update_resource_pool(
             {template_name: (resampled_template, "resampled_template")}

CPAC/registration/tests/test_registration.py

@@ -130,7 +130,7 @@ def test_registration_lesion():
 
     anat_preproc.inputs.inputspec.anat = anat_file
 
-    lesion_preproc = create_lesion_preproc(wf_name="lesion_preproc")
+    lesion_preproc = create_lesion_preproc(cfg, wf_name="lesion_preproc")
 
     lesion_preproc.inputs.inputspec.lesion = lesion_file
 

CPAC/resources/configs/pipeline_config_blank.yml

@@ -11,6 +11,10 @@ pipeline_setup:
   # Name for this pipeline configuration - useful for identification.
   # This string will be sanitized and used in filepaths
   pipeline_name: cpac-blank-template
+
+  # Desired orientation for the output data. "RPI", "LPI", "RAI", "LAI", "RAS", "LAS", "RPS", "LPS"
+  desired_orientation: RPI
+
   output_directory:
 
     # Quality control outputs

CPAC/resources/tests/test_templates.py

@@ -19,6 +19,7 @@
 import os
 
 import pytest
+import nipype.pipeline.engine as pe
 
 from CPAC.pipeline import ALL_PIPELINE_CONFIGS
 from CPAC.pipeline.engine import ingress_pipeconfig_paths, ResourcePool
@@ -29,11 +30,11 @@
 @pytest.mark.parametrize("pipeline", ALL_PIPELINE_CONFIGS)
 def test_packaged_path_exists(pipeline):
     """
-    Check that all local templates are included in image at at
-    least one resolution.
+    Check that all local templates are included in image at atleast one resolution.
     """
-    rpool = ingress_pipeconfig_paths(
-        Preconfiguration(pipeline), ResourcePool(), "pytest"
+    wf = pe.Workflow(name="test")
+    wf, rpool = ingress_pipeconfig_paths(
+        wf, Preconfiguration(pipeline), ResourcePool(), "pytest"
     )
     for resource in rpool.rpool.values():
         node = next(iter(resource.values())).get("data")[0]

CPAC/utils/datasource.py

@@ -1156,7 +1156,7 @@ def res_string_to_tuple(resolution):
     return (float(resolution.replace("mm", "")),) * 3
 
 
-def resolve_resolution(resolution, template, template_name, tag=None):
+def resolve_resolution(orientation, resolution, template, template_name, tag=None):
     """Resample a template to a given resolution."""
     from nipype.interfaces import afni
 
@@ -1203,6 +1203,7 @@ def resolve_resolution(resolution, template, template_name, tag=None):
         resample.inputs.resample_mode = "Cu"
         resample.inputs.in_file = local_path
         resample.base_dir = "."
+        resample.inputs.orientation = orientation
 
         resampled_template = resample.run()
         local_path = resampled_template.outputs.out_file

CPAC/utils/test_mocks.py

@@ -235,6 +235,7 @@ def configuration_strategy_mock(method="FSL"):
         resampled_template.inputs.template = template
         resampled_template.inputs.template_name = template_name
         resampled_template.inputs.tag = tag
+        resampled_template.inputs.orientation = "RPI"
 
         strat.update_resource_pool(
             {template_name: (resampled_template, "resampled_template")}