docs/builtin.rst

@@ -453,6 +453,16 @@ Available
        | Architecture
        | Cerebral Cortex, Volume 26(8), Pages 3508–3526 (2016).
        | https://doi.org/10.1093/cercor/bhw157
+   * - FreeSurfer 7.4.1 anatomical segmentation atlas
+     - None
+     - ``aseg-7_4_1``
+     - ``fsaverage``
+     - 0.0.7
+     - | Fischl B, Salat DH, Busa E, et al.
+       | Whole brain segmentation: automated labeling of neuroanatomical
+       | structures in the human brain.
+       | Neuron., Volume 33(3), Pages 341-355 (2002).
+       | https://doi:10.1016/s0896-6273(02)00569-x
 
 
 Planned
@@ -492,12 +502,6 @@ Planned
        | anatomical nomenclature.
        | NeuroImage, Volume 53(1), Pages 1–15 (2010).
        | http://doi.org/10.1016/j.neuroimage.2010.06.010.
-   * - Fan
-     - | Fan, L., Li, H., Zhuo, J. et al.
-       | The human brainnetome atlas: a new brain atlas based on connectional
-       | architecture.
-       | Cerebral cortex, Volume 26(8), Pages 3508-3526 (2016).
-       | https://doi.org/10.1093/cercor/bhw157
    * - Buckner
      - | Buckner, R.L., Krienen, F.M., Castellanos, A., Diaz, J.C., Yeo, B.T.T.
        | The organization of the human cerebellum estimated by intrinsic

docs/changes/newsfragments/470.enh

@@ -0,0 +1 @@
+Add FreeSurfer 7.4.1 aseg parcellation to :class:`.ParcellationRegistry` by `Synchon Mandal`_

docs/changes/newsfragments/470.misc

@@ -0,0 +1 @@
+Bump ``junifer-data`` to ``v5`` by `Synchon Mandal`_

junifer/data/parcellations/_parcellations.py

@@ -190,6 +190,15 @@ class ParcellationRegistry(BasePipelineDataRegistry):
                     },
                 }
             )
+        # Add FreeSurfer 7.4.1 aseg
+        self._builtin.update(
+            {
+                "aseg-7_4_1": {
+                    "family": "FreeSurfer",
+                    "space": "fsaverage",
+                }
+            }
+        )
 
         # Update registry with built-in ones
         self._registry.update(self._builtin)
@@ -355,6 +364,7 @@ class ParcellationRegistry(BasePipelineDataRegistry):
             "Shen",
             "Yan2023",
             "Brainnetome",
+            "FreeSurfer",
         ]:
             # Load parcellation and labels
             if t_family == "Schaefer2018":
@@ -394,6 +404,10 @@ class ParcellationRegistry(BasePipelineDataRegistry):
                         **parcellation_definition,
                     )
                 )
+            elif t_family == "FreeSurfer":
+                parcellation_fname, parcellation_labels = _retrieve_aseg(
+                    resolution=resolution,
+                )
         else:
             raise_error(f"Unknown parcellation family: {t_family}")
 
@@ -1307,6 +1321,106 @@ def _retrieve_brainnetome(
     return parcellation_img_path, labels
 
 
+def _retrieve_aseg(
+    resolution: Optional[float] = None,
+) -> tuple[Path, list[str]]:
+    """Retrieve aseg generated from FreeSurfer 7.4.1 .
+
+    Parameters
+    ----------
+    resolution : 1.0, optional
+        The desired resolution of the parcellation to load. If it is not
+        available, the closest resolution will be loaded. Preferably, use a
+        resolution higher than the desired one. By default, will load the
+        highest one (default None). Available resolution for this
+        parcellation is 1mm.
+
+    Returns
+    -------
+    pathlib.Path
+        File path to the parcellation image.
+    list of str
+        Parcellation labels.
+
+    """
+    logger.info("Parcellation parameters:")
+    logger.info(f"\tresolution: {resolution}")
+
+    _valid_resolutions = [1.0]
+    _ = closest_resolution(resolution, _valid_resolutions)
+
+    path_prefix = Path("parcellations/FreeSurfer-7_4_1")
+    parcellation_img_path = get(
+        file_path=path_prefix / "aseg.nii",
+        dataset_path=get_dataset_path(),
+        **JUNIFER_DATA_PARAMS,
+    )
+    parcellation_label_path = get(
+        file_path=path_prefix / "ASegStatsLUT.txt",
+        dataset_path=get_dataset_path(),
+        **JUNIFER_DATA_PARAMS,
+    )
+    # Explicitly indexed to get proper labels
+    idxs = [
+        2,
+        3,
+        4,
+        5,
+        7,
+        8,
+        10,
+        11,
+        12,
+        13,
+        14,
+        15,
+        16,
+        17,
+        18,
+        24,
+        26,
+        28,
+        30,
+        31,
+        41,
+        42,
+        43,
+        44,
+        46,
+        47,
+        49,
+        50,
+        51,
+        52,
+        53,
+        54,
+        58,
+        60,
+        62,
+        63,
+        77,
+        85,
+        251,
+        252,
+        253,
+        254,
+        255,
+    ]
+    labels = (
+        pd.read_csv(
+            parcellation_label_path,
+            sep=r"\s+",
+            skiprows=6,
+            header=None,
+            index_col=0,
+        )
+        .loc[idxs][1]
+        .to_list()
+    )
+
+    return parcellation_img_path, labels
+
+
 def merge_parcellations(
     parcellations_list: list["Nifti1Image"],
     parcellations_names: list[str],

junifer/data/parcellations/tests/test_parcellations.py

@@ -941,6 +941,27 @@ def test_retrieve_brainnetome_incorrect_threshold() -> None:
         )
 
 
+def test_aseg() -> None:
+    """Test FreeSurfer 7.4.1 aseg parcellation."""
+    parcellations = list_data(kind="parcellation")
+    assert "aseg-7_4_1" in parcellations
+
+    # Load parcellation
+    img, label, img_path, space = load_data(
+        kind="parcellation",
+        name="aseg-7_4_1",
+        target_space="fsaverage",
+    )
+    assert img is not None
+    assert img_path.name == "aseg.nii"
+    assert space == "fsaverage"
+    assert len(label) == 43
+    assert_array_equal(
+        img.header["pixdim"][1:4],
+        3 * [1],
+    )
+
+
 def test_merge_parcellations() -> None:
     """Test merging parcellations."""
     # load some parcellations for testing

junifer/data/utils.py

@@ -24,10 +24,10 @@ __all__ = [
 
 
 # junifer-data version constant
-JUNIFER_DATA_VERSION = "4"
+JUNIFER_DATA_VERSION = "5"
 
 # junifer-data hexsha constant
-JUNIFER_DATA_HEXSHA = "d178bddf383fede04742d7020312a574de47f0ab"
+JUNIFER_DATA_HEXSHA = "62a0e3d187259a3c3ba7be638ee39cfb40df0a61"
 
 JUNIFER_DATA_PARAMS = {
     "tag": JUNIFER_DATA_VERSION,