docs/changes/newsfragments/346.enh

@@ -0,0 +1 @@
+Adapt :class:`.DataladAOMICID1000`, :class:`.DataladAOMICPIOP1` and :class:`.DataladAOMICPIOP2` to support ``FreeSurfer`` data type by `Synchon Mandal`_

docs/changes/newsfragments/346.feature

@@ -0,0 +1 @@
+Add support for ``FreeSurfer`` data type for :class:`.PatternDataGrabber` by `Synchon Mandal`_

docs/understanding/data.rst

@@ -115,6 +115,9 @@ Data Types
    * - ``VBM_WM``
      - VBM White Matter segmentation (3D)
      - CAT output (`m0wp2` images)
+   * - ``VBM_CSF``
+     - VBM Central Spinal Fluid segmentation (3D)
+     - CAT output (`m0wp3` images)
    * - ``fALFF``
      - Voxel-wise fALFF image (3D)
      - fALFF computed with CONN toolbox
@@ -124,3 +127,9 @@ Data Types
    * - ``LCOR``
      - Local Correlation image (3D)
      - LCOR computed with CONN toolbox
+   * - ``DWI``
+     - Diffusion-weighted image (3D)
+     - Diffusion-weighted image (FSL or MRtrix output)
+   * - ``FreeSurfer``
+     - T1 image (3D)
+     - T1 image computed by FreeSurfer

junifer/datagrabber/aomic/id1000.py

@@ -24,8 +24,8 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
         The directory where the datalad dataset will be cloned. If None,
         the datalad dataset will be cloned into a temporary directory
         (default None).
-    types: {"BOLD", "T1w", "VBM_CSF", "VBM_GM", "VBM_WM", "DWI"} or \
+    types: {"BOLD", "T1w", "VBM_CSF", "VBM_GM", "VBM_WM", "DWI", \
-           list of the options, optional
+           "FreeSurfer"} or list of the options, optional
         AOMIC data types. If None, all available data types are selected.
         (default None).
     native_t1w : bool, optional
@@ -112,6 +112,39 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
                     "{subject}_desc-preproc_dwi.nii.gz"
                 ),
             },
+            "FreeSurfer": {
+                "pattern": "derivatives/freesurfer/[!f]{subject}/mri/T1.mg[z]",
+                "aseg": {
+                    "pattern": (
+                        "derivatives/freesurfer/[!f]{subject}/mri/aseg.mg[z]"
+                    )
+                },
+                "norm": {
+                    "pattern": (
+                        "derivatives/freesurfer/[!f]{subject}/mri/norm.mg[z]"
+                    )
+                },
+                "lh_white": {
+                    "pattern": (
+                        "derivatives/freesurfer/[!f]{subject}/surf/lh.whit[e]"
+                    )
+                },
+                "rh_white": {
+                    "pattern": (
+                        "derivatives/freesurfer/[!f]{subject}/surf/rh.whit[e]"
+                    )
+                },
+                "lh_pial": {
+                    "pattern": (
+                        "derivatives/freesurfer/[!f]{subject}/surf/lh.pia[l]"
+                    )
+                },
+                "rh_pial": {
+                    "pattern": (
+                        "derivatives/freesurfer/[!f]{subject}/surf/rh.pia[l]"
+                    )
+                },
+            },
         }
         # Use native T1w assets
         self.native_t1w = False

junifer/datagrabber/aomic/piop1.py

@@ -26,8 +26,8 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
         The directory where the datalad dataset will be cloned. If None,
         the datalad dataset will be cloned into a temporary directory
         (default None).
-    types: {"BOLD", "T1w", "VBM_CSF", "VBM_GM", "VBM_WM", "DWI"} or \
+    types: {"BOLD", "T1w", "VBM_CSF", "VBM_GM", "VBM_WM", "DWI", \
-           list of the options, optional
+           "FreeSurfer"} or list of the options, optional
         AOMIC data types. If None, all available data types are selected.
         (default None).
     tasks : {"restingstate", "anticipation", "emomatching", "faces", \
@@ -147,6 +147,39 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
                     "{subject}_desc-preproc_dwi.nii.gz"
                 ),
             },
+            "FreeSurfer": {
+                "pattern": "derivatives/freesurfer/[!f]{subject}/mri/T1.mg[z]",
+                "aseg": {
+                    "pattern": (
+                        "derivatives/freesurfer/[!f]{subject}/mri/aseg.mg[z]"
+                    )
+                },
+                "norm": {
+                    "pattern": (
+                        "derivatives/freesurfer/[!f]{subject}/mri/norm.mg[z]"
+                    )
+                },
+                "lh_white": {
+                    "pattern": (
+                        "derivatives/freesurfer/[!f]{subject}/surf/lh.whit[e]"
+                    )
+                },
+                "rh_white": {
+                    "pattern": (
+                        "derivatives/freesurfer/[!f]{subject}/surf/rh.whit[e]"
+                    )
+                },
+                "lh_pial": {
+                    "pattern": (
+                        "derivatives/freesurfer/[!f]{subject}/surf/lh.pia[l]"
+                    )
+                },
+                "rh_pial": {
+                    "pattern": (
+                        "derivatives/freesurfer/[!f]{subject}/surf/rh.pia[l]"
+                    )
+                },
+            },
         }
         # Use native T1w assets
         self.native_t1w = False

junifer/datagrabber/aomic/piop2.py

@@ -26,8 +26,8 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
         The directory where the datalad dataset will be cloned. If None,
         the datalad dataset will be cloned into a temporary directory
         (default None).
-    types: {"BOLD", "T1w", "VBM_CSF", "VBM_GM", "VBM_WM", "DWI"} or \
+    types: {"BOLD", "T1w", "VBM_CSF", "VBM_GM", "VBM_WM", "DWI", \
-           list of the options, optional
+           "FreeSurfer"} or list of the options, optional
         AOMIC data types. If None, all available data types are selected.
         (default None).
     tasks : {"restingstate", "stopsignal", "workingmemory"} or \
@@ -144,6 +144,39 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
                     "{subject}_desc-preproc_dwi.nii.gz"
                 ),
             },
+            "FreeSurfer": {
+                "pattern": "derivatives/freesurfer/[!f]{subject}/mri/T1.mg[z]",
+                "aseg": {
+                    "pattern": (
+                        "derivatives/freesurfer/[!f]{subject}/mri/aseg.mg[z]"
+                    )
+                },
+                "norm": {
+                    "pattern": (
+                        "derivatives/freesurfer/[!f]{subject}/mri/norm.mg[z]"
+                    )
+                },
+                "lh_white": {
+                    "pattern": (
+                        "derivatives/freesurfer/[!f]{subject}/surf/lh.whit[e]"
+                    )
+                },
+                "rh_white": {
+                    "pattern": (
+                        "derivatives/freesurfer/[!f]{subject}/surf/rh.whit[e]"
+                    )
+                },
+                "lh_pial": {
+                    "pattern": (
+                        "derivatives/freesurfer/[!f]{subject}/surf/lh.pia[l]"
+                    )
+                },
+                "rh_pial": {
+                    "pattern": (
+                        "derivatives/freesurfer/[!f]{subject}/surf/rh.pia[l]"
+                    )
+                },
+            },
         }
         # Use native T1w assets
         self.native_t1w = False

junifer/datagrabber/aomic/tests/test_id1000.py

@@ -7,7 +7,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import List, Union
+from typing import List, Optional, Union
 
 import pytest
 
@@ -17,112 +17,58 @@ from junifer.datagrabber.aomic.id1000 import DataladAOMICID1000
 URI = "https://gin.g-node.org/juaml/datalad-example-aomic1000"
 
 
-def test_DataladAOMICID1000() -> None:
+@pytest.mark.parametrize(
-    """Test DataladAOMICID1000 DataGrabber."""
+    "type_, nested_types",
-    dg = DataladAOMICID1000()
+    [
+        ("BOLD", ["confounds", "mask"]),
+        ("T1w", ["mask"]),
+        ("VBM_CSF", None),
+        ("VBM_GM", None),
+        ("VBM_WM", None),
+        ("DWI", None),
+        ("FreeSurfer", None),
+    ],
+)
+def test_DataladAOMICID1000(
+    type_: str,
+    nested_types: Optional[List[str]],
+) -> None:
+    """Test DataladAOMICID1000 DataGrabber.
+
+    Parameters
+    ----------
+    type_ : str
+        The parametrized type.
+    nested_types : list of str or None
+        The parametrized nested types.
+
+    """
+    dg = DataladAOMICID1000(types=type_)
     # Set URI to Gin
     dg.uri = URI
 
     with dg:
+        # Get all elements
         all_elements = dg.get_elements()
+        # Get test element
         test_element = all_elements[0]
-
+        # Get test element data
         out = dg[test_element]
-
+        # Assert data type
-        # asserts type "BOLD"
+        assert type_ in out
-        assert "BOLD" in out
+        assert out[type_]["path"].exists()
-
+        assert out[type_]["path"].is_file()
-        assert (
+        # Asserts data type metadata
-            out["BOLD"]["path"].name == f"{test_element}_task-moviewatching_"
+        assert "meta" in out[type_]
-            "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
+        meta = out[type_]["meta"]
-        )
-
-        assert out["BOLD"]["path"].exists()
-        assert out["BOLD"]["path"].is_file()
-
-        # asserts type BOLD.confounds
-        assert "confounds" in out["BOLD"]
-
-        assert (
-            out["BOLD"]["confounds"]["path"].name
-            == f"{test_element}_task-moviewatching_"
-            "desc-confounds_regressors.tsv"
-        )
-
-        assert out["BOLD"]["confounds"]["path"].exists()
-        assert out["BOLD"]["confounds"]["path"].is_file()
-
-        # assert BOLD.mask
-        assert out["BOLD"]["mask"]["path"].exists()
-
-        # asserts type "T1w"
-        assert "T1w" in out
-
-        assert (
-            out["T1w"]["path"].name
-            == f"{test_element}_space-MNI152NLin2009cAsym_"
-            "desc-preproc_T1w.nii.gz"
-        )
-
-        assert out["T1w"]["path"].exists()
-        assert out["T1w"]["path"].is_file()
-
-        # asserts T1w.mask
-        assert out["T1w"]["mask"]["path"].exists()
-
-        # asserts type "VBM_CSF"
-        assert "VBM_CSF" in out
-
-        assert (
-            out["VBM_CSF"]["path"].name
-            == f"{test_element}_space-MNI152NLin2009cAsym_label-"
-            "CSF_probseg.nii.gz"
-        )
-
-        assert out["VBM_CSF"]["path"].exists()
-        assert out["VBM_CSF"]["path"].is_file()
-
-        # asserts type "VBM_GM"
-        assert "VBM_GM" in out
-
-        assert (
-            out["VBM_GM"]["path"].name
-            == f"{test_element}_space-MNI152NLin2009cAsym_label-"
-            "GM_probseg.nii.gz"
-        )
-
-        assert out["VBM_GM"]["path"].exists()
-        assert out["VBM_GM"]["path"].is_file()
-
-        # asserts type "VBM_WM"
-        assert "VBM_WM" in out
-
-        assert (
-            out["VBM_WM"]["path"].name
-            == f"{test_element}_space-MNI152NLin2009cAsym_label-"
-            "WM_probseg.nii.gz"
-        )
-
-        assert out["VBM_WM"]["path"].exists()
-        assert out["VBM_WM"]["path"].is_file()
-
-        # asserts type "DWI"
-        assert "DWI" in out
-
-        assert (
-            out["DWI"]["path"].name
-            == f"{test_element}_desc-preproc_dwi.nii.gz"
-        )
-
-        assert out["DWI"]["path"].exists()
-        assert out["DWI"]["path"].is_file()
-
-        # asserts meta
-        assert "meta" in out["BOLD"]
-        meta = out["BOLD"]["meta"]
         assert "element" in meta
         assert "subject" in meta["element"]
         assert test_element == meta["element"]["subject"]
+        # Assert nested data type if not None
+        if nested_types is not None:
+            for nested_type in nested_types:
+                assert out[type_][nested_type]["path"].exists()
+                assert out[type_][nested_type]["path"].is_file()
 
 
 @pytest.mark.parametrize(

junifer/datagrabber/aomic/tests/test_piop1.py

@@ -18,33 +18,65 @@ URI = "https://gin.g-node.org/juaml/datalad-example-aomicpiop1"
 
 
 @pytest.mark.parametrize(
-    "tasks",
+    "type_, nested_types, tasks",
-    [None, "restingstate"],
+    [
+        ("BOLD", ["confounds", "mask"], None),
+        ("BOLD", ["confounds", "mask"], ["anticipation"]),
+        ("BOLD", ["confounds", "mask"], ["emomatching", "faces"]),
+        ("BOLD", ["confounds", "mask"], ["restingstate"]),
+        ("BOLD", ["confounds", "mask"], ["workingmemory", "gstroop"]),
+        (
+            "BOLD",
+            ["confounds", "mask"],
+            ["anticipation", "faces", "restingstate"],
+        ),
+        ("T1w", ["mask"], None),
+        ("VBM_CSF", None, None),
+        ("VBM_GM", None, None),
+        ("VBM_WM", None, None),
+        ("DWI", None, None),
+        ("FreeSurfer", None, None),
+    ],
 )
-def test_DataladAOMICPIOP1(tasks: Optional[str]) -> None:
+def test_DataladAOMICPIOP1(
+    type_: str,
+    nested_types: Optional[List[str]],
+    tasks: Optional[List[str]],
+) -> None:
     """Test DataladAOMICPIOP1 DataGrabber.
 
     Parameters
     ----------
-    tasks : str or None
+    type_ : str
+        The parametrized type.
+    nested_types : list of str or None
+        The parametrized nested types.
+    tasks : list of str or None
         The parametrized task values.
 
     """
-    dg = DataladAOMICPIOP1(tasks=tasks)
+    dg = DataladAOMICPIOP1(types=type_, tasks=tasks)
     # Set URI to Gin
     dg.uri = URI
 
     with dg:
+        # Get all elements
         all_elements = dg.get_elements()
+        # Get test element
         test_element = all_elements[0]
-        sub, task = test_element
+        # Get test element data
-
         out = dg[test_element]
-
+        # Get all elements
-        # asserts type "BOLD"
+        all_elements = dg.get_elements()
-        assert "BOLD" in out
+        # Get test element
-
+        test_element = all_elements[0]
-        # depending on task 'acquisition is different'
+        # Get test element data
+        out = dg[test_element]
+        # Assert data type
+        assert type_ in out
+        # Check task name if BOLD
+        if type_ == "BOLD" and tasks is not None:
+            # Depending on task 'acquisition is different'
             task_acqs = {
                 "anticipation": "seq",
                 "emomatching": "seq",
@@ -53,94 +85,20 @@ def test_DataladAOMICPIOP1(tasks: Optional[str]) -> None:
                 "restingstate": "mb3",
                 "workingmemory": "seq",
             }
-        acq = task_acqs[task]
+            assert task_acqs[test_element[1]] in out[type_]["path"].name
-        new_task = f"{task}_acq-{acq}"
+        assert out[type_]["path"].exists()
-        assert (
+        assert out[type_]["path"].is_file()
-            out["BOLD"]["path"].name == f"{sub}_task-{new_task}_"
+        # Asserts data type metadata
-            "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
+        assert "meta" in out[type_]
-        )
+        meta = out[type_]["meta"]
-
-        assert out["BOLD"]["path"].exists()
-        assert out["BOLD"]["path"].is_file()
-
-        # asserts type BOLD.confounds
-        assert "confounds" in out["BOLD"]
-
-        assert (
-            out["BOLD"]["confounds"]["path"].name == f"{sub}_task-{new_task}_"
-            "desc-confounds_regressors.tsv"
-        )
-
-        assert out["BOLD"]["confounds"]["path"].exists()
-        assert out["BOLD"]["confounds"]["path"].is_file()
-
-        # assert BOLD.mask
-        assert out["BOLD"]["mask"]["path"].exists()
-
-        # asserts type "T1w"
-        assert "T1w" in out
-
-        assert (
-            out["T1w"]["path"].name == f"{sub}_space-MNI152NLin2009cAsym_"
-            "desc-preproc_T1w.nii.gz"
-        )
-
-        assert out["T1w"]["path"].exists()
-        assert out["T1w"]["path"].is_file()
-
-        # asserts T1w.mask
-        assert out["T1w"]["mask"]["path"].exists()
-
-        # asserts type "VBM_CSF"
-        assert "VBM_CSF" in out
-
-        assert (
-            out["VBM_CSF"]["path"].name
-            == f"{sub}_space-MNI152NLin2009cAsym_label-"
-            "CSF_probseg.nii.gz"
-        )
-
-        assert out["VBM_CSF"]["path"].exists()
-        assert out["VBM_CSF"]["path"].is_file()
-
-        # asserts type "VBM_GM"
-        assert "VBM_GM" in out
-
-        assert (
-            out["VBM_GM"]["path"].name
-            == f"{sub}_space-MNI152NLin2009cAsym_label-"
-            "GM_probseg.nii.gz"
-        )
-
-        assert out["VBM_GM"]["path"].exists()
-        assert out["VBM_GM"]["path"].is_file()
-
-        # asserts type "VBM_WM"
-        assert "VBM_WM" in out
-
-        assert (
-            out["VBM_WM"]["path"].name
-            == f"{sub}_space-MNI152NLin2009cAsym_label-"
-            "WM_probseg.nii.gz"
-        )
-
-        assert out["VBM_WM"]["path"].exists()
-        assert out["VBM_WM"]["path"].is_file()
-
-        # asserts type "DWI"
-        assert "DWI" in out
-
-        assert out["DWI"]["path"].name == f"{sub}_desc-preproc_dwi.nii.gz"
-
-        assert out["DWI"]["path"].exists()
-        assert out["DWI"]["path"].is_file()
-
-        # asserts meta
-        assert "meta" in out["BOLD"]
-        meta = out["BOLD"]["meta"]
         assert "element" in meta
         assert "subject" in meta["element"]
-        assert sub == meta["element"]["subject"]
+        assert test_element[0] == meta["element"]["subject"]
+        # Assert nested data type if not None
+        if nested_types is not None:
+            for nested_type in nested_types:
+                assert out[type_][nested_type]["path"].exists()
+                assert out[type_][nested_type]["path"].is_file()
 
 
 @pytest.mark.parametrize(

junifer/datagrabber/aomic/tests/test_piop2.py

@@ -18,123 +18,67 @@ URI = "https://gin.g-node.org/juaml/datalad-example-aomicpiop2"
 
 
 @pytest.mark.parametrize(
-    "tasks",
+    "type_, nested_types, tasks",
-    [None, "restingstate"],
+    [
+        ("BOLD", ["confounds", "mask"], None),
+        ("BOLD", ["confounds", "mask"], ["restingstate"]),
+        ("BOLD", ["confounds", "mask"], ["restingstate", "stopsignal"]),
+        ("BOLD", ["confounds", "mask"], ["workingmemory", "stopsignal"]),
+        ("BOLD", ["confounds", "mask"], ["workingmemory"]),
+        ("T1w", ["mask"], None),
+        ("VBM_CSF", None, None),
+        ("VBM_GM", None, None),
+        ("VBM_WM", None, None),
+        ("DWI", None, None),
+        ("FreeSurfer", None, None),
+    ],
 )
-def test_DataladAOMICPIOP2(tasks: Optional[str]) -> None:
+def test_DataladAOMICPIOP2(
+    type_: str,
+    nested_types: Optional[List[str]],
+    tasks: Optional[List[str]],
+) -> None:
     """Test DataladAOMICPIOP2 DataGrabber.
 
     Parameters
     ----------
-    tasks : str or None
+    type_ : str
+        The parametrized type.
+    nested_types : list of str or None
+        The parametrized nested types.
+    tasks : list of str or None
         The parametrized task values.
 
     """
-    dg = DataladAOMICPIOP2(tasks=tasks)
+    dg = DataladAOMICPIOP2(types=type_, tasks=tasks)
     # Set URI to Gin
     dg.uri = URI
 
     with dg:
+        # Get all elements
         all_elements = dg.get_elements()
-
+        # Get test element
-        if tasks == "restingstate":
-            for el in all_elements:
-                assert el[1] == "restingstate"
-
         test_element = all_elements[0]
-        sub, task = test_element
+        # Get test element data
         out = dg[test_element]
-
+        # Assert data type
-        # asserts type "BOLD"
+        assert type_ in out
-        assert "BOLD" in out
+        # Check task name if BOLD
-
+        if type_ == "BOLD" and tasks is not None:
-        new_task = f"{task}_acq-seq"
+            assert test_element[1] in out[type_]["path"].name
-        assert (
+        assert out[type_]["path"].exists()
-            out["BOLD"]["path"].name == f"{sub}_task-{new_task}_"
+        assert out[type_]["path"].is_file()
-            "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
+        # Asserts data type metadata
-        )
+        assert "meta" in out[type_]
-
+        meta = out[type_]["meta"]
-        assert out["BOLD"]["path"].exists()
-        assert out["BOLD"]["path"].is_file()
-
-        # asserts type BOLD.confounds
-        assert "confounds" in out["BOLD"]
-
-        assert (
-            out["BOLD"]["confounds"]["path"].name == f"{sub}_task-{new_task}_"
-            "desc-confounds_regressors.tsv"
-        )
-
-        assert out["BOLD"]["confounds"]["path"].exists()
-        assert out["BOLD"]["confounds"]["path"].is_file()
-
-        # assert BOLD.mask
-        assert out["BOLD"]["mask"]["path"].exists()
-
-        # asserts type "T1w"
-        assert "T1w" in out
-
-        assert (
-            out["T1w"]["path"].name == f"{sub}_space-MNI152NLin2009cAsym_"
-            "desc-preproc_T1w.nii.gz"
-        )
-
-        assert out["T1w"]["path"].exists()
-        assert out["T1w"]["path"].is_file()
-
-        # asserts T1w.mask
-        assert out["T1w"]["mask"]["path"].exists()
-
-        # asserts type "VBM_CSF"
-        assert "VBM_CSF" in out
-
-        assert (
-            out["VBM_CSF"]["path"].name
-            == f"{sub}_space-MNI152NLin2009cAsym_label-"
-            "CSF_probseg.nii.gz"
-        )
-
-        assert out["VBM_CSF"]["path"].exists()
-        assert out["VBM_CSF"]["path"].is_file()
-
-        # asserts type "VBM_GM"
-        assert "VBM_GM" in out
-
-        assert (
-            out["VBM_GM"]["path"].name
-            == f"{sub}_space-MNI152NLin2009cAsym_label-"
-            "GM_probseg.nii.gz"
-        )
-
-        assert out["VBM_GM"]["path"].exists()
-        assert out["VBM_GM"]["path"].is_file()
-
-        # asserts type "VBM_WM"
-        assert "VBM_WM" in out
-
-        assert (
-            out["VBM_WM"]["path"].name
-            == f"{sub}_space-MNI152NLin2009cAsym_label-"
-            "WM_probseg.nii.gz"
-        )
-
-        assert out["VBM_WM"]["path"].exists()
-        assert out["VBM_WM"]["path"].is_file()
-
-        # asserts type "DWI"
-        assert "DWI" in out
-
-        assert out["DWI"]["path"].name == f"{sub}_desc-preproc_dwi.nii.gz"
-
-        assert out["DWI"]["path"].exists()
-        assert out["DWI"]["path"].is_file()
-
-        # asserts meta
-        assert "meta" in out["BOLD"]
-        meta = out["BOLD"]["meta"]
         assert "element" in meta
         assert "subject" in meta["element"]
-        assert sub == meta["element"]["subject"]
+        assert test_element[0] == meta["element"]["subject"]
+        # Assert nested data type if not None
+        if nested_types is not None:
+            for nested_type in nested_types:
+                assert out[type_][nested_type]["path"].exists()
+                assert out[type_][nested_type]["path"].is_file()
 
 
 @pytest.mark.parametrize(

junifer/datagrabber/utils.py

@@ -53,6 +53,17 @@ PATTERNS_SCHEMA = {
         "mandatory": ["pattern"],
         "optional": {},
     },
+    "FreeSurfer": {
+        "mandatory": ["pattern"],
+        "optional": {
+            "aseg": {"mandatory": ["pattern"], "optional": []},
+            "norm": {"mandatory": ["pattern"], "optional": []},
+            "lh_white": {"mandatory": ["pattern"], "optional": []},
+            "rh_white": {"mandatory": ["pattern"], "optional": []},
+            "lh_pial": {"mandatory": ["pattern"], "optional": []},
+            "rh_pial": {"mandatory": ["pattern"], "optional": []},
+        },
+    },
 }
 
 

junifer/datareader/default.py

@@ -103,8 +103,8 @@ class DefaultDataReader(PipelineStepMixin, UpdateMetaMixin):
             params = {}
         # For each type of data, try to read it
         for type_key, type_val in input.items():
-            # Skip Warp data type
+            # Skip Warp and FreeSurfer data type
-            if type_key == "Warp":
+            if type_key in ["Warp", "FreeSurfer"]:
                 continue
 
             # Check for malformed datagrabber specification

tools/create_aomic1000_example_dataset.py

@@ -24,7 +24,7 @@ with TemporaryDirectory() as tmpdir_name:
     base_dir = tmpdir / "derivatives"
     base_dir.mkdir(exist_ok=True, parents=True)
 
-    for dtype in ["dwipreproc", "fmriprep"]:
+    for dtype in ["dwipreproc", "fmriprep", "freesurfer"]:
         dtype_dir = base_dir / dtype
         dtype_dir.mkdir()
 
@@ -88,10 +88,46 @@ with TemporaryDirectory() as tmpdir_name:
                     (f"{dname}/{t_sub}_desc-preproc_dwi.nii.gz"),
                 ]
 
+            elif dtype == "freesurfer":
+                for dname in ["mri", "surf"]:
+                    (sub_dir / dname).mkdir()
+
+                fnames = [
+                    ("mri/T1.mgz"),
+                    ("mri/aseg.mgz"),
+                    ("mri/norm.mgz"),
+                    ("surf/lh.white"),
+                    ("surf/rh.white"),
+                    ("surf/lh.pial"),
+                    ("surf/rh.pial"),
+                ]
+
             for fname in fnames:
                 with open(sub_dir / fname, "w") as f:
                     f.write("placeholder")
 
+        if dtype == "freesurfer":
+            for extra in ["fsaverage", "fsaverage5"]:
+                extra_dir = dtype_dir / extra
+                extra_dir.mkdir()
+
+                for dname in ["mri", "surf"]:
+                    (extra_dir / dname).mkdir()
+
+                fnames = [
+                    ("mri/T1.mgz"),
+                    ("mri/aseg.mgz"),
+                    ("mri/norm.mgz"),
+                    ("surf/lh.white"),
+                    ("surf/rh.white"),
+                    ("surf/lh.pial"),
+                    ("surf/rh.pial"),
+                ]
+
+                for fname in fnames:
+                    with open(extra_dir / fname, "w") as f:
+                        f.write("placeholder")
+
     ds.save(recursive=True)
     # use this to create the repo automatically, only possible for juaml owner
     # ds.create_sibling_gin(

tools/create_aomicpiop1_example_dataset.py

@@ -20,7 +20,7 @@ with TemporaryDirectory() as tmpdir_name:
     base_dir = tmpdir / "derivatives"
     base_dir.mkdir(exist_ok=True, parents=True)
 
-    for dtype in ["dwipreproc", "fmriprep"]:
+    for dtype in ["dwipreproc", "fmriprep", "freesurfer"]:
         dtype_dir = base_dir / dtype
         dtype_dir.mkdir()
 
@@ -94,10 +94,46 @@ with TemporaryDirectory() as tmpdir_name:
                     (f"{dname}/{t_sub}_desc-preproc_dwi.nii.gz"),
                 ]
 
+            elif dtype == "freesurfer":
+                for dname in ["mri", "surf"]:
+                    (sub_dir / dname).mkdir()
+
+                fnames = [
+                    ("mri/T1.mgz"),
+                    ("mri/aseg.mgz"),
+                    ("mri/norm.mgz"),
+                    ("surf/lh.white"),
+                    ("surf/rh.white"),
+                    ("surf/lh.pial"),
+                    ("surf/rh.pial"),
+                ]
+
             for fname in fnames:
                 with open(sub_dir / fname, "w") as f:
                     f.write("placeholder")
 
+        if dtype == "freesurfer":
+            for extra in ["fsaverage", "fsaverage5"]:
+                extra_dir = dtype_dir / extra
+                extra_dir.mkdir()
+
+                for dname in ["mri", "surf"]:
+                    (extra_dir / dname).mkdir()
+
+                fnames = [
+                    ("mri/T1.mgz"),
+                    ("mri/aseg.mgz"),
+                    ("mri/norm.mgz"),
+                    ("surf/lh.white"),
+                    ("surf/rh.white"),
+                    ("surf/lh.pial"),
+                    ("surf/rh.pial"),
+                ]
+
+                for fname in fnames:
+                    with open(extra_dir / fname, "w") as f:
+                        f.write("placeholder")
+
     ds.save(recursive=True)
     # use this to create the repo automatically, only possible for juaml owner
     # ds.create_sibling_gin(

tools/create_aomicpiop2_example_dataset.py

@@ -20,7 +20,7 @@ with TemporaryDirectory() as tmpdir_name:
     base_dir = tmpdir / "derivatives"
     base_dir.mkdir(exist_ok=True, parents=True)
 
-    for dtype in ["dwipreproc", "fmriprep"]:
+    for dtype in ["dwipreproc", "fmriprep", "freesurfer"]:
         dtype_dir = base_dir / dtype
         dtype_dir.mkdir()
 
@@ -92,10 +92,46 @@ with TemporaryDirectory() as tmpdir_name:
                     (f"{dname}/{t_sub}_desc-preproc_dwi.nii.gz"),
                 ]
 
+            elif dtype == "freesurfer":
+                for dname in ["mri", "surf"]:
+                    (sub_dir / dname).mkdir()
+
+                fnames = [
+                    ("mri/T1.mgz"),
+                    ("mri/aseg.mgz"),
+                    ("mri/norm.mgz"),
+                    ("surf/lh.white"),
+                    ("surf/rh.white"),
+                    ("surf/lh.pial"),
+                    ("surf/rh.pial"),
+                ]
+
             for fname in fnames:
                 with open(sub_dir / fname, "w") as f:
                     f.write("placeholder")
 
+        if dtype == "freesurfer":
+            for extra in ["fsaverage", "fsaverage5"]:
+                extra_dir = dtype_dir / extra
+                extra_dir.mkdir()
+
+                for dname in ["mri", "surf"]:
+                    (extra_dir / dname).mkdir()
+
+                fnames = [
+                    ("mri/T1.mgz"),
+                    ("mri/aseg.mgz"),
+                    ("mri/norm.mgz"),
+                    ("surf/lh.white"),
+                    ("surf/rh.white"),
+                    ("surf/lh.pial"),
+                    ("surf/rh.pial"),
+                ]
+
+                for fname in fnames:
+                    with open(extra_dir / fname, "w") as f:
+                        f.write("placeholder")
+
     ds.save(recursive=True)
     # use this to create the repo automatically, only possible for juaml owner
     # ds.create_sibling_gin(