junifer 0.0.4.dev814__tar.gz → 0.0.4.dev824__tar.gz

{junifer-0.0.4.dev814 → junifer-0.0.4.dev824}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.4.dev814
+Version: 0.0.4.dev824
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>

junifer-0.0.4.dev824/docs/changes/newsfragments/320.change

@@ -0,0 +1 @@
+Change all ``probseg_`` types to ``VBM_`` types by `Fede Raimondo`_

junifer-0.0.4.dev824/docs/changes/newsfragments/320.fix

@@ -0,0 +1 @@
+Add a validation step on the :func:`.run` function to validate the marker collection by `Fede Raimondo`_

junifer-0.0.4.dev824/docs/changes/newsfragments/322.bugfix

@@ -0,0 +1 @@
+Force ``str`` dtype when parsing elements from file by `Synchon Mandal`_

{junifer-0.0.4.dev814 → junifer-0.0.4.dev824}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.4.dev814'
-__version_tuple__ = version_tuple = (0, 0, 4, 'dev814')
+__version__ = version = '0.0.4.dev824'
+__version_tuple__ = version_tuple = (0, 0, 4, 'dev824')

{junifer-0.0.4.dev814 → junifer-0.0.4.dev824}/junifer/api/cli.py

@@ -114,14 +114,13 @@ def _parse_elements_file(filepath: Path) -> List[Tuple[str, ...]]:
         filepath,
         header=None,  # no header  # type: ignore
         index_col=False,  # no index column
+        dtype=str,
         skipinitialspace=True,  # no leading space after delimiter
     )
     # Remove trailing whitespace in cell entries
-    csv_df_trimmed = csv_df.apply(
-        lambda x: x.str.strip() if x.dtype == "object" else x
-    )
+    csv_df_trimmed = csv_df.apply(lambda x: x.str.strip())
     # Convert to list of tuple of str
-    return list(map(tuple, csv_df_trimmed.to_numpy().astype(str)))
+    return list(map(tuple, csv_df_trimmed.to_numpy()))
 
 
 def _validate_verbose(

{junifer-0.0.4.dev814 → junifer-0.0.4.dev824}/junifer/api/functions.py

@@ -165,6 +165,8 @@ def run(
         preprocessors=built_preprocessors,
         storage=storage_object,
     )
+    mc.validate(datagrabber_object)
+
     # Fit elements
     with datagrabber_object:
         if elements is not None:

{junifer-0.0.4.dev814 → junifer-0.0.4.dev824}/junifer/api/tests/test_cli.py

@@ -156,6 +156,21 @@ def test_run_using_element_file(tmp_path: Path, elements: str) -> None:
             " sub-01 , ses-01 \n sub-02, ses-01 ",
             [("sub-01", "ses-01"), ("sub-02", "ses-01")],
         ),
+        ("001,01", [("001", "01")]),
+        (
+            "001,01\n002,02",
+            [("001", "01"), ("002", "02")],
+        ),
+        ("001, 01", [("001", "01")]),
+        (
+            "001, 01\n002, 02",
+            [("001", "01"), ("002", "02")],
+        ),
+        (" 001 , 01 ", [("001", "01")]),
+        (
+            " 001 , 01 \n 002, 02 ",
+            [("001", "01"), ("002", "02")],
+        ),
     ],
 )
 def test_multi_element_access(

{junifer-0.0.4.dev814 → junifer-0.0.4.dev824}/junifer/configs/juseless/datagrabbers/tests/test_ucla.py

@@ -29,9 +29,9 @@ def test_JuselessUCLA() -> None:
             "BOLD",
             "BOLD_confounds",
             "T1w",
-            "probseg_CSF",
-            "probseg_GM",
-            "probseg_WM",
+            "VBM_CSF",
+            "VBM_GM",
+            "VBM_WM",
         ]
 
         for t in types:
@@ -45,12 +45,12 @@ def test_JuselessUCLA() -> None:
         "BOLD",
         "BOLD_confounds",
         "T1w",
-        "probseg_CSF",
-        "probseg_GM",
-        "probseg_WM",
+        "VBM_CSF",
+        "VBM_GM",
+        "VBM_WM",
         ["BOLD", "BOLD_confounds"],
-        ["T1w", "probseg_CSF"],
-        ["probseg_GM", "probseg_WM"],
+        ["T1w", "VBM_CSF"],
+        ["VBM_GM", "VBM_WM"],
         ["BOLD", "T1w"],
     ],
 )

{junifer-0.0.4.dev814 → junifer-0.0.4.dev824}/junifer/configs/juseless/datagrabbers/ucla.py

@@ -23,8 +23,8 @@ class JuselessUCLA(PatternDataGrabber):
     datadir : str or Path, optional
         The directory where the dataset is stored.
         (default "/data/project/psychosis_thalamus/data/fmriprep").
-    types: {"BOLD", "BOLD_confounds", "T1w", "probseg_CSF", "probseg_GM", \
-           "probseg_WM"} or a list of the options, optional
+    types: {"BOLD", "BOLD_confounds", "T1w", "VBM_CSF", "VBM_GM", \
+           "VBM_WM"} or a list of the options, optional
         UCLA data types. If None, all available data types are selected.
         (default None).
     tasks : {"rest", "bart", "bht", "pamenc", "pamret", \
@@ -91,21 +91,21 @@ class JuselessUCLA(PatternDataGrabber):
                 ),
                 "space": "MNI152NLin2009cAsym",
             },
-            "probseg_CSF": {
+            "VBM_CSF": {
                 "pattern": (
                     "sub-{subject}/anat/sub-{subject}_T1w_space-"
                     "MNI152NLin2009cAsym_class-CSF_probtissue.nii.gz"
                 ),
                 "space": "MNI152NLin2009cAsym",
             },
-            "probseg_GM": {
+            "VBM_GM": {
                 "pattern": (
                     "sub-{subject}/anat/sub-{subject}_T1w_space-"
                     "MNI152NLin2009cAsym_class-GM_probtissue.nii.gz"
                 ),
                 "space": "MNI152NLin2009cAsym",
             },
-            "probseg_WM": {
+            "VBM_WM": {
                 "pattern": (
                     "sub-{subject}/anat/sub-{subject}_T1w_space"
                     "-MNI152NLin2009cAsym_class-WM_probtissue.nii.gz"

{junifer-0.0.4.dev814 → junifer-0.0.4.dev824}/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", "BOLD_confounds", "T1w", "probseg_CSF", "probseg_GM", \
-           "probseg_WM", "DWI"} or a list of the options, optional
+    types: {"BOLD", "BOLD_confounds", "T1w", "VBM_CSF", "VBM_GM", \
+           "VBM_WM", "DWI"} or a list of the options, optional
         AOMIC data types. If None, all available data types are selected.
         (default None).
     native_t1w : bool, optional
@@ -84,7 +84,7 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
                 ),
                 "space": "MNI152NLin2009cAsym",
             },
-            "probseg_CSF": {
+            "VBM_CSF": {
                 "pattern": (
                     "derivatives/fmriprep/sub-{subject}/anat/"
                     "sub-{subject}_space-MNI152NLin2009cAsym_label-"
@@ -92,7 +92,7 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
                 ),
                 "space": "MNI152NLin2009cAsym",
             },
-            "probseg_GM": {
+            "VBM_GM": {
                 "pattern": (
                     "derivatives/fmriprep/sub-{subject}/anat/"
                     "sub-{subject}_space-MNI152NLin2009cAsym_label-"
@@ -100,7 +100,7 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
                 ),
                 "space": "MNI152NLin2009cAsym",
             },
-            "probseg_WM": {
+            "VBM_WM": {
                 "pattern": (
                     "derivatives/fmriprep/sub-{subject}/anat/"
                     "sub-{subject}_space-MNI152NLin2009cAsym_label-"

{junifer-0.0.4.dev814 → junifer-0.0.4.dev824}/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", "BOLD_confounds", "T1w", "probseg_CSF", "probseg_GM", \
-           "probseg_WM", "DWI"} or a list of the options, optional
+    types: {"BOLD", "BOLD_confounds", "T1w", "VBM_CSF", "VBM_GM", \
+           "VBM_WM", "DWI"} or a list of the options, optional
         AOMIC data types. If None, all available data types are selected.
         (default None).
     tasks : {"restingstate", "anticipation", "emomatching", "faces", \
@@ -119,7 +119,7 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
                 ),
                 "space": "MNI152NLin2009cAsym",
             },
-            "probseg_CSF": {
+            "VBM_CSF": {
                 "pattern": (
                     "derivatives/fmriprep/sub-{subject}/anat/"
                     "sub-{subject}_space-MNI152NLin2009cAsym_label-"
@@ -127,7 +127,7 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
                 ),
                 "space": "MNI152NLin2009cAsym",
             },
-            "probseg_GM": {
+            "VBM_GM": {
                 "pattern": (
                     "derivatives/fmriprep/sub-{subject}/anat/"
                     "sub-{subject}_space-MNI152NLin2009cAsym_label-"
@@ -135,7 +135,7 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
                 ),
                 "space": "MNI152NLin2009cAsym",
             },
-            "probseg_WM": {
+            "VBM_WM": {
                 "pattern": (
                     "derivatives/fmriprep/sub-{subject}/anat/"
                     "sub-{subject}_space-MNI152NLin2009cAsym_label-"

{junifer-0.0.4.dev814 → junifer-0.0.4.dev824}/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", "BOLD_confounds", "T1w", "probseg_CSF", "probseg_GM", \
-           "probseg_WM", "DWI"} or a list of the options, optional
+    types: {"BOLD", "BOLD_confounds", "T1w", "VBM_CSF", "VBM_GM", \
+           "VBM_WM", "DWI"} or a list of the options, optional
         AOMIC data types. If None, all available data types are selected.
         (default None).
     tasks : {"restingstate", "stopsignal", "workingmemory"} \
@@ -116,7 +116,7 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
                 ),
                 "space": "MNI152NLin2009cAsym",
             },
-            "probseg_CSF": {
+            "VBM_CSF": {
                 "pattern": (
                     "derivatives/fmriprep/sub-{subject}/anat/"
                     "sub-{subject}_space-MNI152NLin2009cAsym_label-"
@@ -124,7 +124,7 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
                 ),
                 "space": "MNI152NLin2009cAsym",
             },
-            "probseg_GM": {
+            "VBM_GM": {
                 "pattern": (
                     "derivatives/fmriprep/sub-{subject}/anat/"
                     "sub-{subject}_space-MNI152NLin2009cAsym_label-"
@@ -132,7 +132,7 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
                 ),
                 "space": "MNI152NLin2009cAsym",
             },
-            "probseg_WM": {
+            "VBM_WM": {
                 "pattern": (
                     "derivatives/fmriprep/sub-{subject}/anat/"
                     "sub-{subject}_space-MNI152NLin2009cAsym_label-"

{junifer-0.0.4.dev814 → junifer-0.0.4.dev824}/junifer/datagrabber/aomic/tests/test_id1000.py

@@ -71,41 +71,41 @@ def test_DataladAOMICID1000() -> None:
         # asserts T1w_mask
         assert out["T1w_mask"]["path"].exists()
 
-        # asserts type "probseg_CSF"
-        assert "probseg_CSF" in out
+        # asserts type "VBM_CSF"
+        assert "VBM_CSF" in out
 
         assert (
-            out["probseg_CSF"]["path"].name
+            out["VBM_CSF"]["path"].name
             == f"sub-{test_element}_space-MNI152NLin2009cAsym_label-"
             "CSF_probseg.nii.gz"
         )
 
-        assert out["probseg_CSF"]["path"].exists()
-        assert out["probseg_CSF"]["path"].is_file()
+        assert out["VBM_CSF"]["path"].exists()
+        assert out["VBM_CSF"]["path"].is_file()
 
-        # asserts type "probseg_GM"
-        assert "probseg_GM" in out
+        # asserts type "VBM_GM"
+        assert "VBM_GM" in out
 
         assert (
-            out["probseg_GM"]["path"].name
+            out["VBM_GM"]["path"].name
             == f"sub-{test_element}_space-MNI152NLin2009cAsym_label-"
             "GM_probseg.nii.gz"
         )
 
-        assert out["probseg_GM"]["path"].exists()
-        assert out["probseg_GM"]["path"].is_file()
+        assert out["VBM_GM"]["path"].exists()
+        assert out["VBM_GM"]["path"].is_file()
 
-        # asserts type "probseg_WM"
-        assert "probseg_WM" in out
+        # asserts type "VBM_WM"
+        assert "VBM_WM" in out
 
         assert (
-            out["probseg_WM"]["path"].name
+            out["VBM_WM"]["path"].name
             == f"sub-{test_element}_space-MNI152NLin2009cAsym_label-"
             "WM_probseg.nii.gz"
         )
 
-        assert out["probseg_WM"]["path"].exists()
-        assert out["probseg_WM"]["path"].is_file()
+        assert out["VBM_WM"]["path"].exists()
+        assert out["VBM_WM"]["path"].is_file()
 
         # asserts type "DWI"
         assert "DWI" in out
@@ -132,13 +132,13 @@ def test_DataladAOMICID1000() -> None:
         "BOLD",
         "BOLD_confounds",
         "T1w",
-        "probseg_CSF",
-        "probseg_GM",
-        "probseg_WM",
+        "VBM_CSF",
+        "VBM_GM",
+        "VBM_WM",
         "DWI",
         ["BOLD", "BOLD_confounds"],
-        ["T1w", "probseg_CSF"],
-        ["probseg_GM", "probseg_WM"],
+        ["T1w", "VBM_CSF"],
+        ["VBM_GM", "VBM_WM"],
         ["DWI", "BOLD"],
     ],
 )

{junifer-0.0.4.dev814 → junifer-0.0.4.dev824}/junifer/datagrabber/aomic/tests/test_piop1.py

@@ -91,41 +91,41 @@ def test_DataladAOMICPIOP1(tasks: Optional[str]) -> None:
         # asserts T1w_mask
         assert out["T1w_mask"]["path"].exists()
 
-        # asserts type "probseg_CSF"
-        assert "probseg_CSF" in out
+        # asserts type "VBM_CSF"
+        assert "VBM_CSF" in out
 
         assert (
-            out["probseg_CSF"]["path"].name
+            out["VBM_CSF"]["path"].name
             == f"sub-{sub}_space-MNI152NLin2009cAsym_label-"
             "CSF_probseg.nii.gz"
         )
 
-        assert out["probseg_CSF"]["path"].exists()
-        assert out["probseg_CSF"]["path"].is_file()
+        assert out["VBM_CSF"]["path"].exists()
+        assert out["VBM_CSF"]["path"].is_file()
 
-        # asserts type "probseg_GM"
-        assert "probseg_GM" in out
+        # asserts type "VBM_GM"
+        assert "VBM_GM" in out
 
         assert (
-            out["probseg_GM"]["path"].name
+            out["VBM_GM"]["path"].name
             == f"sub-{sub}_space-MNI152NLin2009cAsym_label-"
             "GM_probseg.nii.gz"
         )
 
-        assert out["probseg_GM"]["path"].exists()
-        assert out["probseg_GM"]["path"].is_file()
+        assert out["VBM_GM"]["path"].exists()
+        assert out["VBM_GM"]["path"].is_file()
 
-        # asserts type "probseg_WM"
-        assert "probseg_WM" in out
+        # asserts type "VBM_WM"
+        assert "VBM_WM" in out
 
         assert (
-            out["probseg_WM"]["path"].name
+            out["VBM_WM"]["path"].name
             == f"sub-{sub}_space-MNI152NLin2009cAsym_label-"
             "WM_probseg.nii.gz"
         )
 
-        assert out["probseg_WM"]["path"].exists()
-        assert out["probseg_WM"]["path"].is_file()
+        assert out["VBM_WM"]["path"].exists()
+        assert out["VBM_WM"]["path"].is_file()
 
         # asserts type "DWI"
         assert "DWI" in out
@@ -149,13 +149,13 @@ def test_DataladAOMICPIOP1(tasks: Optional[str]) -> None:
         "BOLD",
         "BOLD_confounds",
         "T1w",
-        "probseg_CSF",
-        "probseg_GM",
-        "probseg_WM",
+        "VBM_CSF",
+        "VBM_GM",
+        "VBM_WM",
         "DWI",
         ["BOLD", "BOLD_confounds"],
-        ["T1w", "probseg_CSF"],
-        ["probseg_GM", "probseg_WM"],
+        ["T1w", "VBM_CSF"],
+        ["VBM_GM", "VBM_WM"],
         ["DWI", "BOLD"],
     ],
 )

{junifer-0.0.4.dev814 → junifer-0.0.4.dev824}/junifer/datagrabber/aomic/tests/test_piop2.py

@@ -85,41 +85,41 @@ def test_DataladAOMICPIOP2(tasks: Optional[str]) -> None:
         # asserts T1w_mask
         assert out["T1w_mask"]["path"].exists()
 
-        # asserts type "probseg_CSF"
-        assert "probseg_CSF" in out
+        # asserts type "VBM_CSF"
+        assert "VBM_CSF" in out
 
         assert (
-            out["probseg_CSF"]["path"].name
+            out["VBM_CSF"]["path"].name
             == f"sub-{sub}_space-MNI152NLin2009cAsym_label-"
             "CSF_probseg.nii.gz"
         )
 
-        assert out["probseg_CSF"]["path"].exists()
-        assert out["probseg_CSF"]["path"].is_file()
+        assert out["VBM_CSF"]["path"].exists()
+        assert out["VBM_CSF"]["path"].is_file()
 
-        # asserts type "probseg_GM"
-        assert "probseg_GM" in out
+        # asserts type "VBM_GM"
+        assert "VBM_GM" in out
 
         assert (
-            out["probseg_GM"]["path"].name
+            out["VBM_GM"]["path"].name
             == f"sub-{sub}_space-MNI152NLin2009cAsym_label-"
             "GM_probseg.nii.gz"
         )
 
-        assert out["probseg_GM"]["path"].exists()
-        assert out["probseg_GM"]["path"].is_file()
+        assert out["VBM_GM"]["path"].exists()
+        assert out["VBM_GM"]["path"].is_file()
 
-        # asserts type "probseg_WM"
-        assert "probseg_WM" in out
+        # asserts type "VBM_WM"
+        assert "VBM_WM" in out
 
         assert (
-            out["probseg_WM"]["path"].name
+            out["VBM_WM"]["path"].name
             == f"sub-{sub}_space-MNI152NLin2009cAsym_label-"
             "WM_probseg.nii.gz"
         )
 
-        assert out["probseg_WM"]["path"].exists()
-        assert out["probseg_WM"]["path"].is_file()
+        assert out["VBM_WM"]["path"].exists()
+        assert out["VBM_WM"]["path"].is_file()
 
         # asserts type "DWI"
         assert "DWI" in out
@@ -143,13 +143,13 @@ def test_DataladAOMICPIOP2(tasks: Optional[str]) -> None:
         "BOLD",
         "BOLD_confounds",
         "T1w",
-        "probseg_CSF",
-        "probseg_GM",
-        "probseg_WM",
+        "VBM_CSF",
+        "VBM_GM",
+        "VBM_WM",
         "DWI",
         ["BOLD", "BOLD_confounds"],
-        ["T1w", "probseg_CSF"],
-        ["probseg_GM", "probseg_WM"],
+        ["T1w", "VBM_CSF"],
+        ["VBM_GM", "VBM_WM"],
         ["DWI", "BOLD"],
     ],
 )

{junifer-0.0.4.dev814 → junifer-0.0.4.dev824}/junifer/datagrabber/dmcc13_benchmark.py

@@ -25,8 +25,8 @@ class DMCC13Benchmark(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", "BOLD_confounds", "T1w", "probseg_CSF", "probseg_GM", \
-           "probseg_WM"} or a list of the options, optional
+    types: {"BOLD", "BOLD_confounds", "T1w", "VBM_CSF", "VBM_GM", \
+           "VBM_WM"} or a list of the options, optional
         DMCC data types. If None, all available data types are selected.
         (default None).
     sessions: {"wave1bas", "wave1pro", "wave1rea"} or list of the options, \
@@ -181,21 +181,21 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
                 ),
                 "space": "MNI152NLin2009cAsym",
             },
-            "probseg_CSF": {
+            "VBM_CSF": {
                 "pattern": (
                     "derivatives/fmriprep-1.3.2/sub-{subject}/anat/"
                     "sub-{subject}_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz"
                 ),
                 "space": "MNI152NLin2009cAsym",
             },
-            "probseg_GM": {
+            "VBM_GM": {
                 "pattern": (
                     "derivatives/fmriprep-1.3.2/sub-{subject}/anat/"
                     "sub-{subject}_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz"
                 ),
                 "space": "MNI152NLin2009cAsym",
             },
-            "probseg_WM": {
+            "VBM_WM": {
                 "pattern": (
                     "derivatives/fmriprep-1.3.2/sub-{subject}/anat/"
                     "sub-{subject}_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz"

{junifer-0.0.4.dev814 → junifer-0.0.4.dev824}/junifer/datagrabber/tests/test_dmcc13_benchmark.py

@@ -95,9 +95,9 @@ def test_DMCC13Benchmark(
             "BOLD",
             "BOLD_confounds",
             "BOLD_mask",
-            "probseg_CSF",
-            "probseg_GM",
-            "probseg_WM",
+            "VBM_CSF",
+            "VBM_GM",
+            "VBM_WM",
             "T1w",
             "T1w_mask",
         ]
@@ -159,18 +159,18 @@ def test_DMCC13Benchmark(
         ("BOLD", False),
         ("T1w", True),
         ("T1w", False),
-        ("probseg_CSF", True),
-        ("probseg_CSF", False),
-        ("probseg_GM", True),
-        ("probseg_GM", False),
-        ("probseg_WM", True),
-        ("probseg_WM", False),
+        ("VBM_CSF", True),
+        ("VBM_CSF", False),
+        ("VBM_GM", True),
+        ("VBM_GM", False),
+        ("VBM_WM", True),
+        ("VBM_WM", False),
         (["BOLD", "BOLD_confounds"], True),
         (["BOLD", "BOLD_confounds"], False),
-        (["T1w", "probseg_CSF"], True),
-        (["T1w", "probseg_CSF"], False),
-        (["probseg_GM", "probseg_WM"], True),
-        (["probseg_GM", "probseg_WM"], False),
+        (["T1w", "VBM_CSF"], True),
+        (["T1w", "VBM_CSF"], False),
+        (["VBM_GM", "VBM_WM"], True),
+        (["VBM_GM", "VBM_WM"], False),
     ],
 )
 def test_DMCC13Benchmark_partial_data_access(

{junifer-0.0.4.dev814 → junifer-0.0.4.dev824}/junifer/datagrabber/utils.py

@@ -51,15 +51,7 @@ PATTERNS_SCHEMA = {
         "mandatory": ["pattern", "space"],
         "optional": [],
     },
-    "probseg_CSF": {
-        "mandatory": ["pattern", "space"],
-        "optional": [],
-    },
-    "probseg_GM": {
-        "mandatory": ["pattern", "space"],
-        "optional": [],
-    },
-    "probseg_WM": {
+    "VBM_CSF": {
         "mandatory": ["pattern", "space"],
         "optional": [],
     },

{junifer-0.0.4.dev814 → junifer-0.0.4.dev824}/junifer/markers/parcel_aggregation.py

@@ -42,8 +42,8 @@ class ParcelAggregation(BaseMarker):
         The specification of the masks to apply to regions before extracting
         signals. Check :ref:`Using Masks <using_masks>` for more details.
         If None, will not apply any mask (default None).
-    on : {"T1w", "BOLD", "VBM_GM", "VBM_WM", "fALFF", "GCOR", "LCOR"} \
-         or list of the options, optional
+    on : {"T1w", "T2w", "BOLD", "VBM_GM", "VBM_WM", "VBM_CSF", "fALFF", \
+        "GCOR", "LCOR"} or list of the options, optional
         The data types to apply the marker to. If None, will work on all
         available data (default None).
     name : str, optional
@@ -102,7 +102,17 @@ class ParcelAggregation(BaseMarker):
             The list of data types that can be used as input for this marker.
 
         """
-        return ["T1w", "BOLD", "VBM_GM", "VBM_WM", "fALFF", "GCOR", "LCOR"]
+        return [
+            "T1w",
+            "T2w",
+            "BOLD",
+            "VBM_GM",
+            "VBM_WM",
+            "VBM_CSF",
+            "fALFF",
+            "GCOR",
+            "LCOR",
+        ]
 
     def get_output_type(self, input_type: str) -> str:
         """Get output type.
@@ -124,7 +134,14 @@ class ParcelAggregation(BaseMarker):
 
         """
 
-        if input_type in ["VBM_GM", "VBM_WM", "fALFF", "GCOR", "LCOR"]:
+        if input_type in [
+            "VBM_GM",
+            "VBM_WM",
+            "VBM_CSF",
+            "fALFF",
+            "GCOR",
+            "LCOR",
+        ]:
             return "vector"
         elif input_type == "BOLD":
             return "timeseries"