junifer 0.0.4.dev831__tar.gz → 0.0.5__tar.gz

{junifer-0.0.4.dev831 → junifer-0.0.5}/.github/workflows/ci.yml

@@ -66,36 +66,43 @@ jobs:
         sudo tcsh @update.afni.binaries -package linux_ubuntu_16_64 -bindir /afni
         echo "/afni" >> $GITHUB_PATH
       if: matrix.python-version == 3.11
+      # Bypass AFNI installation failure
+      continue-on-error: true
     - name: Check AFNI
       run: |
         echo "Using AFNI : $(afni --version)"
       if: matrix.python-version == 3.11
+      # Bypass AFNI installation failure
+      continue-on-error: true
     - name: Install ANTs
       run: |
         sudo apt-get install -y -qq unzip
-        curl -fsSL -o ants.zip https://github.com/ANTsX/ANTs/releases/download/v2.5.1/ants-2.5.1-ubuntu-22.04-X64-gcc.zip
+        curl -fsSL -o ants.zip https://github.com/ANTsX/ANTs/releases/download/v2.5.2/ants-2.5.2-ubuntu-22.04-X64-gcc.zip
         unzip ants.zip -d /opt
-        mv /opt/ants-2.5.1/bin/* /opt/ants-2.5.1
+        mv /opt/ants-2.5.2/bin/* /opt/ants-2.5.2
         rm ants.zip
-        echo "/opt/ants-2.5.1" >> $GITHUB_PATH
+        echo "/opt/ants-2.5.2" >> $GITHUB_PATH
       if: matrix.python-version == 3.11
+      # Bypass ANTs installation failure
+      continue-on-error: true
     - name: Check ANTs
       run: |
         echo "Using ANTs : $(antsRegistration --version)"
       if: matrix.python-version == 3.11
+      # Bypass ANTs installation failure
+      continue-on-error: true
     - name: Install FSL
       run: |
-        sudo apt-get install -y -qq python3
-        curl -fsSL https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py | python3 - -d /opt/fsl-6.0.6.4 -V 6.0.6.4
+        curl -fsSL https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py | python - -d /opt/fsl/
         FSLOUTPUTTYPE="NIFTI_GZ"
         FSLMULTIFILEQUIT="TRUE"
-        FSLTCLSH="/opt/fsl-6.0.6.4/bin/fsltclsh"
-        FSLWISH="/opt/fsl-6.0.6.4/bin/fslwish"
+        FSLTCLSH="/opt/fsl/bin/fsltclsh"
+        FSLWISH="/opt/fsl/bin/fslwish"
         FSLLOCKDIR=""
         FSLMACHINELIST=""
         FSLREMOTECALL=""
         FSLGECUDAQ="cuda.q"
-        echo "/opt/fsl-6.0.6.4" >> $GITHUB_PATH
+        echo "/opt/fsl" >> $GITHUB_PATH
       if: matrix.python-version == 3.11
       # Bypass FSL installation failure
       continue-on-error: true

{junifer-0.0.4.dev831 → junifer-0.0.5}/.github/workflows/docs.yml

@@ -68,7 +68,7 @@ jobs:
         touch docs/_build/.nojekyll
         cp docs/redirect.html docs/_build/index.html
     - name: Publish docs to gh-pages
-      uses: peaceiris/actions-gh-pages@v3
+      uses: peaceiris/actions-gh-pages@v4
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         publish_dir: docs/_build

junifer-0.0.5/.gitmodules

@@ -0,0 +1,6 @@
+[submodule "junifer/external/h5io"]
+	path = junifer/external/h5io
+	url = https://github.com/juaml/h5io
+[submodule "junifer/external/BrainPrint"]
+	path = junifer/external/BrainPrint
+	url = https://github.com/juaml/BrainPrint.git

{junifer-0.0.4.dev831 → junifer-0.0.5}/.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
       - id: check-ast
       - id: check-docstring-first
@@ -20,14 +20,14 @@ repos:
     rev: v0.16
     hooks:
       - id: validate-pyproject
-  - repo: https://github.com/psf/black
-    rev: 24.1.1
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 24.4.2
     hooks:
       - id: black
         exclude: ^(docs/|examples/|tools/)
         args: [--check]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.15
+    rev: v0.4.2
     hooks:
       - id: ruff
         types_or: [python, jupyter]
@@ -38,7 +38,7 @@ repos:
     hooks:
       - id: codespell
         exclude: ^(.github/|docs/)
-        args: [--config, tox.ini]
+        args: [--toml, pyproject.toml]
   - repo: https://github.com/pre-commit/pygrep-hooks
     rev: v1.10.0
     hooks:
@@ -47,3 +47,10 @@ repos:
       - id: rst-backticks
       - id: rst-directive-colons
       - id: rst-inline-touching-normal
+  - repo: https://github.com/adamchainz/blacken-docs
+    rev: "1.16.0"
+    hooks:
+      - id: blacken-docs
+        additional_dependencies:
+          - black==24.4.2
+        args: [-l 79]

{junifer-0.0.4.dev831 → junifer-0.0.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.4.dev831
+Version: 0.0.5
 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>
@@ -29,19 +29,20 @@ Description-Content-Type: text/markdown
 License-File: LICENSE.md
 License-File: AUTHORS.rst
 Requires-Dist: click<8.2,>=8.1.3
-Requires-Dist: numpy<1.27,>=1.24
-Requires-Dist: scipy<=1.11.4,>=1.9.0
-Requires-Dist: datalad<0.20,>=0.15.4
-Requires-Dist: pandas<2.2,>=1.4.0
-Requires-Dist: nibabel<5.11,>=3.2.0
-Requires-Dist: nilearn<=0.10.2,>=0.9.0
-Requires-Dist: sqlalchemy<=2.1.0,>=1.4.27
+Requires-Dist: numpy<2.0.0,>=1.24.0
+Requires-Dist: scipy<=1.14.0,>=1.10.0
+Requires-Dist: datalad<1.2.0,>=1.0.0
+Requires-Dist: pandas<2.3.0,>=2.0.0
+Requires-Dist: nibabel<5.3.0,>=5.2.0
+Requires-Dist: nilearn<=0.10.4,>=0.10.3
+Requires-Dist: sqlalchemy<=2.1.0,>=2.0.25
 Requires-Dist: ruamel.yaml<0.18,>=0.17
 Requires-Dist: h5py>=3.10
 Requires-Dist: httpx[http2]==0.26.0
 Requires-Dist: tqdm==4.66.1
 Requires-Dist: templateflow>=23.0.0
-Requires-Dist: importlib_metadata; python_version < "3.10"
+Requires-Dist: lapy<2.0.0,>=1.0.0
+Requires-Dist: importlib_metadata; python_version < "3.9"
 Requires-Dist: looseversion==1.3.0; python_version >= "3.12"
 Provides-Extra: all
 Requires-Dist: bctpy==0.6.0; extra == "all"
@@ -56,14 +57,14 @@ Provides-Extra: dev
 Requires-Dist: tox; extra == "dev"
 Requires-Dist: pre-commit; extra == "dev"
 Provides-Extra: docs
-Requires-Dist: seaborn<0.13,>=0.11.2; extra == "docs"
-Requires-Dist: sphinx<7.3,>=5.3.0; extra == "docs"
-Requires-Dist: sphinx-gallery<0.15.0,>=0.11.0; extra == "docs"
-Requires-Dist: furo<2023.10.0,>=2022.9.29; extra == "docs"
-Requires-Dist: numpydoc<1.6,>=1.5.0; extra == "docs"
-Requires-Dist: julearn<0.4,>=0.3.0; extra == "docs"
+Requires-Dist: seaborn<0.14.0,>=0.13.0; extra == "docs"
+Requires-Dist: sphinx<7.4.0,>=7.3.0; extra == "docs"
+Requires-Dist: sphinx-gallery<0.17.0,>=0.15.0; extra == "docs"
+Requires-Dist: furo<2024.6.0,>=2024.4.27; extra == "docs"
+Requires-Dist: numpydoc<1.8.0,>=1.6.0; extra == "docs"
+Requires-Dist: julearn==0.3.3; extra == "docs"
 Requires-Dist: sphinx-copybutton<0.5.3,>=0.5.1; extra == "docs"
-Requires-Dist: towncrier<23.7,>=22.12.0; extra == "docs"
+Requires-Dist: towncrier<23.12.0,>=23.10.0; extra == "docs"
 Requires-Dist: sphinxcontrib-mermaid<0.10,>=0.8.1; extra == "docs"
 
 ![Junifer logo](docs/images/junifer_logo.png "junifer logo")

{junifer-0.0.4.dev831 → junifer-0.0.5}/docs/api/nilearn.rst

@@ -1,8 +1,6 @@
 Nilearn
 =======
 
-This package provides re-implementations of some of the functions in `nilearn`_.
-
 .. automodule:: junifer.external.nilearn
    :members:
    :imported-members:

{junifer-0.0.4.dev831 → junifer-0.0.5}/docs/api/onthefly.rst

@@ -1,8 +1,6 @@
 On-the-fly
 ==========
 
-This package provides functions for quick transform operations on stored data.
-
 .. automodule:: junifer.onthefly
    :members:
    :imported-members:

{junifer-0.0.4.dev831 → junifer-0.0.5}/docs/builtin.rst

@@ -729,14 +729,6 @@ Available
      - | Compute a brain mask for the images by guessing the value of the
        | background from the border of the image.
        | See :func:`nilearn.masking.compute_background_mask`
-   * - ``nilearn``'s ICBM152 template gray-matter mask
-     - | ``fetch_icbm152_brain_gm_mask``
-     - ``MNI152NLin2009aAsym``
-     - 0.0.2
-     - | Compute a gray-matter mask from the asymmetrical ICBM152 2009 template,
-       | release a.
-       | See :func:`nilearn.datasets.fetch_icbm152_brain_gm_mask`
-
 
 ..
    Planned

{junifer-0.0.4.dev831 → junifer-0.0.5}/docs/conf.py

@@ -170,6 +170,7 @@ numpydoc_xref_ignore = {
     "Engine",
     "positive",
     "negative",
+    "estimator",
 }
 # numpydoc_validation_checks = {
 #     "all",

{junifer-0.0.4.dev831 → junifer-0.0.5}/docs/extending/coordinates.rst

@@ -70,10 +70,7 @@ with the DMN. Here, we use the DMN coordinates used in a
 .. code-block:: python
 
   dmn_coords = np.array(
-      [[0, -52, 18],
-      [-46, -68, 32],
-      [46, -68, 32],
-      [1, 50, -5]]
+      [[0, -52, 18], [-46, -68, 32], [46, -68, 32], [1, 50, -5]]
   )
   voi_names = [
       "Posterior Cingulate Cortex",
@@ -90,10 +87,7 @@ simply use this to register our coordinates:
 .. code-block:: python
 
   register_coordinates(
-      name="DMNCustom",
-      coordinates=dmn_coords,
-      voi_names=voi_names,
-      space="MNI"
+      name="DMNCustom", coordinates=dmn_coords, voi_names=voi_names, space="MNI"
   )
 
 Now, when we run this script, ``junifer`` registers these coordinates and we can

{junifer-0.0.4.dev831 → junifer-0.0.5}/docs/extending/datagrabber.rst

@@ -115,14 +115,14 @@ For example, in our BIDS example, the variables will be:
 
     types = ["T1w", "BOLD"]
     patterns = {
-       "T1w": {
-           "pattern": "{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz",
-           "space": "native",
-       },
-       "BOLD": {
-           "pattern": "{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz",
-           "space": "MNI152NLin6Asym",
-       },
+        "T1w": {
+            "pattern": "{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz",
+            "space": "native",
+        },
+        "BOLD": {
+            "pattern": "{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz",
+            "space": "MNI152NLin6Asym",
+        },
     }
     replacements = ["subject", "session"]
 
@@ -144,25 +144,24 @@ With the variables defined above, we can create our DataGrabber and name it
 
 
     class ExampleBIDSDataGrabber(PatternDataGrabber):
-
         def __init__(self, datadir: str | Path) -> None:
             types = ["T1w", "BOLD"]
             patterns = {
-               "T1w": {
-                   "pattern": "{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz",
-                   "space": "native",
-               },
-               "BOLD": {
-                   "pattern": "{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz",
-                   "space": "MNI152NLin6Asym",
-               },
+                "T1w": {
+                    "pattern": "{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz",
+                    "space": "native",
+                },
+                "BOLD": {
+                    "pattern": "{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz",
+                    "space": "MNI152NLin6Asym",
+                },
             }
             replacements = ["subject", "session"]
             super().__init__(
-               datadir=datadir,
-               types=types,
-               patterns=patterns,
-               replacements=replacements,
+                datadir=datadir,
+                types=types,
+                patterns=patterns,
+                replacements=replacements,
             )
 
 Our DataGrabber is ready to be used by ``junifer``. However, it is still unknown
@@ -180,25 +179,24 @@ use the :func:`.register_datagrabber` decorator.
 
     @register_datagrabber
     class ExampleBIDSDataGrabber(PatternDataGrabber):
-
         def __init__(self, datadir: str | Path) -> None:
             types = ["T1w", "BOLD"]
             patterns = {
-               "T1w": {
-                   "pattern": "{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz",
-                   "space": "native",
-               },
-               "BOLD": {
-                   "pattern": "{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz",
-                   "space": "MNI152NLin6Asym",
-               },
+                "T1w": {
+                    "pattern": "{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz",
+                    "space": "native",
+                },
+                "BOLD": {
+                    "pattern": "{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz",
+                    "space": "MNI152NLin6Asym",
+                },
             }
             replacements = ["subject", "session"]
             super().__init__(
-               datadir=datadir,
-               types=types,
-               patterns=patterns,
-               replacements=replacements,
+                datadir=datadir,
+                types=types,
+                patterns=patterns,
+                replacements=replacements,
             )
 
 
@@ -267,29 +265,28 @@ And we can create our DataGrabber:
 
     @register_datagrabber
     class ExampleBIDSDataGrabber(PatternDataladDataGrabber):
-
         def __init__(self) -> None:
             types = ["T1w", "BOLD"]
             patterns = {
-               "T1w": {
-                   "pattern": "{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz",
-                   "space": "native",
-               },
-               "BOLD": {
-                   "pattern": "{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz",
-                   "space": "MNI152NLin6Asym",
-               },
+                "T1w": {
+                    "pattern": "{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz",
+                    "space": "native",
+                },
+                "BOLD": {
+                    "pattern": "{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz",
+                    "space": "MNI152NLin6Asym",
+                },
             }
             replacements = ["subject", "session"]
             uri = "https://gin.g-node.org/juaml/datalad-example-bids"
             rootdir = "example_bids_ses"
             super().__init__(
-               datadir=None,
-               uri=uri,
-               rootdir=rootdir,
-               types=types,
-               patterns=patterns,
-               replacements=replacements,
+                datadir=None,
+                uri=uri,
+                rootdir=rootdir,
+                types=types,
+                patterns=patterns,
+                replacements=replacements,
             )
 
 This approach can be used directly from the YAML, like so:
@@ -297,22 +294,69 @@ This approach can be used directly from the YAML, like so:
 .. code-block:: yaml
 
    datagrabber:
-     - kind: PatternDataladDataGrabber
-       types:
-         - BOLD
-         - T1w
-       patterns:
-         BOLD:
-           pattern: "{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz"
-           space: MNI152NLin6Asym
-         T1w:
-           pattern: "{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz"
-           space: native
-       replacements:
-         - subject
-         - session
-       uri: "https://gin.g-node.org/juaml/datalad-example-bids"
-       rootdir: example_bids_ses
+     kind: PatternDataladDataGrabber
+     types:
+       - BOLD
+       - T1w
+     patterns:
+       BOLD:
+         pattern: "{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz"
+         space: MNI152NLin6Asym
+       T1w:
+         pattern: "{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz"
+         space: native
+     replacements:
+       - subject
+       - session
+     uri: "https://gin.g-node.org/juaml/datalad-example-bids"
+     rootdir: example_bids_ses
+
+Advanced: Using Unix-like path expansion directives
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+It is also possible to use some advanced Unix-like path expansion tricks to
+define our patterns.
+
+A very common thing would be to use ``*`` to match any number of
+characters but we cannot use it right after a replacement like:
+
+.. code-block:: python
+
+    "derivatives/freesurfer/{subject}*"
+
+or if there are multiple files or no files which can be globbed.
+
+We can also use ``[]`` and ``[!]`` to glob certain tricky files like with the
+case of FreeSurfer derivatives. The file structure seen in a typical
+FreeSurfer derivative of a dataset (like ``AOMIC`` ones) is like so:
+
+.. code-block::
+
+      .
+      └── derivatives
+          └── freesurfer
+             ├── fsaverage
+             │   ├── mri
+             │   |   ├── T1.mgz
+             │   |   └── ...
+             │   └── ...
+             ├── sub-01
+             │   ├── mri
+             │   |   ├── T1.mgz
+             │   |   └── ...
+             │   |   └── ...
+             │   └── ...
+             ...
+
+With a structure like this, it would be cumbersome to write custom methods
+for the class and thus we could use a pattern like this:
+
+.. code-block:: python
+
+    "derivatives/freesurfer/[!f]{subject}/mri/T1.mg[z]"
+
+This would ignore the ``fsaverage`` directory as a subject and let ``T1.mgz`` be
+fetched as there can be many files with the same prefix.
 
 .. _extending_datagrabbers_base:
 
@@ -344,17 +388,17 @@ and ``session``, we will use them as parameters of ``get_item``:
 .. code-block:: python
 
    def get_item(self, subject: str, session: str) -> dict[str, dict[str, str]]:
-      out = {
-         "T1w": {
-             "path": f"{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz",
-             "space": "native",
-         },
-         "BOLD": {
-             "path": f"{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz",
-             "space": "MNI152NLin6Asym",
-         },
-      }
-      return out
+       out = {
+           "T1w": {
+               "path": f"{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz",
+               "space": "native",
+           },
+           "BOLD": {
+               "path": f"{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz",
+               "space": "MNI152NLin6Asym",
+           },
+       }
+       return out
 
 
 The second method, ``get_elements``, needs to return a list of all the elements
@@ -368,16 +412,16 @@ need to remember that for session *ses-03* there is no BOLD data.
 
 
    def get_elements(self) -> list[str]:
-      subjects = ["sub-01", "sub-02", "sub-03"]
-      sessions = ["ses-01", "ses-02"]
+       subjects = ["sub-01", "sub-02", "sub-03"]
+       sessions = ["ses-01", "ses-02"]
 
-      # If we are not working on BOLD data, we can add "ses-03"
-      if "BOLD" not in self.types:
-         sessions.append("ses-03")
-      elements = []
-      for subject, element in product(subjects, sessions):
-         elements.append({"subject": subject, "session": session})
-      return elements
+       # If we are not working on BOLD data, we can add "ses-03"
+       if "BOLD" not in self.types:
+           sessions.append("ses-03")
+       elements = []
+       for subject, element in product(subjects, sessions):
+           elements.append({"subject": subject, "session": session})
+       return elements
 
 
 And finally, we can implement the ``get_element_keys`` method. This method needs
@@ -388,7 +432,7 @@ method, in the same order.
 .. code-block:: python
 
    def get_element_keys(self) -> list[str]:
-      return ["subject", "session"]
+       return ["subject", "session"]
 
 
 So, to summarise, our DataGrabber will look like this:
@@ -401,35 +445,36 @@ So, to summarise, our DataGrabber will look like this:
 
    @register_datagrabber
    class ExampleBIDSDataGrabber(BaseDataGrabber):
+       def get_item(
+           self, subject: str, session: str
+       ) -> dict[str, dict[str, str]]:
+           out = {
+               "T1w": {
+                   "path": f"{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz",
+                   "space": "native",
+               },
+               "BOLD": {
+                   "path": f"{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz",
+                   "space": "MNI152NLin6Asym",
+               },
+           }
+           return out
+
+       def get_elements(self) -> list[str]:
+           subjects = ["sub-01", "sub-02", "sub-03"]
+           sessions = ["ses-01", "ses-02"]
 
-      def get_item(self, subject: str, session: str) -> dict[str, dict[str, str]]:
-         out = {
-            "T1w": {
-                "path": f"{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz",
-                "space": "native",
-            },
-            "BOLD": {
-                "path": f"{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz",
-                "space": "MNI152NLin6Asym",
-            },
-         }
-         return out
-
-      def get_elements(self) -> list[str]:
-         subjects = ["sub-01", "sub-02", "sub-03"]
-         sessions = ["ses-01", "ses-02"]
-
-         # If we are not working on BOLD data, we can add "ses-03"
-         if "BOLD" not in self.types:
-            sessions.append("ses-03")
-         elements = []
-         for subject in subjects:
-            for session in sessions:
-               elements.append({"subject": subject, "session": session})
-         return elements
-
-      def get_element_keys(self) -> list[str]:
-         return ["subject", "session"]
+           # If we are not working on BOLD data, we can add "ses-03"
+           if "BOLD" not in self.types:
+               sessions.append("ses-03")
+           elements = []
+           for subject in subjects:
+               for session in sessions:
+                   elements.append({"subject": subject, "session": session})
+           return elements
+
+       def get_element_keys(self) -> list[str]:
+           return ["subject", "session"]
 
 Optional: Using datalad
 ~~~~~~~~~~~~~~~~~~~~~~~
@@ -442,11 +487,11 @@ Step 4: Optional: Adding *BOLD confounds*
 -----------------------------------------
 
 For some analyses, it is useful to have the confounds associated with the BOLD
-data. This corresponds to the ``BOLD_confounds`` item in the
+data. This corresponds to the ``BOLD.confounds`` item in the
 :ref:`Data Object <data_object>` (see :ref:`data_types`). However, the
-``BOLD_confounds`` element does not only consists of a ``path``, but it requires
+``BOLD.confounds`` element does not only consists of a ``path``, but it requires
 more information about the format of the confounds file. Thus, the
-``BOLD_confounds`` element is a dictionary with the following keys:
+``BOLD.confounds`` element is a dictionary with the following keys:
 
 - ``path``: the path to the confounds file.
 - ``format``: the format of the confounds file. Currently, this can be either
@@ -475,26 +520,24 @@ this:
 
 .. code-block:: python
 
-   def get_item(
-      self, subject: str, session: str
-   ) -> dict:
-      out = {
-         "BOLD": {
-             "path": f"{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz",
-             "space": "MNI152NLin6Asym",
-         },
-         "BOLD_confounds": {
-             "path": f"{subject}/{session}/func/{subject}_{session}_confounds.tsv",
-             "format": "adhoc",
-             "mappings": {
-                 "fmriprep": {
-                    "variable1": "rot_x",
-                    "variable2": "rot_z",
-                    "variable3": "rot_y",
-                 },
-             },
-         },
-      }
+   def get_item(self, subject: str, session: str) -> dict:
+       out = {
+           "BOLD": {
+               "path": f"{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz",
+               "space": "MNI152NLin6Asym",
+               "confounds": {
+                   "path": f"{subject}/{session}/func/{subject}_{session}_confounds.tsv",
+                   "format": "adhoc",
+                   "mappings": {
+                       "fmriprep": {
+                           "variable1": "rot_x",
+                           "variable2": "rot_z",
+                           "variable3": "rot_y",
+                       },
+                   },
+               },
+           },
+       }
 
 .. note::