docs/builtin.rst

@@ -25,7 +25,7 @@ Data Grabber
     - In Progress
     - Done
 
-    Version added: If the status is "Done", the Junifer version in which the
+    Version added: If the status is "Done", the junifer version in which the
     dataset was added. Else, a link to the Github issue or pull request
     implementing the dataset. Links to github can be added by using the
     following syntax: :gh:`<issue number>`
@@ -122,6 +122,54 @@ Planned
      - :gh:`47`
 
 
+Preprocessor
+------------
+
+..
+    Provide a list of the Preprocessors that are implemented or planned.
+
+    State: this should indicate the state of the preprocessor. Valid options are
+    - Planned
+    - In Progress
+    - Done
+
+    Version added: If the status is "Done", the junifer version in which the
+    preprocessor was added. Else, a link to the Github issue or pull request
+    implementing the preprocessor. Links to github can be added by using the
+    following syntax: :gh:`<issue number>`
+
+Available
+~~~~~~~~~
+
+.. list-table::
+   :widths: auto
+   :header-rows: 1
+
+   * - Class
+     - Description
+     - State
+     - Version Added
+   * - :class:`.fMRIPrepConfoundRemover`
+     - Remove confounds from ``fMRIPrep``-ed data
+     - Done
+     - 0.0.1
+   * - :class:`.SpaceWarper`
+     - | Warp / transform data from one space to another
+       | (subject-native or other template spaces)
+     - Done
+     - 0.0.4
+   * - ``Smoothing``
+     - | Apply smoothing to data, particularly useful when dealing with
+       | ``fMRIPrep``-ed data
+     - In Progress
+     - :gh:`161`
+
+
+..
+   Planned
+   ~~~~~~~
+
+
 Marker
 ------
 
@@ -133,7 +181,7 @@ Marker
     - In Progress
     - Done
 
-    Version added: If the status is "Done", the Junifer version in which the
+    Version added: If the status is "Done", the junifer version in which the
     marker was added. Else, a link to the Github issue or pull request
     implementing the marker. Links to github can be added by using the
     following syntax: :gh:`<issue number>`
@@ -254,10 +302,6 @@ Planned
    * - Connectedness
      - Compute connectedness
      - :gh:`34`
-   * - Permutation entropy, Range entropy, Multiscale entropy and Hurst exponent
-     - | Calculate Permutation entropy, Range entropy, Multiscale entropy and
-       | Hurst exponent
-     - :gh:`61`
 
 Parcellation
 ------------
@@ -265,7 +309,7 @@ Parcellation
 ..
     Provide a list of the Parcellations that are implemented or planned.
 
-    Version added: The Junifer version in which the parcellation was added.
+    Version added: The junifer version in which the parcellation was added.
 
 Available
 ~~~~~~~~~
@@ -277,8 +321,8 @@ Available
    * - Name
      - Options
      - Keys
-     - Spaces
+     - Template Spaces
-     - Version added
+     - Version Added
      - Publication
    * - Schaefer
      - ``n_rois``, ``yeo_networks``
@@ -439,7 +483,7 @@ Coordinates
 ..
     Provide a list of the Coordinates that are implemented or planned.
 
-    Version added: The Junifer version in which the parcellation was added.
+    Version added: The junifer version in which the parcellation was added.
 
 Available
 ~~~~~~~~~
@@ -450,7 +494,7 @@ Available
 
    * - Name
      - Keys
-     - Version added
+     - Version Added
      - Publication
    * - Cognitive action control
      - ``CogAC``
@@ -635,7 +679,7 @@ Mask
 ..
     Provide a list of the masks that are implemented or planned.
 
-    Version added: The Junifer version in which the mask was added.
+    Version added: The junifer version in which the mask was added.
 
 Available
 ~~~~~~~~~
@@ -646,8 +690,8 @@ Available
 
    * - Name
      - Keys
-     - Spaces
+     - Template Space
-     - Version added
+     - Version Added
      - Description - Publication
    * - Vickery-Patil (Gray Matter)
      - | ``GM_prob0.2``
@@ -663,14 +707,14 @@ Available
      - | Vickery, Sam, & Patil, Kaustubh. (2022).
        | Chimpanzee and Human Gray Matter Masks [Data set]. Zenodo.
        | https://doi.org/10.5281/zenodo.6463123
-   * - Nilearn's MNI152 1mm-resolution mask
+   * - ``junifer``'s custom brain mask
      - | ``compute_brain_mask``
      - Adapts to the target data
      - 0.0.2
-     - | Compute the whole-brain mask. This mask is calculated using
+     - | Compute the whole-brain, gray-matter or white-matter mask using
-       | MNI152 1mm-resolution template mask onto the target image.
+       | the template and the resolution from the target image. The
-       | See :func:`nilearn.masking.compute_brain_mask`
+       | templates are obtained via ``templateflow``.
-   * - Nilearn's mask computed from FMRI data
+   * - ``nilearn``'s mask computed from fMRI data
      - | ``compute_epi_mask``
      - Adapts to the target data
      - 0.0.2
@@ -678,15 +722,14 @@ Available
        | proposed by T.Nichols: find the least dense point of the histogram,
        | between fractions ``lower_cutoff`` and ``upper_cutoff`` of the total
        | image histogram. See :func:`nilearn.masking.compute_epi_mask`
-   * - Nilearn's background mask
+   * - ``nilearn``'s background mask
      - | ``compute_background_mask``
      - Adapts to the target data
      - 0.0.2
      - | 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
-   * - Nilearn's ICBM152 template gray-matter mask
      - | ``fetch_icbm152_brain_gm_mask``
      - ``MNI152NLin2009aAsym``
      - 0.0.2
@@ -695,8 +738,9 @@ Available
        | See :func:`nilearn.datasets.fetch_icbm152_brain_gm_mask`
 
 
-Planned
+..
-~~~~~~~
+   Planned
+   ~~~~~~~
 
 ..
   helpful site for creating tables: https://rest-sphinx-memo.readthedocs.io/en/latest/ReST.html#tables

docs/changes/newsfragments/317.doc

@@ -0,0 +1 @@
+Improve documentation by adding information about space transformation and writing custom Preprocessors by `Synchon Mandal`_

docs/contribution.rst

@@ -164,6 +164,8 @@ In case you remove some files or change their filenames, you can run into
 errors when using ``make local``. In this situation you can use ``make clean``
 to clean up the already build files and then re-run ``make local``.
 
+Also, we follow British English for the documentation.
+
 
 Writing Examples
 ----------------

docs/extending/coordinates.rst

@@ -6,19 +6,20 @@ Adding Coordinates
 ==================
 
 Instead of using whole-brain parcellations to aggregate voxel-wise signals from
-MR images (as for example in the :class:`.ParcelAggregation` marker), junifer
+MR images (as for example in the :class:`.ParcelAggregation` marker), ``junifer``
 allows you to specify a set of coordinates around which to draw spheres to
 aggregate (for example using the :class:`.SphereAggregation` marker) the MR
 signals from individual voxels. Now, before you start specifying your own sets
-of coordinates, check the coordinates that junifer already has
+of coordinates, check the coordinates that ``junifer`` already has
 :ref:`built in <builtin>`. If you simply want to use a well known set of
-coordinates from the literature, there is a reasonable chance, that junifer
+coordinates from the literature, there is a reasonable chance, that ``junifer``
 provides them already.
 
 If you checked the in-built coordinates, and they are not there already (for
-example if you came up with your own set of coordinates), then junifer provides
+example if you came up with your own set of coordinates), then ``junifer``
-an easy way for you to register them using the :func:`.register_coordinates`
+provides an easy way for you to register them using the
-function, so you can use your own set of coordinates within a junifer pipeline.
+:func:`.register_coordinates` function, so you can use your own set of
+coordinates within a ``junifer`` pipeline.
 
 From the API reference, we can see that it has 4 positional arguments
 (``name``, ``coordinates``, ``voi_names`` and ``space``) as well as one
@@ -26,7 +27,7 @@ optional keyword argument (``overwrite``).
 
 The ``name`` argument takes a string indicating the name you want to give to
 this set of coordinates. This ``name`` can be used to obtain and operate on a
-set of coordinates in junifer. For example, you can obtain your coordinates
+set of coordinates in ``junifer``. For example, you can obtain your coordinates
 after registration by providing ``name`` to :func:`.load_coordinates`. We could
 simply call it ``"my_set_of_coordinates"``, but likely you want a more
 descriptive and more informative name most of the time.
@@ -36,9 +37,7 @@ The ``coordinates`` argument takes the actual coordinates as a 2-dimensional
 columns (one for each spatial dimension). That is, the first, second, and third
 columns indicate the x-, y-, and z-coordinates in MNI space respectively.
 The number of rows in the array correspond to the number of coordinates that
-belong to this set. Note, that junifer (as of yet) only works in MNI space, and
+belong to this set.
-so therefore these coordinates should always be real-world coordinates of the
-MNI space.
 
 The ``voi_names`` argument takes a list of strings
 indicating the names of each coordinate (i.e. volume-of-interest) in the
@@ -47,7 +46,7 @@ the number of rows in the coordinates array. Now, we know everything we need to
 know to register a set of coordinates.
 
 Lastly, we specify the ``space`` that the coordinates are in, for example,
-``"MNI"`` or ``"Native"`` (scanner-native space).
+``"MNI"`` or ``"native"`` (scanner-native space).
 
 Step 1: Prepare code to register a set of coordinates
 -----------------------------------------------------
@@ -62,8 +61,8 @@ packages:
   import numpy as np
 
 For the sake of this example, we can create a set of coordinates that belong
-to the default mode network (DMN), and register this set of coordinates with
+to the Default Mode Network (DMN), and register this set of coordinates with
-junifer. Note, that junifer already has a
+``junifer``. Note, that ``junifer`` already has a
 :ref:`set of coordinates built-in <builtin>` ("DMNBuckner") that is associated
 with the DMN. Here, we use the DMN coordinates used in a
 `nilearn example <https://nilearn.github.io/dev/auto_examples/03_connectivity/plot_sphere_based_connectome.html>`_.
@@ -97,7 +96,7 @@ simply use this to register our coordinates:
       space="MNI"
   )
 
-Now, when we run this script, junifer registers these coordinates and we can
+Now, when we run this script, ``junifer`` registers these coordinates and we can
 use them in subsequent analyses. Let's now consider how to use coordinate
 registration in combination with
 :ref:`codeless configuration using a YAML file <codeless>`.
@@ -106,7 +105,7 @@ Step 2: Add coordinate registration to the YAML file
 ----------------------------------------------------
 
 In order to register your coordinates for a pipeline configured by a YAML file,
-you can use the ``with`` keyword provided by junifer:
+you can use the ``with`` keyword provided by ``junifer``:
 
 .. code-block:: yaml
 

docs/extending/datagrabber.rst

@@ -12,8 +12,8 @@ the structure of a dataset and provide two specific functionalities:
    element (e.g. the path to the T1 image, the path to the T2 image, etc.)
 #. Provide the list of *elements* available in the dataset.
 
-In this section, we will see how to create a datagrabber for a dataset. Basic
+In this section, we will see how to create a DataGrabber for a dataset. Basic
-aspects of datagrabbers are covered in the
+aspects of DataGrabbers are covered in the
 :ref:`Understanding Data Grabbers <datagrabber>` section.
 
 .. _extending_datagrabbers_think:
@@ -22,7 +22,7 @@ Step 1: Think about the element
 -------------------------------
 
 Like with any programming-related task, the first step is to think. When
-creating a Data Grabber, we need to first define what an *element* is.
+creating a DataGrabber, we need to first define what an *element* is.
 The *element* should be the smallest unit of data that can be processed. That
 is, for each element, there should be a set of data that can be processed, but
 only one of each *data type* (see :ref:`data_types`).
@@ -42,28 +42,28 @@ then the *element* should be composed of 3 items:
 If any of these items were not part of the element, then we will have more than
 one ``T1w`` and / or ``BOLD`` image for each subject, which is not allowed.
 
-Importantly, nothing prevents that one image is part of two different elements.
+Importantly, nothing prevents that one image being part of two different
-For example, it is usually the case that the ``T1w`` image is not acquired for
+elements. For example, it is usually the case that the ``T1w`` image is not
-each task, but once in the entire session. So in this case, the ``T1w`` image
+acquired for each task, but once in the entire session. So in this case, the
-for the element (``sub001``, ``ses1``, ``rest``) will be the same as the
+``T1w`` image for the element (``sub001``, ``ses1``, ``rest``) will be the same
-``T1w`` image for the element (``sub001``, ``ses1``, ``stroop``).
+as the ``T1w`` image for the element (``sub001``, ``ses1``, ``stroop``).
 
 We will now continue this section using as an example, a dataset in BIDS format
 in which 9 subjects (``sub-01`` to ``sub-09``) were scanned each during 3
 sessions (``ses-01``, ``ses-02``, ``ses-03``) and each session included a
 ``T1w`` and a ``BOLD`` image (resting-state), except for ``ses-03`` which was
-only anatomical.
+only anatomical data.
 
 Step 2: Think about the dataset's structure
 -------------------------------------------
 
 Now that we have our element defined, we need to think about the structure of
 the dataset. Mainly, because the structure of the dataset will determine how
-the Data Grabber needs to be implemented.
+the DataGrabber needs to be implemented.
 
-Junifer provides an abstract class to deal with datasets that can be thought in
+``junifer`` provides an abstract class to deal with datasets that can be thought
-terms of *patterns*. A *pattern* is a string that contains placeholders that are
+in terms of *patterns*. A *pattern* is a string that contains placeholders that
-replaced by the actual values of the element. In our BIDS example, the path
+are replaced by the actual values of the element. In our BIDS example, the path
 to the T1w image of subject ``sub-01`` and session ``ses-01``, relative to the
 dataset location, is ``sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz``. By
 replacing ``sub-01`` with ``sub-02``, we can obtain the T1w image of the first
@@ -88,7 +88,7 @@ discussion in the `junifer Discussions`_ page. Most probably we can help you
 get your dataset in order.
 
 If there is no other way, then you can follow :ref:`extending_datagrabbers_base`
-to create a Data Grabber from scratch.
+to create a DataGrabber from scratch.
 
 .. _extending_datagrabbers_pattern:
 
@@ -101,7 +101,7 @@ Option A: Extending from PatternDataGrabber
 The :class:`.PatternDataGrabber` class is an abstract class that has the
 functionality of understanding patterns embedded in it.
 
-Before creating the datagrabber, we need to define 3 variables:
+Before creating the DataGrabber, we need to define 3 variables:
 
 * ``types``: A list with the available :ref:`data_types` in our dataset.
 * ``patterns``: A dictionary that specifies the pattern for each data type.
@@ -126,7 +126,7 @@ where the dataset is located. For example, if the dataset is located in
 location of the dataset, we can expose the variable in the constructor, as in
 the following example.
 
-With the variables defined above, we can create our datagrabber and name it
+With the variables defined above, we can create our DataGrabber and name it
 ``ExampleBIDSDataGrabber``:
 
 .. code-block:: python
@@ -152,7 +152,7 @@ With the variables defined above, we can create our datagrabber and name it
                replacements=replacements,
             )
 
-Our datagrabber is ready to be used by junifer. However, it is still unknown
+Our DataGrabber is ready to be used by ``junifer``. However, it is still unknown
 to the library. We need to register it in the library. To do so, we need to
 use the :func:`.register_datagrabber` decorator.
 
@@ -183,9 +183,9 @@ use the :func:`.register_datagrabber` decorator.
             )
 
 
-Now, we can use our datagrabber in junifer, by setting the ``datagrabber`` kind
+Now, we can use our DataGrabber in ``junifer``, by setting the ``datagrabber``
-in the yaml file to ``ExampleBIDSDataGrabber``. Remember that we still need to
+kind in the yaml file to ``ExampleBIDSDataGrabber``. Remember that we still need
-set the ``datadir``.
+to set the ``datadir``.
 
 .. code-block:: yaml
 
@@ -209,7 +209,7 @@ temporary directory. To set the location of the dataset, you can use the
 be used to specify the path to the root directory of the dataset after doing
 ``datalad clone``.
 
-In the example, the dataset is hosted in gin
+In the example, the dataset is hosted in Gin
 (``https://gin.g-node.org/juaml/datalad-example-bids``).
 
 When we clone this dataset, we will see the following structure:
@@ -238,7 +238,7 @@ Now we have our 2 additional variables:
     uri = "https://gin.g-node.org/juaml/datalad-example-bids"
     rootdir = "example_bids_ses"
 
-And we can create our datagrabber:
+And we can create our DataGrabber:
 
 .. code-block:: python
 
@@ -267,17 +267,34 @@ And we can create our datagrabber:
                replacements=replacements,
             )
 
+This approach can be used directly from the YAML, like so:
+
+.. code-block:: yaml
+
+   datagrabber:
+     - kind: PatternDataladDataGrabber
+       types:
+         - BOLD
+         - T1w
+       patterns:
+         BOLD: "{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz"
+         T1w: "{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz"
+       replacements:
+         - subject
+         - session
+       uri: "https://gin.g-node.org/juaml/datalad-example-bids"
+       rootdir: "example_bids_ses"
 
 .. _extending_datagrabbers_base:
 
 Option B: Extending from BaseDataGrabber
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-While we could not think of a use case in which the pattern-based datagrabber
+While we could not think of a use case in which the pattern-based DataGrabber
-would not be suitable, it is still possible to create a datagrabber extending
+would not be suitable, it is still possible to create a DataGrabber extending
 from the :class:`.BaseDataGrabber` class.
 
-In order to create a datagrabber extending from :class:`.BaseDataGrabber`, we
+In order to create a DataGrabber extending from :class:`.BaseDataGrabber`, we
 need to implement the following methods:
 
 - ``get_item``: to get a single item from the dataset.
@@ -287,7 +304,7 @@ need to implement the following methods:
 .. note::
 
    The ``__init__`` method could also be implemented, but it is not mandatory.
-   This is required if the datagrabber requires any extra parameter.
+   This is required if the DataGrabber requires any extra parameter.
 
 We will now implement our BIDS example with this method.
 
@@ -339,7 +356,7 @@ method, in the same order.
       return ["subject", "session"]
 
 
-So, to summarize, our datagrabber will look like this:
+So, to summarise, our DataGrabber will look like this:
 
 .. code-block:: python
 
@@ -403,7 +420,7 @@ not standardised.
    The ``mappings`` key is only required if the ``format`` is ``adhoc``. If the
    ``format`` is ``fmriprep``, the ``mappings`` key is not required.
 
-Currently, junifer provides only one confound remover step
+Currently, ``junifer`` provides only one confound remover step
 (:class:`.fMRIPrepConfoundRemover`), which relies entirely on the ``fmriprep``
 confound variable names. Thus, if the confounds are not in ``fmriprep`` format,
 the user will need to provide the mappings between the *ad-hoc* variable names

docs/extending/dependencies.rst

@@ -0,0 +1,141 @@
+.. include:: ../links.inc
+
+.. _specifying_dependencies:
+
+Specifying Dependencies
+=======================
+
+This section describes how you can tackle different situations when writing
+your custom Marker and / or Preprocessor and take care of the dependencies for
+them.
+
+You might have already come across listing out dependencies for your
+:ref:`custom Markers <extending_markers>` and / or
+:ref:`custom Preprocessors <extending_preprocessors>`, if not, check them out
+first. If you have already gone through them, you are already familiar with using
+class attribute ``_DEPENDENCIES`` to keep track of its dependencies. ``junifer``
+is a bit more sophisticated about them and we will see here how you can make the
+best use of them.
+
+.. _component_dependencies:
+
+Handling dependencies that come as Python packages
+--------------------------------------------------
+
+You have already seen this case handled by having a class attribute
+``_DEPENDENCIES`` whose value is a set of all the package names that the
+component depends on. For example, for :class:`.RSSETSMarker`, we have:
+
+.. code-block:: python
+
+    _DEPENDENCIES: ClassVar[Set[str]] = {"nilearn"}
+
+The type annotation is for documentation and static type checking purposes.
+Although not required, we highly recommend you use them, your future self
+and others who use it will thank you.
+
+.. _component_external_dependencies:
+
+Handling external dependencies from toolboxes
+---------------------------------------------
+
+You can also specify dependencies of external toolboxes like AFIN, FSL and ANTs,
+by having a class attribute like so:
+
+.. code-block:: python
+
+    _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, List[str]]]]] = [
+        {
+            "name": "afni",
+            "commands": ["3dReHo", "3dAFNItoNIFTI"],
+        },
+    ]
+
+The above example is taken from the class which computes regional homogeneity
+(ReHo) using AFNI. The general pattern is that you need to have the value of
+``_EXT_DEPENDENCIES`` as a list of dictionary with two keys:
+
+* ``name`` (str) : lowercased name of the toolbox
+* ``commands`` (list of str) : actual names of the commands you need to use
+
+This is simple but powerful as we will see in the following sub-sections.
+
+.. _component_conditional_dependencies:
+
+Handling conditional dependencies
+---------------------------------
+
+You might encounter situations where your Marker or Preprocessor needs to have
+option for the user to either use a dependency that comes as a package or
+use a dependency that relies on external toolboxes. With the foundation we laid
+above, it is really simple to solve it while having validation before running
+and letting the user know if some dependency is missing.
+
+Let's look at an actual implementation, in this case :class:`.SpaceWarper`, so
+that it shows the problem a bit better and how we solve it:
+
+.. code-block:: python
+
+    class SpaceWarper(BasePreprocessor):
+        # docstring
+        _CONDITIONAL_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, Type]]]] = [
+            {
+                "using": "fsl",
+                "depends_on": FSLWarper,
+            },
+            {
+                "using": "ants",
+                "depends_on": ANTsWarper,
+            },
+        ]
+
+        def __init__(
+            self, using: str, reference: str, on: Union[List[str], str]
+        ) -> None:
+            # validation and setting up
+
+
+Here, you see a new class attribute ``_CONDITIONAL_DEPENDENCIES`` which is a
+list of dictionaries with two keys:
+
+* ``using`` (str) : lowercased name of the toolbox
+* ``depends_on`` (object) : a class which implements the particular tool's use
+
+It is mandatory to have the ``using`` positional argument in the constructor in
+this case as the validation starts with this and moves further. It is also
+mandatory to only allow the value of ``using`` argument to be one of them
+specified in the ``using`` key of ``_CONDITIONAL_DEPENDENCIES`` entries.
+
+For brevity, we only show the ``FSLWarper`` here but ``ANTsWarper`` looks very
+similar. ``FSLWarper`` looks like this (only the relevant part is shown here):
+
+.. code-block:: python
+
+    class FSLWarper:
+        # docstring
+
+        _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, List[str]]]]] = [
+            {
+                "name": "fsl",
+                "commands": ["flirt", "applywarp"],
+            },
+        ]
+
+        _DEPENDENCIES: ClassVar[Set[str]] = {"numpy", "nibabel"}
+
+        def preprocess(
+            self,
+            input: Dict[str, Any],
+            extra_input: Dict[str, Any],
+        ) -> Dict[str, Any]:
+            # implementation
+
+Here you can see the familiar ``_DEPENDENCIES`` and ``_EXT_DEPENDENCIES`` class
+attributes. The validation process starts by looking up the ``using`` value of
+the ``_CONDITIONAL_DEPENDENCIES`` entries and then retrieves the object pointed
+by ``depends_on``. After that, the ``_DEPENDENCIES`` and ``_EXT_DEPENDENCIES``
+class attributes are checked.
+
+This might be a bit too much to get it right away so feel free to check the code
+for a better understanding. You can also check ``ALFFBase`` for a Marker
+having this pattern.

docs/extending/extension.rst

@@ -2,19 +2,20 @@
 
 .. _extending_extension:
 
-Creating a junifer extension
+Creating a ``junifer`` extension
-============================
+================================
 
-Junifer is designed to be easily extensible. Through the use of a registry and
+``junifer`` is designed to be easily extensible. Through the use of a registry
-decorators, you can easily add new functionality to junifer during runtime. This
+and decorators, you can easily add new functionality to ``junifer`` during
-is done by creating a new Python module and importing it before running junifer.
+runtime. This is done by creating a new Python module and importing it before
+running ``junifer``.
 
 A special consideration has to be made when using the
 :ref:`code-less configuration<codeless>`. In this case, the
 ``with`` statement can be used to import a module or run a Python file.
 
-In the following example, we instruct junifer to first import ``my_module`` and
+In the following example, we instruct ``junifer`` to first import ``my_module``
-then run the ``my_file.py`` file.
+and then run the ``my_file.py`` file:
 
 .. code-block:: yaml
 
@@ -22,13 +23,13 @@ then run the ``my_file.py`` file.
       - my_module
       - my_file.py
 
-Thus, the code from ``my_file.py`` will be executed before running junifer. This
+Thus, the code from ``my_file.py`` will be executed before running ``junifer``.
-is the ideal place to include junifer extensions.
+This is the ideal place to include ``junifer`` extensions.
 
 .. important::
 
-   Some junifer commands will not consider files imported from files included
+   Some ``junifer`` commands will not consider files imported from files included
    in the ``with`` statement. If ``my_file.py`` imports ``my_other_file.py``,
-   some of the junifer commands will not consider ``my_other_file.py``. Either
+   some of the ``junifer`` commands will not consider ``my_other_file.py``. Either
    place all the code in one file or add multiple files to the ``with``
    statement.

docs/extending/index.rst

@@ -2,20 +2,20 @@
 
 .. _extending:
 
-Extending junifer
+Extending ``junifer``
-=================
+=====================
 
 While we aim to provide as many datasets and markers as possible, we are also
 interested in allowing users to extend the functionality with their own
-datagrabbers, preprocessing, markers, etc., .
+DataGrabbers, Preprocessors, Markers, etc., .
 
-It's not necessary to have the new functionality included in junifer before
+It's not necessary to have the new functionality included in ``junifer`` before
 the user can use them. The user can simply create a new Python file, code the
-desired functionality and use it with junifer. This is the first step towards
+desired functionality and use it with ``junifer``. This is the first step towards
-including the new functionality in the junifer pipeline.
+including the new functionality in the ``junifer`` pipeline.
 
-In this section we will show how to extend junifer, by creating new
+In this section we will show how to extend ``junifer``, by creating new
-datagrabbers, preprocessing, markers, etc.,  following the *junifer* way.
+DataGrabbers, Preprocessors, Markers, etc.,  following the *junifer* way.
 
 
 .. toctree::
@@ -25,6 +25,8 @@ datagrabbers, preprocessing, markers, etc.,  following the *junifer* way.
    extension
    datagrabber
    marker
+   preprocessor
+   dependencies
    parcellations
    coordinates
    masks

docs/extending/marker.rst

@@ -5,35 +5,35 @@
 Creating Markers
 ================
 
-Computing a marker (a.k.a. *feature*) is the main goal of junifer. While we aim
+Computing a marker (a.k.a. *feature*) is the main goal of ``junifer``. While we
-to provide as many markers as possible, it might be the case that the marker you
+aim to provide as many Markers as possible, it might be the case that the Marker
-are looking for is not available. In this case, you can create your own marker
+you are looking for is not available. In this case, you can create your own Marker
 by following this tutorial.
 
-Most of the functionality of a junifer marker has been taken care by the
+Most of the functionality of a ``junifer`` Marker has been taken care by the
 :class:`.BaseMarker` class. Thus, only a few methods are required:
 
 #. ``get_valid_inputs``: The method to obtain the list of valid inputs for the
-   marker. This is used to check that the inputs provided by the user are
+   Marker. This is used to check that the inputs provided by the user are
    valid. This method should return a list of strings, representing
    :ref:`data types <data_types>`.
-#. ``get_output_type``: The method to obtain the kind of output of the marker.
+#. ``get_output_type``: The method to obtain the output type of the Marker.
-   This is used to check that the output of the marker is compatible with the
+   This is used to check that the output of the Marker is compatible with the
    storage. This method should return a string, representing
    :ref:`storage types <storage_types>`.
-#. ``compute``: The method that given the data, computes the marker.
+#. ``compute``: The method that given the data, computes the Marker.
-#. ``__init__``: The initialisation method, where the marker is configured.
+#. ``__init__``: The initialisation method, where the Marker is configured.
 
-As an example, we will develop a ``ParcelMean`` marker, a marker that first
+As an example, we will develop a ``ParcelMean`` Marker, a Marker that first
 applies a parcellation and then computes the mean of the data in each parcel.
-This is a very simple example, but it will show you how to create a new marker.
+This is a very simple example, but it will show you how to create a new Marker.
 
 .. _extending_markers_input_output:
 
 Step 1: Configure input and output
 ----------------------------------
 
-This step is quite simple: we need to define the input and output of the marker.
+This step is quite simple: we need to define the input and output of the Marker.
 Based on the current :ref:`data types <data_types>`, we can have ``BOLD``,
 ``VBM_WM`` and ``VBM_GM`` as valid inputs.
 
@@ -42,32 +42,32 @@ Based on the current :ref:`data types <data_types>`, we can have ``BOLD``,
     def get_valid_inputs(self) -> list[str]:
         return ["BOLD", "VBM_WM", "VBM_GM"]
 
-The output of the marker depends on the input. For ``BOLD``, it will be
+The output of the Marker depends on the input. For ``BOLD``, it will be
 ``timeseries``, while for the rest of the inputs, it will be ``vector``. Thus,
 we can define the output as:
 
 .. code-block:: python
 
-    def get_output_type(self, input_kind: str) -> str:
+    def get_output_type(self, input_type: str) -> str:
-        if input_kind == "BOLD":
+        if input_type == "BOLD":
             return "timeseries"
         else:
             return "vector"
 
 .. _extending_markers_init:
 
-Step 2: Initialize the marker
+Step 2: Initialise the Marker
 -----------------------------
 
-In this step we need to define the parameters of the marker the user can provide
+In this step we need to define the parameters of the Marker the user can provide
-to configure how the marker will behave.
+to configure how the Marker will behave.
 
-The parameters of the marker are defined in the ``__init__`` method. The
+The parameters of the Marker are defined in the ``__init__`` method. The
 :class:`.BaseMarker` class requires two optional parameters:
 
-1. ``name``: the name of the marker. This is used to identify the marker in the
+1. ``name``: the name of the Marker. This is used to identify the Marker in the
    configuration file.
-2. ``on``: a list or string with the data types that the marker will be applied
+2. ``on``: a list or string with the data types that the Marker will be applied
    to.
 
 .. attention::
@@ -92,29 +92,29 @@ parcellation to use. Thus, we can define the ``__init__`` method as follows:
 
 .. caution::
 
-   Parameters of the marker must be stored as object attributes without using
+   Parameters of the Marker must be stored as object attributes without using
    ``_`` as prefix. This is because any attribute that starts with ``_`` will
    not be considered as a parameter and not stored as part of the metadata of
-   the marker.
+   the Marker.
 
 .. _extending_markers_compute:
 
-Step 3: Compute the marker
+Step 3: Compute the Marker
 --------------------------
 
-In this step, we will define the method that computes the marker. This method
+In this step, we will define the method that computes the Marker. This method
-will be called by junifer when needed, using the data provided by the
+will be called by ``junifer`` when needed, using the data provided by the
-datagrabber, as configured by the user. The method ``compute`` has two
+DataGrabber, as configured by the user. The method ``compute`` has two
 arguments:
 
-* ``input``: a dictionary with the data to be used to compute the marker. This
+* ``input``: a dictionary with the data to be used to compute the Marker. This
   will be the corresponding element in the :ref:`Data Object<data_object>`
   already indexed. Thus, the dictionary has at least two keys: ``data`` and
   ``path``. The first one contains the data, while the second one contains the
   path to the data. The dictionary can also contain other keys, depending on the
   data type.
 * ``extra_input``: the rest of the :ref:`Data Object<data_object>`. This is
-  useful if you want to use other data to compute the marker
+  useful if you want to use other data to compute the Marker
   (e.g.: ``BOLD_confounds`` can be used to de-confound the ``BOLD`` data).
 
 Following the example, we will compute the mean of the data in each parcel using
@@ -133,7 +133,7 @@ the ``store`` method.
 
     from typing import Any
 
-    from junifer.data import load_parcellation
+    from junifer.data import get_parcellation
     from nilearn.maskers import NiftiLabelsMasker
 
 
@@ -145,13 +145,11 @@ the ``store`` method.
         # Get the data
         data = input["data"]
 
-        # Get the min of the voxels sizes and use it as the resolution
+        # Get the parcellation tailored for the target
-        resolution = np.min(data.header.get_zooms()[:3])
+        t_parcellation, t_labels, _ = get_parcellation(
-
-        # Load the parcellation
-        t_parcellation, t_labels, _ = load_parcellation(
             name=self.parcellation_name,
-            resolution=resolution,
+            target_data=input,
+            extra_input=extra_input,
         )
 
         # Create a masker
@@ -173,32 +171,33 @@ the ``store`` method.
 
 .. _extending_markers_finalize:
 
-Step 4: Finalise the marker
+Step 4: Finalise the Marker
 ---------------------------
 
-Once all of the above steps are done, we just need to give our marker a name,
+Once all of the above steps are done, we just need to give our Marker a name,
 state its *dependencies* and register it using the ``@register_marker``
 decorator.
 
-The *dependencies* are the core packages that are required to compute the marker.
+The :ref:`dependencies <specifying_dependencies>` are the core packages that are
-This will be later used to keep track of the versions of the packages used to
+required to compute the Marker. This will be later used to keep track of the
-compute the marker. To inform junifer about the dependencies of a marker, we need
+versions of the packages used to compute the Marker. To inform ``junifer``
-to define a ``_DEPENDENCIES`` attribute in the class. This attribute must be a
+about the dependencies of a Marker, we need to define a ``_DEPENDENCIES``
-set, with the names of the packages as strings. For example, the ``ParcelMean``
+attribute in the class. This attribute must be a set, with the names of the
-marker has the following dependencies:
+packages as strings. For example, the ``ParcelMean`` marker has the
+following dependencies:
 
 .. code-block:: python
 
     _DEPENDENCIES = {"nilearn", "numpy"}
 
-Finally, we need to register the marker using the ``@register_marker`` decorator.
+Finally, we need to register the Marker using the ``@register_marker`` decorator.
 
 .. code-block:: python
 
     from typing import Any
 
     from junifer.api.decorators import register_marker
-    from junifer.data import load_parcellation
+    from junifer.data import get_parcellation
     from junifer.markers.base import BaseMarker
     from nilearn.maskers import NiftiLabelsMasker
 
@@ -220,8 +219,8 @@ Finally, we need to register the marker using the ``@register_marker`` decorator
         def get_valid_inputs(self) -> list[str]:
             return ["BOLD", "VBM_WM", "VBM_GM"]
 
-        def get_output_type(self, input_kind: str) -> str:
+        def get_output_type(self, input_type: str) -> str:
-            if input_kind == "BOLD":
+            if input_type == "BOLD":
                 return "timeseries"
             else:
                 return "vector"
@@ -234,13 +233,11 @@ Finally, we need to register the marker using the ``@register_marker`` decorator
             # Get the data
             data = input["data"]
 
-            # Get the min of the voxels sizes and use it as the resolution
+            # Get the parcellation tailored for the target
-            resolution = np.min(data.header.get_zooms()[:3])
+            t_parcellation, t_labels, _ = get_parcellation(
-
-            # Load the parcellation
-            t_parcellation, t_labels, _ = load_parcellation(
                 name=self.parcellation_name,
-                resolution=resolution,
+                target_data=input,
+                extra_input=extra_input,
             )
 
             # Create a masker
@@ -283,8 +280,8 @@ Template for a custom Marker
             valid = []
             return valid
 
-        def get_output_type(self, input_kind):
+        def get_output_type(self, input_type):
-            # TODO: Return the valid output kind for each input kind
+            # TODO: Return the valid output type for each input type
             pass
 
         def compute(self, input, extra_input):

docs/extending/masks.rst

@@ -5,7 +5,7 @@
 Adding Masks
 ============
 
-Many processing steps and markers in junifer allow you to specify a binary
+Many processing steps and Markers in ``junifer`` allow you to specify a binary
 mask to select voxels you want to include in the analysis. There are a number
 of masks :ref:`in-built in junifer already <builtin>`, so check if any of them
 suit your needs. Check how to use these masks :ref:`here <using_masks>`. Once
@@ -14,23 +14,23 @@ suit your needs, and you have found that they don't, you can come back here to
 learn how to use your own masks.
 
 The principle is fairly simple and quite similar to :ref:`adding_parcellations`
-and :ref:`adding_coordinates`. junifer provides a :func:`.register_mask`
+and :ref:`adding_coordinates`. ``junifer`` provides a :func:`.register_mask`
 function that lets you register your own custom masks. It consists of three
 positional arguments (``name``, ``mask_path`` and ``space``) and one optional
 keyword argument (``overwrite``).
 
 The ``name`` argument is a string indicating the name of the mask. This name
-is used to refer to that mask in junifer internally in order to obtain the
+is used to refer to that mask in ``junifer`` internally in order to obtain the
 actual mask data and perform operations on it. For example, using the name you
 can load a mask after registration using the
 :func:`.load_mask` function.
 
 The ``mask_path`` should contain the path to a valid NIfTI image with binary
-voxel values (i.e. 0 or 1). This data can then be used by junifer to mask other
+voxel values (i.e. 0 or 1). This data can then be used by ``junifer`` to mask
-MR images.
+other MR images.
 
 Lastly, we specify the ``space`` that the coordinates are in, for example,
-``"MNI"`` or ``"Native"`` (scanner-native space).
+``"MNI152NLin6Asym"`` or ``"native"`` (scanner-native space).
 
 Step 1: Prepare code to register a mask
 ---------------------------------------
@@ -49,7 +49,7 @@ look as follows:
   # on your system:
   mask_path = Path("..") / ".." / "my_custom_mask.nii.gz"
 
-  register_mask(name="my_custom_mask", mask_path=mask_path, space="Native")
+  register_mask(name="my_custom_mask", mask_path=mask_path, space="native")
 
 Simple, right? Now we just have to configure a YAML file to register this mask
 so we can use it for :ref:`codeless configuration of junifer <codeless>`.
@@ -57,14 +57,14 @@ so we can use it for :ref:`codeless configuration of junifer <codeless>`.
 Step 2: Configure a YAML file for registration of a mask
 --------------------------------------------------------
 
-In order to do this, we can use the ``with`` keyword provided by junifer:
+In order to do this, we can use the ``with`` keyword provided by ``junifer``:
 
 .. code-block:: yaml
 
   with:
     - register_custom_mask.py
 
-Then we can use this mask for any processing step or marker that takes in a
+Then we can use this mask for any processing step or Marker that takes in a
 mask as an argument. For example:
 
 .. code-block:: yaml
@@ -76,12 +76,15 @@ mask as an argument. For example:
       method: mean
       masks: "my_custom_mask"
 
-Now, you can simply use this YAML file to run your pipeline. One important
+Now, you can simply use this YAML file to run your pipeline.
-point to keep in mind is that if the paths given in ``register_custom_mask.py``
+
-are relative paths, they will be interpreted by junifer as relative to the
+.. important::
-jobs directory (i.e. where junifer will create submit files, logs directory and
+
-so on). For simplicity, you may just want to use absolute paths to avoid
+   It's important to keep in mind that if the paths given in
-confusion, yet using relative paths is likely a better way to make your
+   ``register_custom_mask.py`` are relative paths, they will be interpreted
-pipeline directory/repository more portable and therefore more reproducible for
+   by junifer as relative to the jobs directory (i.e. where ``junifer`` will
-others. Really, once you understand how these paths are interpreted by junifer,
+   create submit files, logs directory and so on). For simplicity, you may just
-it is quite easy.
+   want to use absolute paths to avoid confusion, yet using relative paths is
+   likely a better way to make your pipeline directory / repository more portable
+   and therefore more reproducible for others. Really, once you understand how
+   paths are interpreted by ``junifer``, it is quite easy.

docs/extending/parcellations.rst

@@ -5,28 +5,29 @@
 Adding Parcellations
 ====================
 
-Before you start adding your own parcellations, check whether junifer has
+Before you start adding your own parcellations, check whether ``junifer`` has
 the parcellation :ref:`in-built already <builtin>`. Perhaps, what is available
-there will suffice to achieve your goals. However, of course junifer will not
+there will suffice to achieve your goals. However, of course ``junifer`` will not
 have every parcellation available that you may want to use, and if so, it will
-be nice to be able to add it yourself using a format that junifer understands.
+be nice to be able to add it yourself using a format that ``junifer`` understands.
 Similarly, you may even be interested in creating your own custom parcellations
-and then adding them to junifer, so you can use junifer to obtain different
+and then adding them to ``junifer``, so you can use ``junifer`` to obtain
-markers to assess and validate your own parcellation. So, how can you do this?
+different Markers to assess and validate your own parcellation. So, how can you do
+this?
 
 Since both of these use-cases are quite common, and not being able to use your
-favourite parcellation is of course quite a buzzkill, junifer actually provides
+favourite parcellation is of course quite a buzzkill, ``junifer`` actually
-the easy-to-use :func:`.register_parcellation` function to do just that. Let's
+provides the easy-to-use :func:`.register_parcellation` function to do just that.
-try to understand the API reference and then use this function to register our
+Let's try to understand the API reference and then use this function to register our
 own parcellation.
 
 From the API reference, we can see that it has 4 positional arguments
 (``name``, ``parcellation_path``, ``parcels_labels`` and ``space``) as well as
 one optional keyword argument (``overwrite``).
 
-The ``name`` of the parcellation is up to you and will be the name that junifer
+The ``name`` of the parcellation is up to you and will be the name that
-will use to refer to this particular parcellation. You can think of this as
+``junifer`` will use to refer to this particular parcellation. You can think of
-being similar to a key in a python dictionary, i.e. a key that is used to
+this as being similar to a key in a Python dictionary, i.e. a key that is used to
 obtain and operate on the actual parcellation data. This ``name`` must always
 be a string. For example, we could call our parcellation
 ``"my_custom_parcellation"`` (Note, that in a real-world use case this is
@@ -52,14 +53,14 @@ first label in this list corresponds to the first integer label in the
 parcellation and so on).
 
 Lastly, we specify the ``space`` that the parcellation is in, for example,
-``"MNI"`` or ``"Native"`` (scanner-native space).
+``"MNI152NLin2009cAsym"`` or ``"native"`` (scanner-native space).
 
 Step 1: Prepare code to register a parcellation
 -----------------------------------------------
 
-Now we know everything that we need to know to make sure junifer can use our
+Now we know everything that we need to know to make sure ``junifer`` can use our
-own parcellation to compute any parcellation-based marker. For example,
+own parcellation to compute any parcellation-based Marker. A simple example could
-a simple example could look like this:
+look like this:
 
 .. code-block:: python
 
@@ -82,20 +83,20 @@ a simple example could look like this:
       name="my_custom_parcellation",
       parcellation_path=path_to_parcellation,
       parcels_labels=my_labels,
-      space="MNI"
+      space="MNI152NLin2009cAsym"
   )
 
 We can run this code and it seems to work, however, how can we actually
-include the custom parcellation in a junifer pipeline using a
+include the custom parcellation in a ``junifer`` pipeline using a
 :ref:`code-less YAML configuration <codeless>`?
 
 Step 2: Add parcellation registration to the YAML file
 ------------------------------------------------------
 
-In order to use the parcellation in a junifer pipeline configured by a YAML
+In order to use the parcellation in a ``junifer`` pipeline configured by a YAML
-file, we can save the above code in a python file, say
+file, we can save the above code in a Python file, say
 ``registering_my_parcellation.py``. We can then simply add this file using the
-``with`` keyword provided by junifer:
+``with`` keyword provided by ``junifer``:
 
 .. code-block:: yaml
 
@@ -105,7 +106,7 @@ file, we can save the above code in a python file, say
 Afterwards continue configuring the rest of the pipeline in this YAML file, and
 you will be able to use this parcellation using the name you gave the
 parcellation when registering it. For example, we can add a
-:class:`.ParcelAggregation` marker to demonstrate how this can be done:
+:class:`.ParcelAggregation` Marker to demonstrate how this can be done:
 
 .. code-block:: yaml
 
@@ -115,12 +116,15 @@ parcellation when registering it. For example, we can add a
       parcellation: my_custom_parcellation
       method: mean
 
-Now, you can simply use this YAML file to run your pipeline. One important
+Now, you can simply use this YAML file to run your pipeline.
-point to keep in mind is that if the paths given in
+
-``registering_my_parcellation.py`` are relative paths, they will be interpreted
+.. important::
-by junifer as relative to the jobs directory (i.e. where junifer will create
+
-submit files, logs directory and so on). For simplicity, you may just want to
+   It's important to keep in mind that if the paths given in
-use absolute paths to avoid confusion, yet using relative paths is likely a
+   ``registering_my_parcellation.py`` are relative paths, they will be interpreted
-better way to make your pipeline directory/repository more portable and
+   by ``junifer`` as relative to the jobs directory (i.e. where ``junifer`` will
-therefore more reproducible for others. Really, once you understand how these
+   create submit files, logs directory and so on). For simplicity, you may just
-paths are interpreted by junifer, it is quite easy.
+   want to use absolute paths to avoid confusion, yet using relative paths is
+   likely a better way to make your pipeline directory / repository more portable
+   and therefore more reproducible for others. Really, once you understand how
+   these paths are interpreted by ``junifer``, it is quite easy.

docs/extending/preprocessor.rst

@@ -0,0 +1,246 @@
+.. include:: ../links.inc
+
+.. _extending_preprocessors:
+
+Creating Preprocessors
+======================
+
+As already mentioned in the introduction, ``junifer`` does not do traditional
+MRI pre-processing but can perform minimal preprocessing of the data that the
+DataGrabber provides, for example, smoothing after confound regression or
+transforming data to subject-native space before feature extraction. While
+there are a few Preprocessors available already and we are constantly adding
+new ones, you might need something specific and then you can create your
+own Preprocessor.
+
+While implementing your own Preprocessor, you need to always inherit from
+:class:`.BasePreprocessor` and implement a few methods:
+
+#. ``get_valid_inputs``: This method should return a list of strings
+   representing the valid data types that the Preprocessor can work on.
+   Check :ref:`data types <data_types>` for reference.
+#. ``get_output_type``: This method should just return the input as it
+   is unused as of now.
+#. ``preprocess``: The method that given the data, preprocesses the data.
+#. ``__init__``: The initialisation method, where the Preprocessor is
+   configured.
+
+As an example, we will develop a ``NilearnSmoothing`` Preprocessor, which
+smoothens the data using :func:`nilearn.image.smooth_img`. This is often
+desirable in cases where your data is preprocessed using ``fMRIPrep``, as
+``fMRIPrep`` does not perform smoothing.
+
+.. _extending_preprocessors_input_output:
+
+Step 1: Configure input and output
+----------------------------------
+
+In this step, we define the input and output data types of the Preprocessor.
+For input we can accept ``T1w``, ``T2w`` and ``BOLD``
+:ref:`data types <data_types>`.
+
+.. code-block:: python
+
+    ...
+
+    def get_valid_inputs(self) -> list[str]:
+        return ["T1w", "T2w", "BOLD"]
+
+    ...
+
+The output definition of the Preprocessor is unused now but is kept for
+completeness.
+
+.. code-block:: python
+
+    ...
+
+    def get_output_type(self, input_type: str) -> str:
+        return input_type
+
+    ...
+
+.. _extending_preprocessors_init:
+
+Step 2: Initialise the Preprocessor
+-----------------------------------
+
+Now we need to define our Preprocessor class' constructor which is also how
+you configure it. Our class will have the following arguments:
+
+1. ``fwhm``: The smoothing strength as a full-width at half maximum
+   (in millimetres). Since we depend on :func:`nilearn.image.smooth_img`, we
+   pass the value to it.
+2. ``on``: The data type we want the Preprocessor to work on. If the user does
+   not specify, it will work on all the data types given by the
+   ``get_valid_inputs`` function.
+
+.. attention::
+
+   Only basic types (*int*, *bool* and *str*), lists, tuples and dictionaries
+   are allowed as parameters. This is because the parameters are stored in
+   JSON format, and JSON only supports these types.
+
+.. code-block:: python
+
+    from typing import Literal
+
+    from numpy.typing import ArrayLike
+
+
+    ...
+
+    def __init__(
+        self,
+        fwhm: int | float | ArrayLike | Literal["fast"] | None,
+        on: str | list[str] | None = None,
+    ) -> None:
+        self.fwhm = fwhm
+        super().__init__(on=on)
+
+    ...
+
+.. caution::
+
+   Parameters of the Preprocessor must be stored as object attributes without
+   using ``_`` as prefix. This is because any attribute that starts with ``_``
+   will not be considered as a parameter and not stored as part of the metadata
+   of the Preprocessor.
+
+.. _extending_preprocessors_preprocess:
+
+Step 3: Preprocess the data
+---------------------------
+
+Finally, we will write the actual logic of the Preprocessor. This method will
+be called by ``junifer`` when needed, using the data provided by the
+DataGrabber, as configured by the user. The method ``preprocess`` has two
+arguments:
+
+* ``input``: A dictionary with the data to be used by the Preprocessor. This
+  will be the corresponding element in the :ref:`Data Object<data_object>`
+  already indexed. Thus, the dictionary has at least two keys: ``data`` and
+  ``path``. The first one contains the data, while the second one contains the
+  path to the data. The dictionary can also contain other keys, depending on the
+  data type.
+* ``extra_input``: The rest of the :ref:`Data Object<data_object>`. This is
+  useful if you want to use other data (e.g., ``Warp`` can be used to provide
+  the transformation matrix file for transformation to subject-native space).
+
+and it has two return values:
+
+* First is the ``input`` dictionary with necessary data modified. Usually, you
+  want to replace the ``input["data"]`` with the preprocessed data.
+* Second is a dictionary just like ``input`` or ``extra_input`` but with only
+  specific key-value pairs which you would like to pass down to the Markers.
+  For example, if your Preprocessor computes some mask with the preprocessed
+  data, you could pass it through this which would be added and available
+  in the Marker step with the same key you pass here. Usually, you would
+  want to pass ``None``.
+
+.. code-block:: python
+
+    from typing import Any
+
+    from nilearn import image as nimg
+
+
+    ...
+
+    def preprocess(
+        self,
+        input: dict[str, Any],
+        extra_input: dict[str, Any] | None = None,
+    ) -> tuple[dict[str, Any], dict[str, Any] | None]:
+         input["data"] = nimg.smooth_img(imgs=input["data"], fwhm=self.fwhm)
+         return input, None
+
+     ...
+
+Step 4: Finalise the Preprocessor
+---------------------------------
+
+Now we just need to combine everything we have above and throw in a couple of
+other stuff to get our Preprocessor ready.
+
+First, we specify the :ref:`dependencies <specifying_dependencies>` for our
+class, which are basically the packages that are required by the class. This is
+used for validation before running to ensure all the packages are installed and
+also to keep track of the dependencies and their versions in the metadata. We
+define it using a class attribute like so:
+
+.. code-block:: python
+
+    _DEPENDENCIES = {"nilearn"}
+
+Then, we just need to register the Preprocessor using ``@register_preprocessor``
+decorator and our final code should look like this:
+
+.. code-block:: python
+
+    from typing import Any, Literal
+
+    from junifer.api.decorators import register_preprocessor
+    from junifer.preprocess import BasePreprocessor
+
+    from nilearn import image as nimg
+    from numpy.typing import ArrayLike
+
+
+    @register_preprocessor
+    class NilearnSmoothing(BasePreprocessor):
+
+        _DEPENDENCIES = {"nilearn"}
+
+        def __init__(
+            self,
+            fwhm: int | float | ArrayLike | Literal["fast"] | None,
+            on: str | list[str] | None = None,
+        ) -> None:
+            self.fwhm = fwhm
+            super().__init__(on=on)
+
+        def get_valid_inputs(self) -> list[str]:
+            return ["T1w", "T2w", "BOLD"]
+
+        def get_output_type(self, input_type: str) -> str:
+            return input_type
+
+        def preprocess(
+            self,
+            input: dict[str, Any],
+            extra_input: dict[str, Any] | None = None,
+        ) -> tuple[dict[str, Any], dict[str, Any] | None]:
+            input["data"] = nimg.smooth_img(imgs=input["data"], fwhm=self.fwhm)
+            return input, None
+
+
+.. _extending_preprocessors_template:
+
+Template for a custom Preprocessor
+----------------------------------
+
+.. code-block:: python
+
+    from junifer.api.decorators import register_preprocessor
+    from junifer.preprocess import BasePreprocessor
+
+
+    @register_preprocessor
+    class TemplatePreprocessor(BasePreprocessor):
+
+        def __init__(self, on=None):
+            # TODO: add preprocessor-specific parameters
+            super().__init__(on=on)
+
+        def get_valid_inputs(self):
+            # TODO: Complete with the valid inputs
+            valid = []
+            return valid
+
+        def get_output_type(self, input_type):
+            return input_type
+
+        def preprocess(self, input, extra_input):
+            # TODO: add the preprocessor logic
+            return input, None

docs/installation.rst

@@ -1,35 +1,13 @@
 .. include:: links.inc
 
-Installing junifer
+Installing ``junifer``
-==================
+======================
-
-
-Requirements
-------------
-
-junifer is compatible with `Python`_ >= 3.8 and requires the following packages:
-
-* ``click>=8.1.3,<8.2``
-* ``numpy>=1.24,<1.27``
-* ``datalad>=0.15.4,<0.20``
-* ``pandas>=1.4.0,<2.2``
-* ``nibabel>=3.2.0,<5.11``
-* ``nilearn>=0.9.0,<=0.11.0``
-* ``sqlalchemy>=1.4.27,<= 2.1.0``
-* ``ruamel.yaml>=0.17,<0.18``
-* ``h5py>=3.8.0,<3.10``
-
-Depending on the installation method, these packages might be installed
-automatically.
-
-Installation
-------------
 
 Depending on your use-case, ``junifer`` can be installed differently:
 
-* Install the :ref:`install_latest_release`. This is the most suitable approach
+* Install the :ref:`latest stable release <install_latest_release>`. This is the most suitable approach
   for end users.
-* Install from :ref:`install_development_git`. This is the most suitable approach
+* Install from :ref:`latest development release <install_development_git>`. This is the most suitable approach
   for developers.
 
 
@@ -39,8 +17,8 @@ Either way, we strongly recommend using
 
 .. _install_latest_release:
 
-Stable release
+Using a package manager
-~~~~~~~~~~~~~~
+-----------------------
 
 Use ``pip`` to install ``junifer`` from `PyPI <https://pypi.org>`_, like so:
 
@@ -64,8 +42,8 @@ You can also install via ``conda``, like so:
 
 .. _install_development_git:
 
-Local Git repository
+From the source
-~~~~~~~~~~~~~~~~~~~~
+---------------
 
 Follow the `detailed contribution guidelines <contribution.rst>`_.
 
@@ -81,11 +59,11 @@ that are required for specific markers.
 
 .. important::
 
-   The Docker container wrappers add the commands required by junifer. Using
+   The Docker container wrappers add the commands required by ``junifer``. Using
    these commands have some limitations, mostly related to handling files and
-   paths. Junifer knows about this and uses these commands in the proper way.
+   paths. ``junifer`` knows about this and uses these commands in the proper way.
    Keep this in mind if you try to use the Docker wrappers outside of
-   junifer. These caveats and limitations are not documented.
+   ``junifer``. These caveats and limitations are not documented.
 
 AFNI
 ----

docs/links.inc

@@ -23,6 +23,7 @@
 .. _`nilearn`: https://nilearn.github.io
 .. _`nipype`: https://nipype.readthedocs.io
 .. _`datalad`: https://datalad.org
+.. _`templateflow`: https://www.templateflow.org
 
 .. _`venv`: https://docs.python.org/3/tutorial/venv.html
 .. _`conda env`: https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html

docs/starting.rst

@@ -2,8 +2,8 @@
 
 .. _starting:
 
-First steps with junifer
+First steps with ``junifer``
-========================
+============================
 
 .. note::
 
@@ -13,7 +13,7 @@ First steps with junifer
 
    flowchart TD
      start((( Start )))
-     read_understanding(Read Understanding Junifer)
+     read_understanding(Read Understanding junifer)
      start --> read_understanding
      question_features{Can I compute\nthe features I want\nusing junifer?}
      read_understanding --> question_features
@@ -22,7 +22,7 @@ First steps with junifer
      question_features -->|No| question_feature_type
      read_using --> question_features
 
-     read_using(Read Using Junifer)
+     read_using(Read Using junifer)
 
      question_feature_type{"What am I missing\nfrom junifer"}
      question_feature_type --> missing_datagrabber
@@ -30,7 +30,7 @@ First steps with junifer
      question_feature_type --> missing_marker
      question_feature_type --> missing_other
      missing_datagrabber("A Dataset/DataGrabber")
-     missing_preprocessing("A Preprocessing")
+     missing_preprocessing("A Preprocessor")
      missing_marker("A Marker")
      missing_other("Something else")
 
@@ -38,7 +38,7 @@ First steps with junifer
      question_datagrabber_junifarm{Is the\ndataset/datagrabber\nin juni-farm?}
      question_datagrabber_junifarm -->|Yes| read_using_final
      question_datagrabber_junifarm -->|No| read_extending_datagrabber_start
-     read_extending_datagrabber_start(Read Creating a Junifer extension)
+     read_extending_datagrabber_start(Read Creating a junifer extension)
      read_extending_datagrabber_start --> read_extending_datagrabber
      read_extending_datagrabber(Read Creating Data Grabbers)
      read_extending_datagrabber --> question_datagrabber_kind
@@ -55,14 +55,14 @@ First steps with junifer
      question_contribute_datagrabber{Do you think\nyour DataGrabber\nis useful for other users?}
      question_contribute_datagrabber -->|Yes| contribute_datagrabber
      question_contribute_datagrabber -->|No| final_run
-     contribute_datagrabber(Create a\nDATASET REQUEST\nissue on Github)
+     contribute_datagrabber(Create a\nDATASET REQUEST\nissue on GitHub)
      contribute_datagrabber --> final_run
 
      missing_marker --> question_marker_junifarm
      question_marker_junifarm{Is the marker\nin juni-farm?}
      question_marker_junifarm -->|Yes| read_using_final
      question_marker_junifarm -->|No| read_extending_marker_start
-     read_extending_marker_start(Read Creating a Junifer extension)
+     read_extending_marker_start(Read Creating a junifer extension)
      read_extending_marker_start --> read_extending_marker
      read_extending_marker(Read Creating Markers)
      read_extending_marker --> question_marker_solved
@@ -72,7 +72,7 @@ First steps with junifer
      question_contribute_marker{Do you think\nyour Marker\nis useful for other users?}
      question_contribute_marker -->|Yes| contribute_marker
      question_contribute_marker -->|No| final_run
-     contribute_marker(Create a\nMARKER REQUEST\nissue on Github)
+     contribute_marker(Create a\nMARKER REQUEST\nissue on GitHub)
      contribute_marker --> final_run
 
      missing_preprocessing --> contact_help
@@ -87,22 +87,22 @@ First steps with junifer
      missing_other --> missing_other_other
      missing_other_other --> contact_help
 
-     contact_help(((Contact the\nJunifer team)))
+     contact_help(((Contact the\njunifer team)))
 
      missing_mask --> read_adding_mask_start
-     read_adding_mask_start("Read Creating a Junifer extension")
+     read_adding_mask_start("Read Creating a junifer extension")
      read_adding_mask_start --> read_adding_mask
      read_adding_mask("Read Adding Masks")
      read_adding_mask --> missing_other_solved
 
      missing_parcellation --> read_adding_parcellation_start
-     read_adding_parcellation_start("Read Creating a Junifer extension")
+     read_adding_parcellation_start("Read Creating a junifer extension")
      read_adding_parcellation_start --> read_adding_parcellation
      read_adding_parcellation("Read Adding Parcellations")
      read_adding_parcellation --> missing_other_solved
 
      missing_coordinates --> read_adding_coordinates_start
-     read_adding_coordinates_start("Read Creating a Junifer extension")
+     read_adding_coordinates_start("Read Creating a junifer extension")
      read_adding_coordinates_start --> read_adding_coordinates
      read_adding_coordinates("Read Adding Coordinates")
      read_adding_coordinates --> missing_other_solved
@@ -110,11 +110,11 @@ First steps with junifer
      missing_other_solved{Did you solve your issue?}
      missing_other_solved -->|Yes| read_using_final
      missing_other_solved -->|No| missing_other_contact
-     missing_other_contact(Contact the\nJunifer team)
+     missing_other_contact(Contact the\njunifer team)
      missing_other_contact --> missing_other_issue
-     missing_other_issue(((Submit a\nFEATURE REQUEST\nissue in Github)))
+     missing_other_issue(((Submit a\nFEATURE REQUEST\nissue in GitHub)))
 
-     read_using_final(Read Using Junifer)
+     read_using_final(Read Using junifer)
      read_using_final --> final_yaml
      final_yaml(Create/edit the YAML file)
      final_yaml --> final_run
@@ -125,9 +125,9 @@ First steps with junifer
      question_error_run{"Is it an issue\nwith my YAML file?"}
      question_error_run -->|Yes| final_yaml
      question_error_run -->|No| error_contact
-     error_contact(Contact the\nJunifer team)
+     error_contact(Contact the\njunifer team)
      error_contact --> error_issue
-     error_issue(((Submit a\nBUG REPORT issue\nin Github)))
+     error_issue(((Submit a\nBUG REPORT issue\nin GitHub)))
      question_final_run_worked -->|Yes| final_queue
      final_queue(Use junifer queue to compute your features)
      final_queue --> final_magic

docs/understanding/data.rst

@@ -105,7 +105,7 @@ Data Types
      - Preprocessed or Raw T1w image
    * - ``BOLD``
      - BOLD image (4D)
-     - Preprocessed/Denoised BOLD image (fmriprep output)
+     - Preprocessed or Denoised BOLD image (fMRIPrep output)
    * - ``BOLD_confounds``
      - BOLD image confounds (CSV/TSV file)
      - Confounds that can be applied to the BOLD image.

docs/understanding/datagrabber.rst

@@ -9,9 +9,9 @@ Description
 -----------
 
 The ``DataGrabber`` is an object that can provide an interface to datasets you
-want to work with in junifer. Every concrete implementation of a DataGrabber is
+want to work with in ``junifer``. Every concrete implementation of a DataGrabber
-aware of a particular dataset's structure and thus allows you to fetch specific
+is aware of a particular dataset's structure and thus allows you to fetch
-elements of interest from the dataset. It adds the ``path`` key to each
+specific elements of interest from the dataset. It adds the ``path`` key to each
 :ref:`data type <data_types>` in the :ref:`Data object <data_object>`.
 
 DataGrabbers are intended to be used as context managers. When used within a
@@ -20,18 +20,18 @@ the dataset, for example, downloading and cleaning up. As the interface
 is consistent, you always use the same procedure to interact with the DataGrabber.
 
 For example, a concrete implementation of :class:`.DataladDataGrabber` can
-provide junifer with data from a Datalad dataset. Of course, DataGrabbers are not
+provide ``junifer`` with data from a Datalad dataset. Of course, DataGrabbers are
-only meant to work with Datalad datasets but any dataset.
+not only meant to work with Datalad datasets but any dataset.
 
 If you are interested in using already provided DataGrabbers, please go to
 :doc:`../builtin`. And, if you want to implement your own DataGrabber, you need
-to provide concrete implementations of base classes already provided.
+to provide concrete implementations of abstract base classes already provided.
 
 Base Classes
 ------------
 
-In this section, we showcase different abstract base classes you might want to
+In this section, we showcase different abstract and concrete base classes you
-use to implement your own DataGrabber.
+might want to use to implement your own DataGrabber.
 
 .. list-table::
    :widths: auto

docs/understanding/datareader.rst

@@ -9,17 +9,17 @@ Description
 -----------
 
 The ``DataReader`` is an object that is responsible for actually reading data
-files in junifer. It reads the value of the key ``path`` for each
+files in ``junifer``. It reads the value of the key ``path`` for each
 :ref:`data type <data_types>` in the :ref:`Data object <data_object>` and loads
 them into memory. After reading the data into memory, it adds the key ``data``
 to the same level as ``path`` and the value is the actual data in the memory.
 
-DataReaders are meant to be used inside the datagrabber context but you can
+DataReaders are meant to be used inside the DataGrabber context but you can
 operate on them outside the context as long as the actual data is in the memory
 and the Python runtime has not garbage-collected it.
 
-For data formats not supported by junifer yet, you can either make your own
+For data formats not supported by ``junifer`` yet, you can either make your own
-*Data Reader* or open an issue on `junifer Github`_ and we can help you out.
+DataReader or open an issue on `junifer Github`_ and we can help you out.
 
 File Formats
 ------------

docs/understanding/index.rst

@@ -2,14 +2,14 @@
 
 .. _understanding:
 
-Understanding junifer
+Understanding ``junifer``
-=====================
+=========================
 
-Before you start, you should understand how junifer works. Junifer is a
+Before you start, you should understand how ``junifer`` works. ``junifer`` is a
 tool conceived to extract features from neuroimaging data in an easy-to-use
 manner, with minimal coding and minimal user expertise in the internal aspects.
 
-Unlike other tools like FSL, SPM, AFNI, etc., junifer is not a toolbox to
+Unlike other tools like FSL, SPM, AFNI, etc., ``junifer`` is not a toolbox to
 pre-process data, but a toolbox to extract features from previously
 pre-processed data.
 
@@ -20,9 +20,9 @@ julearn_).
 
 .. important::
 
-   Junifer is not a toolbox to create pipelines, but a tool to configure the
+   ``junifer`` is not a toolbox to create pipelines, but a tool to configure the
-   junifer pipeline, which is intended to be fixed and not to be changed. If you
+   ``junifer`` pipeline, which is intended to be fixed and not to be changed. If
-   want to create a pipeline, you should use other tools like nipype_.
+   you want to create a pipeline, you should use other tools like nipype_.
 
 .. toctree::
    :maxdepth: 2

docs/understanding/marker.rst

@@ -21,12 +21,12 @@ the pipeline.
    SPM, AFNI, etc., . For example, one can perform confound removal on loaded
    data and then perform feature extraction.
 
-Markers are meant to be used inside the datagrabber context but you can operate
+Markers are meant to be used inside the DataGrabber context but you can operate
 on them outside the context as long as the actual data is in the memory and the
 Python runtime has not garbage-collected it.
 
-If you are interested in using already provided markers, please go to
+If you are interested in using already provided Markers, please go to
-:doc:`../builtin`. And, if you want to implement your own marker, you need to
+:doc:`../builtin`. And, if you want to implement your own Marker, you need to
 provide concrete implementation of :class:`.BaseMarker`. Specifically, you
 need to override ``get_valid_inputs``, ``get_output_type`` and ``compute``
 methods.

docs/understanding/pipeline.rst

@@ -2,8 +2,8 @@
 
 .. _pipeline:
 
-The junifer Pipeline
+The ``junifer`` Pipeline
-====================
+========================
 
 The junifer pipeline is the main execution path of junifer. It consists of five
 steps:
@@ -11,10 +11,10 @@ steps:
 1. :ref:`Data Grabber <datagrabber>`: Interpret the dataset and provide a list
    of files.
 2. :ref:`Data Reader <datareader>`: Read the files.
-3. :ref:`Pre-processing <preprocess>`: Prepare the images for marker
+3. :ref:`Preprocess <preprocess>`: Prepare the files' data for marker
    computation.
-4. :ref:`Marker Computation <marker>`: Compute the marker.
+4. :ref:`Marker Computation <marker>`: Compute the marker(s).
-5. :ref:`Storage <storage>`: Store the marker values.
+5. :ref:`Storage <storage>`: Store the marker(s) values.
 
 The element that is passed across the pipeline is called the
 :ref:`Data Object<data_object>`.
@@ -26,7 +26,7 @@ The following is a graphical representation of the pipeline:
    flowchart LR
      dg[Data Grabber]
      dr[Data Reader]
-     pp[Pre-processing]
+     pp[Preprocess]
      mc[Marker Computation]
      st[Storage]
      dg --> dr
@@ -45,7 +45,7 @@ on multiple markers:
    flowchart LR
      dg[Data Grabber]
      dr[Data Reader]
-     pp[Pre-processing]
+     pp[Preprocess]
      mc1[Marker Computation]
      mc2[Marker Computation]
      mc3[Marker Computation]

docs/understanding/preprocess.rst

@@ -22,12 +22,12 @@ want to perform confound removal on ``BOLD`` data before feature extraction.
 Confound Removal
 ----------------
 
-The *Confound Removal* step is meant to remove *confounds* from the ``BOLD``
+This step is meant to remove *confounds* from the ``BOLD`` data. The confounds
-data. The confounds are extracted from the ``BOLD_confounds`` data (must be
+are extracted from the ``BOLD_confounds`` data (must be provided by the
-provided by the :ref:`Data Grabber <datagrabber>`). The confounds are then
+:ref:`Data Grabber <datagrabber>`). The confounds are then regressed out from
-regressed out from the ``BOLD`` data using :func:`nilearn.image.clean_img`.
+the ``BOLD`` data using :func:`nilearn.image.clean_img`.
 
-Currently, junifer supports only one confound removal class:
+Currently, ``junifer`` supports only one confound removal class:
 :class:`.fMRIPrepConfoundRemover`. This class is meant to remove confounds as
 described before, using the output of `fMRIPrep`_ as reference.
 
@@ -128,3 +128,69 @@ parameters:
        | If not, a mask is computed using
        | :func:`nilearn.masking.compute_brain_mask`.
      - compute
+
+.. _preprocess_warping:
+
+Warping or Transformation to other spaces
+-----------------------------------------
+
+``junifer`` can also warp or transform any supported
+:ref:`data type <data_types>` from the template space provided by the dataset
+(e.g., ``MNI152NLin6Asym``) to either  the subject's
+:ref:`native space <preprocess_warping_native>` or to any other
+:ref:`template space <preprocess_warping_template>`
+(e.g., ``MNI152NLin2009cAsym``). This functionality is provided by
+:class:`.SpaceWarper` and depends on external tools like FSL and / or ANTs.
+
+.. _preprocess_warping_native:
+
+Warping to subject's native space
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+To warp to subject's native space, the dataset needs to provide ``T1w`` and
+``Warp`` data types and the DataGrabber needs to at least have
+``["BOLD", "T1w", "Warp"]`` (if you are warping ``BOLD``) as the ``types``
+parameter's value. The :class:`.SpaceWarper`'s ``reference`` parameter needs
+to be set to ``T1w``, which means that the ``BOLD`` data will be transformed
+using the ``T1w`` as reference (it's resampled internally to match the
+resolution of the ``BOLD``). The ``Warp`` data type is new and it's only purpose
+is to provide the warp or transformation file (can be linear, non-linear or
+linear + non-linear transform) for the purpose. For ``using`` parameter, you can
+pass either ``"fsl"`` or ``"ants"`` depending on the warp or transformation file
+format.
+
+An example YAML might look like this:
+
+.. code-block:: yaml
+
+      preprocess:
+         - kind: SpaceWarper
+           using: fsl
+           reference: T1w
+
+.. _preprocess_warping_template:
+
+Warping to other template space
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+In a situation where your dataset might provide the ``BOLD`` data (or any other
+data type that you want to work on) in ``MNI152NLin6Asym`` template space but
+you would like to compute features in ``MNI152NLin2009cAsym`` template space,
+you can also use the :class:`.SpaceWarper` by setting the ``reference``
+parameter to the template space's name, in this case,
+``reference="MNI152NLin2009cAsym"``. The ``using`` parameter needs to be set
+to ``"ants"`` as we need it to warp the data.
+
+.. note::
+
+   We only support template spaces provided by `templateflow`_ and the naming
+   is similar except that we omit the ``tpl-`` prefix used by ``templateflow``.
+
+For an YAML example:
+
+.. code-block:: yaml
+
+      preprocess:
+         - kind: SpaceWarper
+           using: ants
+           reference: MNI152NLin2009cAsym

docs/understanding/storage.rst

@@ -13,7 +13,7 @@ as computed from :ref:`Marker <marker>` step of the pipeline. If the pipeline is
 provided with a ``storage-like`` object, the extracted features are stored via
 that object else they are kept in memory.
 
-Storage is meant to be used inside the datagrabber context but you can operate
+Storage is meant to be used inside the DataGrabber context but you can operate
 on them outside the context as long as the processed data is in the memory and
 the Python runtime has not garbage-collected it.
 
@@ -25,8 +25,8 @@ storage object in turn declares and provides implementation for specific
 ``matrix``, ``vector`` and ``timeseries`` via ``store_matrix``, ``store_vector``
 and ``store_timeseries`` methods respectively.
 
-For storage interfaces not supported by junifer yet, you can either make your
+For storage interfaces not supported by ``junifer`` yet, you can either make
-own ``Storage`` by providing a concrete implementation of
+your own ``Storage`` by providing a concrete implementation of
 :class:`.BaseFeatureStorage` or open an issue on `junifer Github`_ and we can
 help you out.
 

docs/using/codeless.rst

@@ -5,7 +5,7 @@
 Code-less Configuration
 =======================
 
-On of the most important features of junifer is its capacity to run without
+One of the most important features of ``junifer`` is its capacity to run without
 writing a single line of code. This is achieved by using a configuration file
 that is written in YAML_. In this file, we configure the different steps of
 :ref:`pipeline`.
@@ -17,7 +17,7 @@ As a reminder, this is how the pipeline looks like:
    flowchart LR
      dg[Data Grabber]
      dr[Data Reader]
-     pp[Pre-processing]
+     pp[Preprocess]
      mc[Marker Computation]
      st[Storage]
      dg --> dr
@@ -31,21 +31,21 @@ as well as some general parameters.
 
 As an example, we will generate the configuration file for a pipeline that will
 extract the mean ``VBM_GM`` values using two different parcellations and one set
-of coordinates, from the ``Oasis VBM Testing dataset`` included in junifer.
+of coordinates, from the ``Oasis VBM Testing dataset`` included in ``junifer``.
 
 
 General Parameters
 ------------------
 
 The general parameters are the ones that are not specific to any of the sections
-of the pipeline, but configure junifer as a whole. These parameters are:
+of the pipeline, but configure ``junifer`` as a whole. These parameters are:
 
-* ``with``: A section used to specify modules and junifer extensions to use.
+* ``with``: A section used to specify modules and ``junifer`` extensions to use.
-* ``workdir``: The working directory where junifer will store temporary files.
+* ``workdir``: The working directory where ``junifer`` will store temporary files.
 
-Since the example uses a specific datagrabber for testing, we need to add
+Since the example uses a specific DataGrabber for testing, we need to add
-``junifer.testing.registry`` to the ``with`` section. This will allow junifer
+``junifer.testing.registry`` to the ``with`` section. This will allow ``junifer``
-to find the datagrabber. We will set the ``workdir`` to ``/tmp``.
+to find the DataGrabber. We will set the ``workdir`` to ``/tmp``.
 
 .. code-block:: yaml
 
@@ -66,9 +66,9 @@ In order to configure the pipeline, we need to configure each step:
 
 .. important::
 
-   The datareader step configuration is optional, as junifer only provides one
+   The ``datareader`` step configuration is optional, as ``junifer`` only
-   datareader. Nevertheless, it is possible to extend junifer with custom
+   provides one DataReader. Nevertheless, it is possible to extend ``junifer``
-   datareaders, and thus, it is also possible to configure this step.
+   with custom DataReaders, and thus, it is also possible to configure this step.
 
 
 Data Grabber
@@ -107,9 +107,9 @@ In the ``Oasis VBM Testing dataset`` example, the section will look like this:
 Data Reader
 ^^^^^^^^^^^
 
-As mentioned before, this section is entirely optional, as junifer only provides
+As mentioned before, this section is entirely optional, as ``junifer`` only
-one DataReader (:class:`.DefaultDataReader`), which is the default in case the
+provides one DataReader (:class:`.DefaultDataReader`), which is the default in
-section is not specified.
+case the section is not specified.
 
 In any case, the syntax of the section is the same as for the ``datagrabber``
 section, using the ``kind`` key to specify the DataReader to use, and additional
@@ -127,25 +127,26 @@ For the ``Oasis VBM Testing dataset`` example, we will not specify a
 Preprocess
 ^^^^^^^^^^
 
-Pre-processing is also an optional step, as it might be the case that no
+``preprocess`` is also an optional step, as it might be the case that no
-pre-processing is needed. In the case that pre-processing is needed, the section
+pre-processing is needed. As we can perform multiple preprocessing steps, it's
-must be configured using the ``kind`` key to specify the preprocessor to use,
+passed as a list of Preprocessors. In the case that pre-processing is needed,
-and additional keys to pass parameters to the preprocessor.
+each Preprocessord must be configured using the ``kind`` key to specify the
+Preprocessor to use, and additional keys to pass parameters to the Preprocessor.
 
-For example, to use the :class:`.fMRIPrepConfoundRemover` preprocessor, we just
+For example, to use the :class:`.fMRIPrepConfoundRemover` Preprocessor, we just
 need to specify its name as the ``kind`` key, as well as its parameters.
 
 .. code-block:: yaml
 
   preprocess:
-    kind: fMRIPrepConfoundRemover
+    - kind: fMRIPrepConfoundRemover
-    strategy:
+      strategy:
-      motion: full
+        motion: full
-      wm_csf: full
+        wm_csf: full
-      global_signal: basic
+        global_signal: basic
-    spike: 0.2
+      spike: 0.2
-    detrend: false
+      detrend: false
-    standardize: true
+      standardize: true
 
 
 For the ``Oasis VBM Testing dataset`` example, we will not specify a
@@ -155,9 +156,9 @@ preprocessing step.
 Marker
 ^^^^^^
 
-The ``markers`` section diverges from the previous ones, as we need to specify
+The ``markers`` section like the ``preprocess`` section expects a list of
-a list of markers. Each marker has a name that we can use to refer to it later,
+markers. Each Marker has a name that we can use to refer to it later,
-and a set of parameters that will be passed to the marker.
+and a set of parameters that will be passed to the Marker.
 
 For the ``Oasis VBM Testing dataset`` example, we want to compute the mean
 ``VBM_GM`` value for each parcel using the ``Schaefer parcellation (100 parcels,
@@ -190,14 +191,14 @@ Finally, we need to define how and where the results will be stored. This is
 done using the ``storage`` section, which must be configured using the ``kind``
 key to specify the storage to use, and additional keys to pass parameters.
 
-For example, to use the :class:`.SQLiteFeatureStorage` storage, we just need to
+For example, to use the :class:`.HDF5FeatureStorage` storage, we just need to
 specify where we want to store the results:
 
 .. code-block:: yaml
 
     storage:
-      kind: SQLiteFeatureStorage
+      kind: HDF5FeatureStorage
-      uri: /data/junifer/example/oasis_vbm_testing.sqlite
+      uri: /data/junifer/example/oasis_vbm_testing.hdf5
 
 
 Complete Example
@@ -231,5 +232,5 @@ looks like:
       method: mean
 
   storage:
-    kind: SQLiteFeatureStorage
+    kind: HDF5FeatureStorage
-    uri: /data/junifer/example/oasis_vbm_testing.sqlite
+    uri: /data/junifer/example/oasis_vbm_testing.hdf5

docs/using/index.rst

@@ -2,14 +2,14 @@
 
 .. _using:
 
-Using junifer
+Using ``junifer``
-=============
+=================
 
-In this section, we will cover the main aspects behind using junifer. We will
+In this section, we will cover the main aspects behind using ``junifer``. We
-first explain the basics behind junifer's code-less configuration. Then we will
+will first explain the basics behind junifer's code-less configuration. Then we
-show how to use the command line interface to ``run`` junifer and ``collect``
+will show how to use the command line interface to ``run`` the pipeline and
-the results. Finally, we will show how to use the ``queue`` command to interact
+``collect`` the results. Finally, we will show how to use the ``queue`` command
-with HPC and HTC systems.
+to interact with HPC and HTC systems.
 
 .. toctree::
    :maxdepth: 2
@@ -25,7 +25,7 @@ with HPC and HTC systems.
 Using Common Components
 -----------------------
 
-The following sections explains common components of junifer that can be used
+The following sections explains common components of ``junifer`` that can be used
 across many steps of the pipeline.
 
 .. toctree::

docs/using/masks.rst

@@ -12,7 +12,7 @@ contain a certain ratio of gray matter to white matter / cerebrospinal fluid,
 ensuring that the features are not extracted from voxels that contain mostly
 white matter or cerebrospinal fluid, which could add noise to the BOLD signal.
 
-Junifer provides a number of built-in masks, which can be listed using
+``junifer`` provides a number of built-in masks, which can be listed using
 :func:`.list_masks`. Some masks are images, while other masks can be computed
 using :ref:`nilearn` functions.
 
@@ -22,15 +22,14 @@ dictionary in which the **only** key is the built-in mask name and the value is
 a dictionary of keyword arguments to pass to the mask function.
 
 For example, the following is a valid mask specification that specified the
-``GM_prob0.2`` mask.
+``GM_prob0.2`` mask:
 
 .. code-block:: yaml
 
     masks: GM_prob0.2
 
 The following is a valid mask specification that specifies the
-``compute_brain_mask``  mask (function from nilearn), with a threshold of
+``compute_brain_mask`` mask, with a threshold of ``0.5``.
-``0.5``.
 
 .. code-block:: yaml
 

docs/using/queueing.rst

@@ -5,14 +5,15 @@
 Queueing Jobs (HPC, HTC)
 ========================
 
-Yet another interesting feature of junifer is the ability to queue jobs on
+Yet another interesting feature of ``junifer`` is the ability to queue jobs on
 computational clusters. This is done by adding the ``queue`` section in the
 :ref:`codeless` file and executing the  ``junifer queue`` command.
 
 While junifer is meant to support `HTCondor`_, `SLURM`_ and local queueing
 using `GNU Parallel`_, only HTCondor is currently supported. This will be
-implemented in future releases of junifer. If you are in immediate need of any of
+implemented in future releases of ``junifer``. If you are in immediate need of
-these schedulers, please create an issue on the `junifer github`_ repository.
+any of these schedulers, please create an issue on the `junifer github`_
+repository.
 
 The ``queue`` section of the :ref:`codeless` must start by defining the
 following general parameters:
@@ -24,7 +25,7 @@ following general parameters:
 * ``kind``: The kind of scheduler to be used. Currently, only ``HTCondor`` is
   supported.
 
-Example:
+Example in YAML:
 
 .. code-block:: yaml
 
@@ -40,7 +41,7 @@ The rest of the parameters depend on the scheduler you are using.
 HTCondor
 --------
 
-When using HTCondor, junifer will use a DAG to queue one job per element
+When using HTCondor, ``junifer`` will use a DAG to queue one job per element
 (``junifer run``). As an option, the DAG can include a final job
 (``junifer collect``) to collect the results once all of the individual element
 jobs are finished.
@@ -61,12 +62,13 @@ The following parameters are available for HTCondor:
     If relative path is used then it should be relative to the YAML.
 
 * ``mem``: Memory to be used by the job. It must be provided as a string with
-  the units (e.g. ``2GB``).
+  the units (e.g., ``"2GB"``).
-* ``cpus``: Number of CPUs to be used by the job. It must be provided as an int.
+* ``cpus``: Number of CPUs to be used by the job. It must be provided as an
+  integer (e.g., ``1``).
 * ``disk``: Disk space to be used by the job. It must be provided as a string
-  with the units (e.g. ``2GB``). Keep in mind that junifer uses a local working
+  with the units (e.g., ``"2GB"``). Keep in mind that ``junifer`` uses a local
-  directory for each job, and datalad datasets might be cloned in this temporary
+  working directory for each job, and datalad datasets might be cloned in this
-  directory.
+  temporary directory.
 * ``extra_preamble``: Extra lines to be added to the HTCondor submit file. This
   can be used to add extra parameters to the job, such as ``requirements``.
 * ``collect``: This parameter allows to include a collect to the DAG to collect
@@ -81,7 +83,7 @@ The following parameters are available for HTCondor:
   * ``no``: Do not include a collect job to the DAG.
 
 
-Example:
+Example in YAML:
 
 .. code-block:: yaml