.. _sphx_glr_auto_examples_01_datasets:

.. _examples-datasets:

Working with studysets
----------------------

NiMARE's primary collection type is now :class:`~nimare.nimads.Studyset`.
Studysets can be used directly with estimators, workflows, and several transformers,
while the legacy :class:`~nimare.dataset.Dataset` class remains available for backwards compatibility
and migration workflows.

Additionally, NiMARE contains fetching and conversion tools for a number of meta-analytic resources,
including Neurosynth, NeuroQuery, NeuroVault, and, to a limited extent, BrainMap.
In the examples below, we show how to work with Studysets in NiMARE, along with
legacy Dataset-specific examples for interoperability and migration.


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  <div id='sg-tag-list' class='sphx-glr-tag-list'></div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This is a brief walkthrough of the legacy Dataset class and its methods.">

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  .. image:: /auto_examples/01_datasets/images/thumb/sphx_glr_01_plot_dataset_io_thumb.png
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  :doc:`/auto_examples/01_datasets/01_plot_dataset_io`

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      <div class="sphx-glr-thumbnail-title">The legacy NiMARE Dataset object</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Neurosynth and NeuroQuery are the two largest publicly-available coordinate-based databases. NiMARE includes functions for downloading releases of each database and converting the databases to NiMARE collections for analysis.">

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  .. image:: /auto_examples/01_datasets/images/thumb/sphx_glr_02_download_neurosynth_thumb.png
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  :doc:`/auto_examples/01_datasets/02_download_neurosynth`

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      <div class="sphx-glr-thumbnail-title">Neurosynth and NeuroQuery</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Download statistical maps from NeuroVault, then use them in a meta-analysis, with NiMARE.">

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  .. image:: /auto_examples/01_datasets/images/thumb/sphx_glr_03_plot_neurovault_io_thumb.png
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  :doc:`/auto_examples/01_datasets/03_plot_neurovault_io`

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      <div class="sphx-glr-thumbnail-title">Use NeuroVault statistical maps in NiMARE</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Create a dataset with coordinates derived from peak statistic identification in images.">

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  :doc:`/auto_examples/01_datasets/04_transform_images_to_coordinates`

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      <div class="sphx-glr-thumbnail-title">Transform images into coordinates</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates the key functionality of the NeuroImaging Meta-Analysis Data Structure (NIMADS) with NiMARE, including working with Studysets, annotations, coordinates, metadata, and native Studyset-backed meta-analysis.">

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  .. image:: /auto_examples/01_datasets/images/thumb/sphx_glr_05_plot_nimads_thumb.png
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  :doc:`/auto_examples/01_datasets/05_plot_nimads`

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      <div class="sphx-glr-thumbnail-title">The NiMARE Studyset object</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="Here, we present the structure of the JSON/dict input format to create a Dataset class from scratch.">

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  .. image:: /auto_examples/01_datasets/images/thumb/sphx_glr_06_plot_dataset_json_thumb.png
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  :doc:`/auto_examples/01_datasets/06_plot_dataset_json`

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      <div class="sphx-glr-thumbnail-title">Create a legacy NiMARE Dataset object from a JSON file</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="=============================== Loading Studysets from parquet ===============================">

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  .. image:: /auto_examples/01_datasets/images/thumb/sphx_glr_07_plot_parquet_studyset_thumb.png
    :alt:

  :doc:`/auto_examples/01_datasets/07_plot_parquet_studyset`

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      <div class="sphx-glr-thumbnail-title">Loading Studysets from parquet.</div>
    </div>


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    </div>


.. toctree::
   :hidden:

   /auto_examples/01_datasets/01_plot_dataset_io
   /auto_examples/01_datasets/02_download_neurosynth
   /auto_examples/01_datasets/03_plot_neurovault_io
   /auto_examples/01_datasets/04_transform_images_to_coordinates
   /auto_examples/01_datasets/05_plot_nimads
   /auto_examples/01_datasets/06_plot_dataset_json
   /auto_examples/01_datasets/07_plot_parquet_studyset