6.2. Downloading statistical maps from the Neurovault repository

Neurovault is a public repository of unthresholded statistical maps, parcellations, and atlases of the human brain. You can read about it and browse the images it contains at http://www.neurovault.org. You can download maps from Neurovault with Nilearn.

Neurovault was introduced in [1].

Neurovault contains collections of images. We can get information about each collection - such as who uploaded it, a link to a paper, a description - and about each image - the modality, number of subjects, some tags, and more. The nilearn downloaders will fetch this metadata and the images themselves.

Nilearn provides two functions to download statistical maps from Neurovault.

6.2.1. Specific images or collections

In the simplest case, you already know the “id” of the collections or images you want. Maybe you liked a paper and went to http://www.neurovault.org looking for the data. Once on the relevant collection’s webpage, you can click ‘Details’ to see its id (and more). You can then download it using nilearn.datasets.fetch_neurovault_ids :

>>> from nilearn.datasets import fetch_neurovault_ids
>>> brainpedia = fetch_neurovault_ids(collection_ids=[1952]) 

Or if you want some images in particular, rather than whole collections :

>>> brainpedia_subset = fetch_neurovault_ids(image_ids=[32015, 32016]) 

6.2.2. Selection filters

You may not know which collections or images you want. For example, you may be conducting a meta-analysis and want to grab all the images that are related to “language”. Using nilearn.datasets.fetch_neurovault, you can fetch all the images and collections that match your criteria - you don’t need to know their ids.

The filters are applied to images’ and collections’ metadata.

You can describe filters with dictionaries. Each collection’s metadata is compared to the parameter collection_terms. Collections for which collection_metadata['key'] == value is not True for every key, value pair in collection_terms will be discarded. We use image_terms in the same way to filter images.

For example, many images on Neurovault have a “modality” field in their metadata. BOLD images should have it set to “fMRI-BOLD”. We can ask for BOLD images only :

>>> bold = fetch_neurovault(image_terms={'modality': 'fMRI-BOLD'}, 
... max_images=7) 

Here we set the max_images parameter to 7, so that you can try this snippet without waiting for a long time. To get all the images which match your filters, you should set max_images to None, which means “get as many images as possible”. The default for max_images is 100.

The default values for the collection_terms and image_terms parameters filter out empty collections, and exclude an image if one of the following is true:

  • it is not in MNI space.
  • its metadata field “is_valid” is cleared.
  • it is thresholded.
  • its map type is one of “ROI/mask”, “anatomical”, or “parcellation”.
  • its image type is “atlas”

Extra keyword arguments are treated as additional image filters, so if we want to keep the default filters, and add the requirement that the modality should be “fMRI-BOLD”, we can write:

>>> bold = fetch_neurovault(modality='fMRI-BOLD', max_images=7) 

Sometimes the selection criteria are more complex than a simple comparison to a single value. For example, we may also be interested in CBF and CBV images. In nilearn, the dataset.neurovault module provides IsIn which makes this easy :

>>> from nilearn.datasets import neurovault
>>> fmri = fetch_neurovault( 
... modality=neurovault.IsIn('fMRI-BOLD', 'fMRI-CBF', 'fMRI-CBV'), 
... max_images=100) 

We could also have used Contains :

>>> fmri = fetch_neurovault( 
... modality=neurovault.Contains('fMRI'), 
... max_images=7) 

If we need regular expressions, we can also use Pattern :

>>> fmri = fetch_neurovault( 
... modality=neurovault.Pattern('fmri(-.*)?', neurovault.re.IGNORECASE), 
... max_images=7) 

The complete list of such special values available in nilearn.datasets.neurovault is: IsNull, NotNull, NotEqual, GreaterOrEqual, GreaterThan, LessOrEqual, LessThan, IsIn, NotIn, Contains, NotContains, Pattern.

You can also use ResultFilter to easily express boolean logic (AND, OR, XOR, NOT).

If you need more complex filters, and using dictionaries as shown above is not convenient, you can express filters as functions. The parameter collection_filter should be a callable, which will be called once for each collection. The sole argument will be a dictionary containing the metadata for the collection. The filter should return True if the collection is to be kept, and False if it is to be discarded. image_filter does the same job for images. The default values for these parameters don’t filter out anything. Using a filter rather than a dictionary, the first example becomes:

>>> bold = fetch_neurovault( 
...     image_filter=lambda meta: meta.get('modality') == 'fMRI-BOLD', 
...     image_terms={}, max_images=7) 

Note

Even if you specify a filter as a function, the default filters for image_terms and collection_terms still apply; pass an empty dictionary if you want to disable them. Without image_terms={} in the call above, parcellations, images not in MNI space, etc. would be still be filtered out.

The example above can be rewritten using dictionaries, but in some cases you will need to use image_filter or collection_filter. For example, suppose that for some weird reason you only want images that don’t have too many metadata fields - say, an image should only be kept if its metadata has less than 50 fields. This cannot be done by simply comparing each key in a metadata dictionary to a required value, so we need to write our own filter:

>>> small_meta_images = fetch_neurovault(image_filter=lambda meta: len(meta) < 50, 
...                                      max_images=7) 

6.2.3. Output

Both functions return a dict-like object which exposes its items as attributes.

It contains:

  • images, the paths to downloaded files.
  • images_meta, the metadata for the images in a list of dictionaries.
  • collections_meta, the metadata for the collections.
  • description, a short description of the Neurovault dataset.

Note to pandas users: passing images_meta or collections_meta to the DataFrame constructor yields the expected result, with images (or collections) as rows and metadata fields as columns.

6.2.4. Neurosynth annotations

It is also possible to ask Neurosynth to annotate the maps found on Neurovault. Neurosynth is a platform for large-scale, automated synthesis of fMRI data. It can be used to perform decoding. You can learn more about Neurosynth at http://www.neurosynth.org.

Neurosynth was introduced in [2].

If you set the parameter fetch_neurosynth_words when calling fetch_neurovault or fetch_neurovault_ids, we will also download the annotations for the resulting images. They will be stored as json files on your disk. The result will also contain (unless you clear the vectorize_words parameter to save computation time):

  • vocabulary, a list of words
  • word_frequencies, the weight of the words returned by neurosynth.org for each image, such that the weight of word vocabulary[j] for the image found in images[i] is word_frequencies[i, j]

6.2.5. Examples using Neurovault

6.2.6. References

[1]Gorgolewski KJ, Varoquaux G, Rivera G, Schwartz Y, Ghosh SS, Maumet C, Sochat VV, Nichols TE, Poldrack RA, Poline J-B, Yarkoni T and Margulies DS (2015) NeuroVault.org: a web-based repository for collecting and sharing unthresholded statistical maps of the human brain. Front. Neuroinform. 9:8. doi: 10.3389/fninf.2015.00008
[2]Yarkoni, Tal, Russell A. Poldrack, Thomas E. Nichols, David C. Van Essen, and Tor D. Wager. “Large-scale automated synthesis of human functional neuroimaging data.” Nature methods 8, no. 8 (2011): 665-670.