About

Group inference and reporting of neuroimaging studies require that individual’s features are spatially aligned into a common frame where their location can be called standard. To that end, a multiplicity of brain templates with anatomical annotations (i.e., atlases) have been published. However, a centralized resource that allows programmatic access to templates is lacking. TemplateFlow is a modular, version-controlled resource that allows researchers to use templates “off-the-shelf” and share new ones.

Contents

• TemplateFlow Naming
  • Naming information
• Publishing in TemplateFlow
  • Prerequisites to contributing templates to TemplateFlow
    • Are you allowed to share the template?
    • What type of contribution are you making?
    • Prerequisites for uploading nifti files
    • Initializing the TemplateFlow OSF directory
  • Creating a new template space
    • Step 1: create a new dataset
    • Step 2: Add a template_description.json
  • Uploading files to an existing template space
    • Big picture
    • Step 1: Placing the template on the OSF server
    • Step 2: Telling DataLad where the files are
    • Example script when subdirectories are present
• Library API (application program interface)
  • templateflow.api module
  • templateflow.conf package
    • Submodules

What’s new

0.7.1 (December 9, 2020)

Minor release with improvements to the template fetching experience. With thanks to Lea Waller for the contribution.

• FIX: Use BIDSLayoutIndexer when initiating BIDSLayout (#61)

• FIX: Display correct units when downloading templates (#63)

• FIX: GitHub Actions build (#64)

• ENH: Add option to raise exception on empty get queries (#57)

• ENH: Ensure templates layout is re-indexed when updated (#59)

0.7.0 - Withdrawn

Release 0.7.0 was withdrawn because of inconsistencies in deployment.

0.6.3 (July 06, 2020)

Patch release including an updated PyBIDS configuration file for the PyBIDS 0.11.x series.

• FIX: Include leading dots in extensions (#56)

0.6.2 (May 09, 2020)

Patch release including some minimal improvements to package building and CI.

• MAINT: Some additional distribution improvements (#51)

0.6.1 (May 09, 2020)

Patch release to generate and distribute wheels.

• MAINT: Run black (#50)

• MAINT: Distribute wheel + Revise CI framework (#49)

0.6.0 (May 1st, 2020)

Minor release in preparation of a new CalVer versioning following the lead of fMRIPrep. This release contains a fair amount of maintenance work to ensure synchronicity with the TemplateFlow Archive (https://github.com/templateflow/templateflow). These maintenance actions drive the development towards establishing a peer-reviewed, lightweight template submission protocol. The release includes an update mechanism, enabling users of the S3-backed mode of operation (default) to update their local Archive structure without reinstalling the client. This feature is enabled by default on import time, to disable it make sure you export TEMPLATEFLOW_AUTOUPDATE=off. With thanks to Yarik for a datalad-related bug-fix. With thanks to V. Fonov for contributing with the new tpl-MNI152NLin2009cSym.

• FIX: Provide path to the dataset as dataset argument (#48)

• ENH: Run an automatic S3-skeleton update on import by default (#45)

• ENH: Update the internal index of TemplateFlow (#40)

• ENH: Automatic generation of template citations (#35)

• MAINT: Set-up a GitHub action to test installation alternatives (see #23).

• MAINT: Migrate to setuptools_scm (#42)

• MAINT: Run black on the whole tree (#41)

• MAINT: Transfer the burden of keeping the S3-skeleton updated over to the archive (#39)

0.5.2 (March 20, 2020)

Patch release in the 0.5 series, adding a soft brainmask for numerical stability in floating-point rounding of atlas-based brain-extraction methods using the MNI152NLin2009cAsym template.

0.5.1 (March 20, 2020)

Patch of the new 0.5.x series, including a new rodent template and file fixes for fsaverage and fsLR templates. With thanks to E. MacNicol for contributing the new tpl-WHS.

• MAINT: Drop Python 3.5 (#36)

0.5.0 (March 12, 2020)

This release has been removed and should not be used.

Version 0.4.2 (January 28, 2020)

Patch release including a bugfix, adding a DataLad pin, and making PyBIDS pin more flexible.

• MAINT: Update PyBIDS pin and DataLad pin

• FIX: Density key (#31)

Version 0.4.1 (July 22, 2019)

First release after a deep revision of the tests and the continuous integration setup. Also includes minor reliability improvements over the previous release and some bugfixes.

• MAINT: Testing Automatically update CHANGES after merge (51988f8) (#27)

• MAINT: Enable code coverage collection (#25)

• MAINT: Switch to a setup.cfg-style of installation (#24)

• FIX: Check and update $HOME if needed with every installation (#20)

• FIX: Do not merge branches into master when pushing back skell (#19)

• FIX: Commit newly generated S3 skeletons back to repo (#17)

• FIX: Add extension entity for selection (#16) @effigies

Version 0.4.0 (July 9, 2019)

• MAINT: Use PyBIDS 0.9.x (#15) @effigies

Version 0.3.0 (June 4, 2019)

• ENH: Add MNIInfant template.

Version 0.2.0 (June 4, 2019)

• ENH: Added MNIPediatricAsym template.

• ENH: Updated spec to allow several cohorts (cohort-).

Version 0.1.9 (May 28, 2019)

• ENH: Added the Schaefer 2018 atlas) to MNI152NLin6Asym.

• ENH: Mapped the Schaefer atlas and the Harvard-Oxford atlas into MNI152NLin2009cAsym.

Version 0.1.8 (May 9, 2019)

• ENH: Added FSL’s Harvard-Oxford template to MNI152NLin6Asym.

Version 0.1.7 (April 3, 2019)

• ENH: New release including bugfixes for MNI152NLin2009cAsym (particularly https://github.com/templateflow/tpl-MNI152NLin2009cAsym/commit/6e6d5915c7d8055d4af5efbf5e5457a0ab3246b9)

Version 0.1.6 (March 29, 2019)

• ENH: Finish adding MNI152NLin6Sym after curation of NIfTI volumes and exporting to S3.

Version 0.1.5 (March 29, 2019)

• ENH: Add volumetric data to the fsLR template.

• ENH: Rename the segmentation of subcortical structures to be consistent with the new files.

Version 0.1.4 (March 28, 2019)

• ENH: New release to include the new MNI152NLin6Asym template (the default MNI template of FSL).

Version 0.1.3 (March 14, 2019)

• FIX: Update TemplateFlow skeleton to include tpl-fsaverage/tpl-fsaverage_dseg.tsv, after TemplateFlow update.

Version 0.1.2 (March 12, 2019)

• FIX: api.get - robuster fetcher algorithm (allows S3 download on DL repos) and better error messages (#10)

Version 0.1.1 (March 12, 2019)

• FIX: Require environment variable to use DataLad (#8)

Version 0.1.0.post1 (March 05, 2019)

• ENH: Testing a better .zenodo.json settings.

Version 0.1.0 (March 05, 2019)

• ENH: First minimally functional TemplateFlow client release.

Version 0.0.5.post1 (March 04, 2019)

Hotfix release to retrieve correct version when pip installed.

• MAINT: Add a .zenodo.json file.

Version 0.0.5 (March 04, 2019)

• ENH: Datalad-free alternative for TemplateFlow (#7)

• ENH: Use a BIDSLayout to index TemplateFlow (#6)

Version 0.0.4 (January 18, 2019)

• ENH: Add a get_metadata utility

Version 0.0.3 (January 16, 2019)

• ENH: Add api.templates() + one doctest

Version 0.0.2 (January 16, 2019)

• ENH: Add one doctest

Version 0.0.1 (January 16, 2019)

• ENH: First functional release