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

0.5.0 (March 12, 2020)

Minor release including a new rodent template and file fixes for fsaverage and fsLR templates.

• MAINT: Drop Python 3.5 (#36)

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