Automated Fiber Quantification in Python Releases

GitHub_Releases Version 1.3.3 (1.3.3)

arokem@www.nitrc.org (Ariel Rokem) — Tue, 01 Oct 2024 19:24:38 GMT

1.3.3 (October 01, 2024)
========================
Implements option to parallelize tractography using Ray.
Implements option to run GroupAFQ in parallel using Slurm.
Updates to documentation and minor bug fixes.
* [FIX] Do not assume VOX space in clean bundles function (#1161)
* [FIX] bug in finding ROI from freesurfer using pybids (#1160)
* (#1158)
* Fixes small typo in plot_001_afq_api.py (#1145)
* allow identity mapping from CLI (#1153)
* Update kwargs.rst (#1150)
* ... <a href="https://github.com/yeatmanlab/pyAFQ/releases/tag/1.3.3">see more</a>

GitHub_Releases Version 1.3.2 (1.3.2)

arokem@www.nitrc.org (Ariel Rokem) — Fri, 31 May 2024 18:45:17 GMT

1.3.2 (May 31, 2024)
====================
This release adds the ability to do tractography in parallel using ray.
It also adds Pydra integration into GroupAFQ (ParallelGroupAFQ).
We also added RUMBA-SD from DIPY and made other minor changes.
* Streamlines task in parallel using ray (#1136)
* Check bvals on dki (#1139)
* [FIX] different CST ROI 2 for L/R (#1138)
* Adds ParallelGroupAFQ (#1124)
* [DOC] Update kwargs.rst (#1135)
* [ENH] Added RUMBA-SD to data.py (#1129)
* [ ... <a href="https://github.com/yeatmanlab/pyAFQ/releases/tag/1.3.2">see more</a>

GitHub_Releases Version 1.3.1 (1.3.1)

arokem@www.nitrc.org (Ariel Rokem) — Thu, 04 Apr 2024 23:15:44 GMT

Adds the mean signal diffusion kurtosis model as an option.
Adds more information in JSON sidecars. Adds an explanation
of our current bundle orientation system to the documentation.
* [ENH] add mean signal diffusion kurtosis model (#1121)
* [ENH] make source field relative in json sidecars (#1118)
* [ENH] add more information from bundle dict into jsons (#1117)
* [DOC] add bundle orientation explanation (#1120)

GitHub_Releases Version 1.3 (1.3)

arokem@www.nitrc.org (Ariel Rokem) — Mon, 25 Mar 2024 16:25:31 GMT

1.3 (March 25, 2024)
====================
All bundles are now ordered according to LPI+ and
are output as full names instead of abbreviations.
Only the lowest shell is now used in the calculation of
the CSD response function. Corrects typos in babyAFQ and
GPU tracking, pARC/VOF cleaning parameters updated,
along with other minor improvements.
* Adds an example to plot stages of tractometry. (#1073)
* [FIX] fix bundle colors (#1116)
* Fix gpu tracking (#1115)
* Move s3 BIDS to ... <a href="https://github.com/yeatmanlab/pyAFQ/releases/tag/1.3">see more</a>

GitHub_Releases Version 1.2 (1.2)

arokem@www.nitrc.org (Ariel Rokem) — Fri, 05 Jan 2024 0:05:01 GMT

Incorporates TRX, a new tractography file format, makes
a new way for organizing bundle dictionaries, extensive
documentation improvements, and many other minor fixes
* DOC: Small fixes to the visualization example. (#1083)
* [WIP/ENH] add AR from endpoint ROIs (#1078)
* Update grant funding (#1076)
* [FIX] Add exclusion ROI to IFOF (#1074)
* Update fury (#1080)
* [ENH] add some utilities for working with altair and pyafq (#1049)
* [FIX] possible fix to pediatric bundle di ... <a href="https://github.com/yeatmanlab/pyAFQ/releases/tag/1.2">see more</a>

GitHub_Releases Version 1.1 (1.1)

arokem@www.nitrc.org (Ariel Rokem) — Fri, 08 Sep 2023 16:53:53 GMT

1.1 (September 08, 2023)
========================
Add compatibility with GPU based tractography. Speeds
up the Mahalanobis cleaning step. Removes interface for
loading ITK files and using them as maps in pyAFQ, because
it did not work in all cases. Adds more examples and updates
docs to a new system. Other minor fixes.
* [FIX] delete folders in AFQ derivatives when clobbering (#1015)
* Update the pypi action so that it runs on latest ubuntu. (#1012)
* NF: Adds fetcher for cerebell ... <a href="https://github.com/yeatmanlab/pyAFQ/releases/tag/1.1">see more</a>

GitHub_Releases Version 1.0.1 (1.0.1)

arokem@www.nitrc.org (Ariel Rokem) — Wed, 22 Feb 2023 21:42:01 GMT

Fixed two bugs, where max streamline length was not being enforced and the
mean b0 was being calculated incorrectly. Small documenation fixes.
* [FIX] Add max length constraint, b0 fix (#955)
* Small documentation fixes, to improve auto-rendering of API docs. (#949)
* MAINT: Upgrade pytest as a start to tackling CI errors. (#945)
* MAINT: pep517 => build. (#947)

GitHub_Releases Version 1.0 (1.0)

arokem@www.nitrc.org (Ariel Rokem) — Thu, 05 Jan 2023 23:15:44 GMT

This is the first major release of pyAFQ. The API should be stable
from here until the next major release of pyAFQ.
Adds freewater DTI, fiber density maps, VOF and pAF bundles,
and montage and combine bundle visualizations, as well as other
minor additions, fixes, and documentation updates.
* [FIX] Missing underscore in custom tissue property filenames (#944)
* [FIX] finally finish this SLR PR (#937)
* Add fwDTI (#931)
* [FIX] Import tract docs (#936)
* TST: Fixes another fail ... <a href="https://github.com/yeatmanlab/pyAFQ/releases/tag/1.0">see more</a>

GitHub_Releases Version 0.12.2 (0.12.2)

arokem@www.nitrc.org (Ariel Rokem) — Fri, 22 Jul 2022 4:31:26 GMT

This release fixes a critical bug introduced in version 0.11, which caused exclusion ROIs to be ignored.
* [FIX]: Reorder endpoint (#858)
* [FIX] Some ITK map fixes for running with groupAFQ and in CLI (#855)
* [ENH] Add montage and combine bundle to GroupAFQ (#849)
* [DOC] add fatal error when no bundles found at all (#851)
* [ENH] add median bundle len function (#852)

GitHub_Releases Version 0.12.1 (0.12.1)

arokem@www.nitrc.org (Ariel Rokem) — Thu, 30 Jun 2022 19:21:55 GMT

More informative warnings and errors, minor fixes.
* [FIX] warn user about number of invalid streamlines removed (#850)
* TST: Test the nibabel release candidate. (#842)
* MAINT: Refreshes the zenodo metadata file. (#845)
* [ENH] minor docs updates and qsiprep changes (#847)
* [FIX] Error when file not found should be more informative (#844)
* [ENH] Return path to single viz file if its generated (#839)
* [ENH] Add core_bundle functionality to fury backend (#838)
* [FIX] ... <a href="https://github.com/yeatmanlab/pyAFQ/releases/tag/0.12.1">see more</a>