From 14de28241effe6993fff5fbe011856c73a3968ab Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Wed, 31 Jul 2024 13:33:22 -0400 Subject: [PATCH] Prepare for 0.8.0 release (#1221) --- CITATION.cff | 17 +++++++---------- docs/changes.md | 42 ++++++++++++++++++++++++++++++++++++++++-- 2 files changed, 47 insertions(+), 12 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 03884fa83..1c4086239 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -18,16 +18,15 @@ authors: - given-names: Kahini family-names: Mehta email: kahini.mehta@pennmedicine.upenn.edu - affiliation: University of Pennsylvania + affiliation: Columbia University orcid: 'https://orcid.org/0000-0001-9466-100X' - given-names: Azeez family-names: Adebimpe - affiliation: University of Pennsylvania orcid: 'https://orcid.org/0000-0001-9049-0135' - given-names: Maxwell family-names: Bertolero orcid: 'https://orcid.org/0000-0002-2691-3698' - affiliation: University of Pennsylvania + affiliation: Turing Medical - given-names: Kristin family-names: Murtha affiliation: University of Pennsylvania @@ -39,20 +38,18 @@ authors: - given-names: Steven family-names: Meisler orcid: 'https://orcid.org/0000-0002-8888-1572' - affiliation: >- - Harvard-MIT Division of Health Sciences and - Technology + affiliation: University of Pennsylvania - given-names: Thomas family-names: Madison affiliation: University of Minnesota orcid: 'https://orcid.org/0000-0003-3030-6580' - given-names: Valerie family-names: Sydnor - affiliation: University of Pennsylvania + affiliation: University of Pittsburgh Medical Center orcid: 'https://orcid.org/0000-0002-8640-668X' - given-names: Sydney family-names: Covitz - affiliation: University of Pennsylvania + affiliation: Stanford University orcid: 'https://orcid.org/0000-0002-7430-4125' - given-names: Damien family-names: Fair @@ -86,5 +83,5 @@ keywords: - BIDS-App - Neuroimaging license: BSD-3-Clause -version: 0.7.5 -date-released: '2024-06-27' +version: 0.8.0 +date-released: '2024-07-31' diff --git a/docs/changes.md b/docs/changes.md index 4154118a1..994527136 100644 --- a/docs/changes.md +++ b/docs/changes.md @@ -1,6 +1,46 @@ # What's New +## 0.8.0 + +This is a backwards-incompatible release that will be used to postprocess the beta version of the first release of the HBCD dataset. +There are two major breaking changes. +First, there is a new required `--mode` parameter that automatically defines sets of parameters to match recommendations from different studies/labs. +Each parameter that the `--mode` parameter controls can be overridden, so users should be able to reproduce their original settings from previous versions of XCP-D. +Second, XCP-D now loads certain sphere files from the BIDS derivatives, rather than non-BIDS Freesurfer or MCRIBS folders. +This means that the anatomical workflow (`--warp-surfaces-native2std`) will only work for fMRIPrep versions >= 23.1.0 and Nibabies versions >= 23.1.0. +The rest of XCP-D should still work for versions of fMRIPrep and Nibabies that were supported previously, but we cannot guarantee this. + +### 🛠 Breaking Changes + +* Add required `--mode` parameter to define sets of parameters by @tsalo in https://github.com/PennLINC/xcp_d/pull/1109 +* Load spheres for anatomical workflow from TemplateFlow and BIDS derivatives by @tsalo in https://github.com/PennLINC/xcp_d/pull/1207 + +### 🎉 Exciting New Features + +* Add discretized MID-B and Myers-Labonte atlases by @tsalo in https://github.com/PennLINC/xcp_d/pull/1192 +* Plot CIFTI maps on subject-specific surfaces when available by @tsalo in https://github.com/PennLINC/xcp_d/pull/1208 +* Allow bids-filter-file terms for mesh and morphometry files by @tsalo in https://github.com/PennLINC/xcp_d/pull/1210 + +### 🐛 Bug Fixes + +* Generate session-wise executive summaries by @tsalo in https://github.com/PennLINC/xcp_d/pull/1202 +* Look for space entity in T2w-only anatomical inputs by @tsalo in https://github.com/PennLINC/xcp_d/pull/1203 +* Use standard-space anatomical brain mask by @tsalo in https://github.com/PennLINC/xcp_d/pull/1204 +* Drop volumetric Myers-Labonte atlas by @tsalo in https://github.com/PennLINC/xcp_d/pull/1212 +* Enable linc-qc for abcd and hbcd modes by default by @tsalo in https://github.com/PennLINC/xcp_d/pull/1220 + +### Other Changes + +* Document anatomical workflow in more detail by @tsalo in https://github.com/PennLINC/xcp_d/pull/1191 +* Fix up documentation by @tsalo in https://github.com/PennLINC/xcp_d/pull/1209 +* Reorganize QC interfaces by @tsalo in https://github.com/PennLINC/xcp_d/pull/1215 +* Allow `space-fsaverage` for sphere files by @tsalo in https://github.com/PennLINC/xcp_d/pull/1217 +* Continue to improve documentation of anatomical workflow by @tsalo in https://github.com/PennLINC/xcp_d/pull/1216 + +**Full Changelog**: https://github.com/PennLINC/xcp_d/compare/0.7.5...0.8.0 + + ## 0.7.5 This is a patch release that fixes how the correlation matrix plot is generated when users select only one atlas for parcellation. @@ -49,8 +89,6 @@ Small patch release for manuscript's executive summary. **There is a known bug with the band-pass filter settings in this release. Upper and lower band-pass values were hardcoded to 0.01 - 0.1.** -## What's Changed - ### 🐛 Bug Fixes * Drop concatenated rest-as-run section from executive summary by @tsalo in https://github.com/PennLINC/xcp_d/pull/1156