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Prepare for 0.8.0 release (PennLINC#1221)
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tsalo authored Jul 31, 2024
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17 changes: 7 additions & 10 deletions CITATION.cff
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Expand Up @@ -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
Expand All @@ -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
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- 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'
42 changes: 40 additions & 2 deletions docs/changes.md
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# 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.
Expand Down Expand Up @@ -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
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