Osprey: Open-source processing, reconstruction & estimation of magnetic resonance spectroscopy data Releases

GitHub_Releases Osprey v.2.0.0 (v.2.0.0)

zoellner@www.nitrc.org (Helge Zöllner) — Fri, 25 Mar 2022 21:49:08 GMT

### Features
- In case metabolite suppressed data is supplied, OspreyFit has been updated to perform three separate linear-combination modeling runs.: 1) Using parameterized MM basis functions (standard approach with Gaussian functions); 2) Include the cleaned measured MM spectrum (denoised by using a spline function) in the LCM; 3) If multiple subjects are supplied a mean MM spectrum across all subjects is created and included in the last run.
- Analysis of metabolite-suppressed data from edited and multiplexed spectra is now supported.
- Add multiple MRS experiments to a single subject by adding another dimension to your input cell arrays. Osprey will load and process all spectra and concatenate them along the extra dimension. In the current release, the extra dimension is not incorporated into the OspreyFit, OspreyQuantify or OspreyQuantify module. This will be part of a future release. However, this can be used if for example, multiple MRS experiments need to be averaged e.g. two separate scans from the same voxel (See example jobSDAT_MEGA_Multidataset.m). After processing you have to call osp_AverageAllDatasetsAlongExtras to average the acquisitions.

### Changes
- The MRSCont struct has been completely restructured. Therefore the files from older versions are not compatible, please re-run the analysis or use an older release version.

GitHub_Releases Osprey v1.1.0 (v1.1.0)

zoellner@www.nitrc.org (Helge Zöllner) — Thu, 26 Aug 2021 19:29:12 GMT

**New functionalities**

- Automated LCModel integration from within the Osprey pipeline for unedited data. Osprey automatically creates the needed control files and calls LCModel from within MATLAB. The results are imported back into Osprey to be used in the downstream modules. You can also provide your own control files and .BASIS files. You need to add compiled LCModel binaries into the libraries/LCModel folder ([visit for instructions](https://github.com/schorschinho/LCModel)). Currently, Osprey is shipped with compiled binaries for Windows 10 and macos catalina.
- Nifti MRS loader and export functions

**Updates & Bugfixes**

- Reduced file size by removing redundant basis set from the MRS container
- Issues related to the deletion of user supplied strucutral images

**Other changes**
- automated OS identifier and font picker

GitHub_Releases Osprey v1.0.2.1 (v1.0.2.1)

zoellner@www.nitrc.org (Helge Zöllner) — Fri, 09 Jul 2021 21:00:23 GMT

Version check bug fix

GitHub_Releases Osprey v1.0.2 (v1.0.2)

zoellner@www.nitrc.org (Helge Zöllner) — Fri, 09 Jul 2021 20:01:27 GMT

**New functionalities**
- updates to the MRSI module to process three slice edited MRSI data (loading & MoCo)
- GE nifti files accepted
- MRSinMRS markdown function
- 7 T relaxation time lookup table for quantification
- Improved functionality to run Osprey on the server
- Added co-edited MM model to HERCULES modeling
- OspreyOverview can be called after OspreyProcess to generate overview plots without fitting

**Updates & Bugfixes**
- Preliminary fit picks metabolites based on the supplied basis set (e.g. Cho containing compounds instead of Cho)
- FitQA definitions updated to match the original paper
- AllPDF bug fixes
- Updated GE load function
- Updated Siemens DICOM loader
- Updated all example jobFiles to reflect the current functionalities of Osprey and to reflect BIDS structured automated processing
- Updated version numbering and check function to give soft warnings only

**Other changes**
- Prior module check function

GitHub_Releases Osprey v1.0.1.1 (v1.0.1.1)

zoellner@www.nitrc.org (Helge Zöllner) — Mon, 05 Apr 2021 21:03:25 GMT

-This hotfix release was resolves issues related to the version comaprison

GitHub_Releases Osprey v1.0.1 (v1.0.1)

zoellner@www.nitrc.org (Helge Zöllner) — Mon, 05 Apr 2021 14:07:14 GMT

- Resolved issue #75: Instead of relying on Curve Fitting Toolbox functions (spmak, fnval) to generate the cubic spline basis functions, these are now created with an explicit iterative analytical procedure.
- Fixed a major bug in the interactive job file creator, which caused all entries (except for the first) of the water reference file array to be wrongly populated with the file names of the water-suppressed (metabolite) data.
- Added basis set for macromolecule-suppressed GABA-edited Philips MEGA-PRESS.
- Removed separate version definitions for each sub-module - there is now one single version number for all modules.
- Fixed an error occurring when short-TE water, but no water reference, was used.
- Small fixes to errors caused during GUI calls.
- Added fancy shields.io badges to the README file.

GitHub_Releases Osprey v1.0.0 (v1.0.0)

zoellner@www.nitrc.org (Helge Zöllner) — Fri, 12 Mar 2021 18:13:14 GMT

Releasing Osprey v1.0.0