Prepare v.2.2.0 release #427
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Improved user experience for the OspreyGUI which removes unwanted figures and warnings appearing during the OspreyGUI call. Also included foundation to solve the SPM12 path removal issues.
[BUG] - Remove unwanted warnings and windows from Osprey GUI - Helge
Fixes some unwanted bugs related to the introduction of multiple basis sets. This commit also includes foundation for Philips Series data.
[BUG] - Multi-dataset errors and preparation of series - Helge
OspreyJob supports .jason jobfiles
Integrate jason jobFiles
Initial commit of Osprey HTML report. This report creates a short subject-specific HTML report to be created after finishing the whole pipeline. It includes a summary of the alignment process and frequency drift traces. A simplified traffic light system for data quality measures based on Martin Wilson Clinical MRS consensus paper. Summary of the LCM results and fitQA numbers as well as a plot with voxel localization and tissue fractions. Outputs are BIDS compliant.
Create OspreyHTMLReport.m
Added header to the HTML report function.
Added description to HTML report
Added a single line caller to perform a full Osprey analysis.
Create RunOspreyJob
…elge Added support for arbitrary external segmentation results to Osprey. The external *.nii/*.nii.gz. results are defined in the jobfile including a 1x3 cell for each subject pointing to the path for the gray matter, white matter, and csf segmentation tissue class maps. The results have to be in the same coordinate space as the supplied anatomical image (file_nii) and are used during the tissue fraction calculations in OspreySeg(). This feature will be used in HBCD. The example jobfiles were updated accordingly to describe the new feature.
[FEATURE REQUEST] - Add external segmentation results - OspreySeg - H…
This commit includes adaptions of the implementation to allow an easy compilation of Osprey standalone. - The Osprey toolbox check module is called within the RunPreviousModule function and updated flag.didLoadData to didLoad to match the naming convention - addpath functions are removed from OspreySettings and not including SPM12 in the path will result in an error message instead of automatically including it (as this is not possible for compiled MATLAB code). - added a CompileOspreyStandalone function to create compiled Osprey. This includes a HBCD specific version, a command window version to be called in the terminal, and a full GUI version. The compilation includes SPM12 with the needed LICENSE files. -
Prepare Osprey compilation - Helge
- Updated the scaling of the colorbar used in the coregistration and segmentation plots according to the implementation in Gannet.
Update T1w colormap - Resolve scaling issue - Richard Edden
Bug fix related to naming issue of the fit results struct resulting in a crash of the OspreyFit module.
[BUG Fix] - OspreyFit crashing - Yulu Song
- Osprey accepts external tissue segmentation maps as a single file 4D NIfTI (the order of the tissue segmentation has to be changed by the user to accurately perform the segmentation)
[FEATURE REQUEST] - Single file external segmentation - HBCD
- Added pre/post alignment spectra to the OspreyProcess plot
[FEATURE REQUEST] - Add pre/post alignment - Eric Porges
- fixed reported issues when pressing the up/down arrow on the first/last entry. This was related to the 2D structure of nDatasets since the 2.0 update.
[BUG] - Keypress GUI - Yulu Song
Update/upload all basis sets for the HBCD project especially the HERCULES basis sets for all vendors
Upload basis sets for HBCD
- no alignment case for unedited data added
Update OspreyProc
Added GE HERCULES universal basis set
Add GE HERCULES basis set
Fixes loading of STEAM data acquired with the CMRR sequence (was unintentionally mis-classified as MEGA, and didn't recognize the correct number of pre-echo points). Fixes #400
The SPMpath.mat variable which is used to store the SPM is not compatible with compiled MATLAB. It is actually not needed anymore as long as spm12 is included in the path without subfolders. Therefore, it was removed from the osp_Toolbox_Check function.
Remove SPMpath.mat - osp_Toolbox_Check - Helge Zöllner
This commit includes numerous changes needed for the HBCD processing. See details below: - osp_fitInitialise.m had a wrong path for the GE HERCULES basis set - Fixed typo and wrong setup of the cell array for external segmentation files when .json files where used in OspreyJob.m - Changed the reference/reporter signal for the linewidth and SNR to creatine for all sequences with changes in op_get_Mutlispectra_LW,m, op_get_Multispectra_SNR.m, OspreyHTMLReport.m, OspreyMinReport.m, and OspreyProcess.m - Fixed a bug related to the linewidth calculation of creatine for HERMES/HERCULES data related to the included frequency range for the simple FWHM calculation - Added a quick summary to the HTML report showing quality measures (LW, SNR, fit residual), all fits, and localization + segmentation (if available) - Added segmentation based on anatomical labels. This works for HBCD atlas only
HBCD changes - [FEATURE REQUEST] - multiple functions - Helge Zöllner
Bug fix for OS related filesep issue during the setup of the job.
[BUG FIX] - example jobfiles - Helge Zöllner
Update version number for release
Add version number
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Prepare release of Osprey v.2.2.0