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lcmodel-integration

Add support for loading and processing several flavors of Siemens SPECIAL data (including sequences developed by Jamie Near, Masoumeh Dehghani, Layla Riemann). Add a few cosmetic fixes here and there.

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

Update 3T Siemens SPECIAL basis set. Add small tweaks to the LCModel control file generation for data with water reference.

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

-removed unwanted error found during CI

fix MEGA fit

SPECIAL support

Added a decision tree for the OspreySeg call in the RunOspreyJob function. In case a path to the external segmentation is supplied, but the file doesn't exist yet the OspreySeg will be skipped. This script is used in the compiled Osprey version.

HBCD - external segmentation not finished case - Erik Lee

Added a Siemens 97 ms PRESS basis set for optimized 2HG/Cystat quantification.

Add PRESS 97 ms - Todd Parrish

Added Cystat to the example jobfiles

Integrate Cystat - Todd Parrish

- Add Cystat into the GUI job creator

Integrate Cystat - Todd Parrish

Update the MATALB app

Integrate Cystat - Todd Parrish

Added a round function in various functions to account for non-integer spectralwidth.

[BUG FIX] - Osprey crash for non-integer spectralwidth - McNabb