Trigger pipeline

- Added csv file output for CRLBs and h2oarea for LCModel fitting in Osprey

Add CRLB/h2oarea csv files

- Added comments to Quantify module

Add comment to LCModel tables

- add Siemens Mega GSH TE 120

Create basis_siemens_meagpress_gsh120

- merge MEGA MM fit function into the MultiSpectra branch

MEGA-MM

- Update info in the processed plot when the AllPDF option is used

Bug fix plot module

Bug fix related to GUI created jobFiles for multiple RDA files.
- The issue was related to trailing whitespaces generated from the SPM input dialog. Removing those from the file string fixed the problem.

Bug fix osp_create_job_file

- Bug fix related to the MRSinMRS function being non functional for concatenated fitting

Bug Fix Cristian MRSHub

- fixes a possible bug for older Siemens DICOM spectra

Bug Fix Jill

Added a multiplexed, probabilistic approach for aligning HERMES/HERCULES and MEGA data (adapted from Mark Mikkelsen's Gannet implementation). This can be used as a valid option in case of VAPOR WS which introduces different phases to the transients.

This can be envoked by   opts.SpecReg                = 'ProbSpecReg'; in the job file.

Add probabSpecReg

Added an default ordering of the ONOFF spectra for MEGA and HERMES in case the automatic detection fails. This can be changed in the specific function.

It will most likely be replaced by an job file entry in the updated OspreyProcess function

automated ONOFF classifier

This bug fix solves issues related to GUI malfunction for MATLAB 2021b.

This bug fix solves isses related to GUI malfunctions for MATLAB 2021b

Bug Fix MATLAB 2021b

-  enable all toolboxes that are available

Toolbox_Check

-fit style concatenated in MRSinMRS report

Bug Fix conc fit style

- enable external toolboxes only

Add support for CMRR DICOM STEAM data. Rejigs a few bits in the DICOM header read function. Resolves #366.

Add support for multi-file un-edited RDA datasets. Resolves #367.

- Bug fix related to Osprey crash during OspreyLoad for Siemens TWIX unedited data acquried on Connectom Scanner with Software Version VD

Bug fix - Siemens connectom data

-Updated GE loader to support GE HERMES/HERCULES data. Tested with GE data from the HBCD collaboration

Update io_loadspec_GE

- writetable() outputs use '\t' delimiter with .txt extension (writetable doesn't support .tsv extension).
- Modified exportCSV.m, renaming to exportTSV.m and adjusting outputs as above. Also updated calls to this function to reflect new name.

Added a movefile command to exports to apply .tsf extension. Also hard-coded a json encoded sidecar file for the table in OspreyProcess.m.

JSON encoding revised in OspreyProcess.m, and added into OspreySeg and OspreyFit.

Unified TSV outputs to one function call: WriteBIDsTable.m.

Still need to update OspreyQuantify to reflect this.

Finished CSV to TSV by updating the export TSV function. This was renamed exportQuant to avoid confusion with osp_WriteBIDsTable.m

Also reformatted json information to fit with existing Matlab table structure.

The subject_names_and_excludes table is now BIDs formatted.

Updated filename generation for OspreyCoreg and OspreySeg to allign with BIDs standards.

Initial BIDs update

Avoid errors for Matlab versions before 2021a

Update osp_WriteBIDsTable.m

Update OspreyOverview.m

Updated OspreySeg to save volume information. GUI plot requires callback to file locations stored there.

Update OspreySeg

Added complete description to the alignment options and cleaned up some typos regarding the PDF output.

Update example jobfiles

- Added new version number for release

Update version number