Updated io_writeniimrs to work with more general input data. This should now manage any 7D SVS data that uses Matlab MRS structure.

Fixed error in main loop of NIFTI write routine, and added a temporary seq label for NFITI data.

Fixed error in osp_processHERCULES concatenation of ref averages

Rename metabolite models for consistency:
Scyllo -> sI
Ins -> mI
Updated in basis sets, plot routines, example scripts, libraries, GUI text, and main functions.

This work has been supported by NIH grants R01 EB016089, P41 EB15909, P41 EB031771, R01 EB023963, and K99 AG062230.

Edit ReadMe.md

- Bug fix for single average HERMES/HERCULES Siemens data
- Feature request: Update Twix loader to accept combined fMRI/fMRS sequence

Update io_loadspec_twix

GUI related bug fixes:
- nExperiments correctly initialized
- raw size correctly initialized
- metabolite names correctly initialized
- SPM12 crash in MATLAB R2021 and newer
- residual amplitude correctly stored

Bug fixes

- Adapted struct output according to new QM measures

Update OspreyMinReport

Some plot lines in osp_plotLoad and osp_plotProcess did not specify the real part of spectra to be plotted, so the obligatory "Warning: Imaginary parts ignored" would pop up. This commit fixes this behavior.

Added voxel coregistration for Nii MRS. Currently working for Philips data but not Siemens. Main changes:

Added coreg_nifti.m which uses nii_tool to coregister voxel to structural.
Added nii_xform to lib - function used by nii_tool
updated OspreyCoreg to handle NIFTI
Modified osp_fitinitialise to throw warning if sequence type not detected
Modified osp_LoadNii to try and populate vendor/seq fields of MRSCont
Fixed bug in osp_plotSegment

… NIFTIMRS

Intercept and skip read errors during Siemens DICOM header parsing. Add missing flag indicating whether multi-file IMA data have been averaged on-scanner. Fix an error resulting from an unknown `seq` variable. Fixes #395

Empty protocol name handling for NIfTI MRS, and bug fix in osp_combineCoils

Integrate NIfTI MRS read/write/coreg implementaion

Fix RDA writing error (data points were not ordered correctly).

Fixes TWIX coil combination procedure in case no water reference is provided.