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Added azure pipeline success batch to README.md [ci skip]

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Adding scripts to de-identify Philips SPAR, GE P, and Siemens TWIX files.

- removed redundant basis sets from MRS container and updated all functions that need those
- Osprey GUI figure is now overwritten when a new instance is started
- Bug fix related to potential naming issue for the sub-spectra alignment as defined in the example jobFiles

Memory Optimization

- Added new functionalities which allow to share/copy the MRS container between different machines without losing the GUI functionalities. This flag is turned of by default to reduce the file size of the container, but it can be run on already processed containers.

- OspreyAddImages stores the three plane images that are required for the plot functions of coreg and seg into the container.

- osp_extract_three_plane_image.m adds the images for the OspreCoreg plot into the container

- osp_extract_three_plane_image_seg.m adds the images for the OspreSeg plot into the container

- Further updates were added to the OspreyGUI function which automatically checks whether the container has been moved. The LogFile is then recreated on the new machine and the Coreg/Seg buttons are disabled. The coreg/seg tab is activated only for containers where the image files are available or the results are stored in the container. The same is the case for the external nii viewer.

Decouple MRS container from local machine

This update introduces new functions for loading and writing NIfTI-MRS data, tweaks existing ones to ensure compatibility, and adds example data.

At this point, only conventional (non-dynamic) single-voxel data has been tested. Support for spectral editing, MRSI etc. will follow.

- Bug fix wrt reported issues with the GUI being closed during module calls. This was due to the changes of the handle visibility of the GUI which was supposed to overwrite old instance upon GUI call. The handle visibility is now changed dynamically on button click events to avoid crashes.

BugFix accidental GUI crash

New functions to provide, read and write custom LCModel control files.

This reverts commit bc305b5, reversing
changes made to d991f85.

- updated downstream modules to work with lcmodel
- updated GUI to work with lcmodel

- removed metabolite combinations from stack plot
- ensured full GUI functionality
- automated platform check and font picker

Adding an if-statement to intercept cases where no basis set was formally specified in the job file (for use with special LCModel-sptype-settings like lipid-8, which don't require a basis set).

When data from the JHU Universal Sequence (Siemens) is loaded, io_loadspec_twix automatically sorts the sub-experiments for MEGA/HERMES into FID-A sub-spectra. This behaviour crashed data that was collected with less transients than expected sub-spectra. This is now fixed.

Similarly, op_averaging demolished the dimension arrangements when it encountered single-transient data. This is now fixed, too.

- added platform extraction to check for LCM binaries
- updated ver number for release
- avoided accidental nii removal

Added win_10 LCModel binaries

Load nii mrs

Lcmodel integration

-Updated the example jobFiles to include NII MRS and LCModel fitting

Update example jobFiles

Update Nii flag to default settings

Update OspreySettings

- Fix bug related to fit plots of Osprey Model

Fix plot related issues

- removed some bugs with regards to plotFit and plotModule
- OspreySeg bug WRT to gz files removed

lcm-integration