Mrsi

Revert "Mrsi"

Versioning:
-Removed single module versioning
- versioning is defined by single number (Osprey Version)
-Osprey version is used for checking on older containers, which is implemented in the toolbox check function
- Changed logging to Matlab diary function which hopefully allows us logging of MRSI processing etc
- Bugfix of VE11c and VE11E  universal data

Preparation for 1.0.0 Release

-Fixes error that was introduced during merge conflict
-Fixes introduction of multiple new lines in the console during module call

Release 1.0.0 prep

Add a file so GitHub Pages understands it can host the HTML files right away, without building through Jekyll.

Release 1.0.0

Merge pull request schorschinho#238 from schorschinho/develop

-Added basis set for MM suppressed GABA-edited Philips MEGA-PRESS

Add MMsup MP GABA Phillips

-This commit fixes the bug reported in issue schorschinho#242. The title definition in the osp_plotModule were changed in v.1.0.0, as individual version numbers of the modules were removed.

Bugfix for issue schorschinho#242

-Resolves issues reported in schorschinho#244

Fix issue schorschinho#244

Previously, we relied on MATLAB functions only available in the Curve Fitting Toolbox (spmak, fnval) to generate the cubic B-spline spline functions for baseline estimation.
These are now replaced with recursive iteration, eliminating the need for the toolbox altogether. In the process, the function has been cleaned up, removing the second derivatives that were never really used in the first place.

Adding a few lines to the gitignore path, mainly to prevent accidentally committing anything in our own "derivatives" folders in the exampledata folder, as well as overwriting the default SPM path.

Added some fancy shields.io badges to the readme file, like all the other great open source projects have.
Remove the YAML file for the previous Jekyll-style documentation system, which is now obsolete since we switched to bookdown.

Fix small bug in shields.io website-online? badge.

Fix an error that occurred when data with short-TE water, but without water reference, was displayed.

Remove a closed bracket that made the HERMES fitting routine throw an error upon calling.

Fix a bug in the function creating a job file from GUI inputs: Previously, only the first entry in a GUI list of multiple water reference datasets would be parsed correctly into the job file, while the rest of the entries would be erroneously replaced by the metabolite data. This is now corrected.

- Added new version number v.1.0.1 for next release

Update version number

-Fixes version comparison for v1.0.1 . The integrated version comparison was not properly update, therefore the GUI did not show the content of an already processed MRS container.

Hotfix version number

Update basis sets

- Removed H2O from the default metabolite list, so that it is not included in the metabolite fit anymore. It can still be included if the user specifies H2O in his metabolite list manually.
- The water basis function is loaded from the specific basis set if it is needed for the fit of the water scan. This happens regardless of the metabolite list the user specifies.

Update_water_fit

Added a new Osprey module OspreyMinReport.m that creates a markdown table including the minimum parameters for reporting of MRS studies (defined in MRSinMRS). This includes the following changes to other functions:

- Extracting software versions during the loading process (io_loadspec_sdat, io_loadspec_twix, and io_loadspec_GE)
- Automatic generation of md report during OspreyOverview call

Initial_commit_MRSinMRS_markdown

- Bug fix related to vendor-specific naming conventions in the voxel geometry
- Minor layout  changes

Update OspreyMinReport

- Updated the calculation of the fit quality parameter to match the original paper Barros & Slotboom. The quality is defined as a variance ratio between residual in the fitted region and noise

Update osp_fit_Quality

Two minor bug fixes:
1) Possible issues in the metabolite list when new metabolites are added to a default Osprey basis set

2) Avoid crashes when hidden files are stored in the DCM folder

Bug fix

-Added a decision tree, that creates a metabolite list for the preliminary reduced fit according to the input list of the user (e.g. if the user performs a phantom scan with fCho instead of GPC or PCh in the list) this metabolite is picked instead of the default (NAA, Cr, PCh, Glu, and Ins.

Updated prelim fit

Fixes reported Bug in the correlation plot within the GUI where it was not possible to switch between external variables

Bugfix correlation plot GUI

- OspreyQuantify has now relaxation times for 7T metabolites as well
- fieldstrength is automatically picked

Added 7T relaxation time lookup table