twix_slaser_bug

Create Job: an interactive gui to select the data and set the parameters of the analysis to perform. A job.m file is automatically created and loaded

…scanner data

Coregistration of the mrs voxel on a T1 image in nifti format for GE scanner data

Coregistration of the mrs voxel on a T1 image in nifti format for GE …

Interactive create Job GUI

Interactive 'Create Job' GUI and coregistration with T1 data in nifty format for GE scanner

-Inserted credits to Dr. Schuerbeck for his work on developing a GUI to create OspreyJob.m files.

Update_jobFile_app

-Made some adaptions on the jobGUI

UpdatingOspreyJobGUI

- Added Peter Van Schuerbeek for his contributions

-MLaser 7T water reference from Siemens bugfix

7T_subspec

-Bugfix in the jobTwix example jobFile which was introduced by including a short TE water reference and an eddy current reference for undedited data

Update_jobTwix

-Added case with short TE water reference and lineshape reference to the orderFields function

-bugFix for Processed plot

Update orderFields

-Added different MM moddels for the co-edited MMs at 3 ppm for GABA-edited MEGA-PRESS
-Added experimentally derived MM baseline and MMs > 3 ppm

MEGA_PRESS_coMM_model_and_MMexp

Addded dh and h to the LM output

Add_dh

-Added freeGauss model to HERMES GABA-edited spectra

-Addded Philips DATA file support to Osprey
-If no SPAR file is available, the sequence parameters (te, tr, sw, Larmor, and seq) can be passed into Osprey via the stat.csv file.
- Tested on MP data

HERMES_coMM3_model

- Removed bug in case of multiple .data files

Update_ospLoadDATA

-inital upload of PRIAM laod and recosntruction

-Tweaked the HERMES classifier for the GABALac HERMES experiment, bc of weak water suppression

Update_HERMES_Classifier

-Added a subspectra alignment based on the L1 norm (sum of the difference spectrum)
-Added a flag to evoke L1norm alignment in the job
-Added options to change the range of FrequencyRestricted registration in the job
-Added a flag to evoke unstable water option in the job

Adding L1Norm subspec alignment

Small fix to squash a bug when DICOM folders in the job file are provided without the file separating character at the end.

Simplify the parsing of the MRS data file extension; add function to load DICOM files without any extension (don't necessarily have to be .dcm or .ima).

-Added .nii.gz reader for all vendors and overlays
- changed standard output format for the voxel masks and segmentation maps to .nii.gz
- replaced .nii files in the examples to reduce file size

Adding .nii.gz readability

-Re-adding gitignore

- Update .gitignore, needed to recache the repostiory to do so

Update .gitignore

-Re-adding gitignore

_re-cashed and re-added gitignore

Re-add gitignore

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.