Release Push v.2.4.0 #497
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Release Push v.2.4.0 #497
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Updated description of the voxel indices for the process and fit plot functions for external use. Also added better automatic fallback for the plotProcess function
[FEATURE REQUEST] - Update description plotProcess and plotFit - Maari13
The crash was related to having a single average water scan which results in dims.averages = 0 and wrong indexing. Fixed by having an additional case during the plot call.
[BUG FIX] - GUI crashes during load plot - osp_plotLoad - Gaelle Doucet
…kelsen/Hupfeld/Mullins Added a drawnow command which fixes the issue.
Set plotPDF flag back to 0 for the example file.
[BUG FIX] - plotPDF crashes for ref/water scan - osp_plotModule - Mikkelsen/Hupfeld/Mullins
Add new basis set and control file for 7T Siemens STEAM (CMRR sequence) data (TE = 5 ms). Very kindly provided by Dr. Dinesh Deelchand. Add request for acknowledgement of Dr. Deelchand's and Dr. Ariane Fillmer's contributions to the readme.
… load functions - Muhammad Saleh - You can add any water scan as water reference now. - Introduced a new function that combines subspectra from the water scan during the loading - Additionally, added a case for the coil-combination to use the water reference scan if no lineshape reference is provided.
[NEW FEATURE] - Process 'any' water scan as water reference - various…
…oschutnig Modified io_loadspec_twix to support XA31 data.
[FEATURE REQUEST] - Import Siemens XA (31) data - OspreyLoad - Karl K…
Added a proper fix for the reported issue. This was related to the interleaved water scan for GE P files. Also updated some of the indices for MultiSpectraLoader in the same script as well as GE P files related GUI issues due to the absence of files_ref names.
[BUG FIX] - Issue with Special Flag - osp_combineCoils - marilenad
- Added a 40 ms sLASER Siemens unedited basis set - Added a new function (osp_remove_noise_scan) to remove noise reference scans from the CMRR sequence. This has to be run before OspreyProcess to remove the noise reference scan.
[FEATURE] - Add basis and remove noise scan - Gaelle Doucet
…onite & DeMayo Removed a redundant LR flip form the coreg_ge_nifti function. Test data reproduces voxel locations for DCM and nifti input.
[BUG FIX] - GE MRS & nifti anatomical LR flip - coreg_ge_nifti - Simm…
Re-added code to remove uncombined raw data after coil combination to reduce the file size of the MRS container.
[BUG FIX] - remove uncombined raw - OspreyLoad - Helge
Added a missing round statement to avoid an additional . during the construction of the struct.
[BUG FIX] - crash during osp_plotModule - osp_plotModule - Gaelle Doucet
…- Koen Cuypers This was related to hardcoded window size and a non-resizable window. We have added an optional scroll bar and made the window resizable. We did not include an automated window size due to compatibility with the MATLAB App designer.
[BUG FIX] - OspreyJobGUI not showing 1. header - CreateOspreyJob_app …
…llner Added an additional loop to parse all sub options from the .m jobfile.
[BUG FIX] - pars all sub options in OspreyJob - OspreyJob - Helge Zoe…
…se - Helge Zoellner Fixed FID-A functions to allow for multi-dimensional data with >1 sub-spectra.
[BUG FIX] - FID-A functions for multi-dim data - op_ppmref/op_autopha…
Added a try catch block for unreasonable high frequency shifts during the pre-referencing step. The catch block uses a cropped frequency range and the magnitude spectra instead.
[BUG FIX] - pre_referencing unreliable - op_preref - Helge Zoellner
Added round() statement to GUI functions to avoid crashes related to non-integer spectral width
[BUG FIX] - non-integer spectral width - GUI functions - Helge Zoellner
…bine - Helge Zoellner file_w spectra were skipped when a reference file was supplied.
[BUG FIX] - file_w not loaded when file_ref is supplied - osp_CoilCo…
This crash is related to the the spar loader and how it recognizes whether a 'Series' scan has been acquired. It falsely identified the MEGA data as a series data resulting in a crash. Added a new flag to indicate series data in the container.
[BUG FIX] - GUI crash during Load window - ? - Koen Cuypers
Added a new feature that creates BIDS compliant voxel mask names if the user is not using BIDS compliant naming.
[FEATURE] - Autodetect Same Name Masks - OspreyCoreg - Helge Zoellner
…lge Zoellner - Changed the segmentation output to match BIDS - Export Deformation Field during the segmentation to calculate SPM152 overlap masks - Updated OspreySeg to calculate voxel masks in SPM152 space. To make this work on an older analysis you have to remove the old SPM outputs from your folder. - New function to generate a voxel consistency figure. It calculates the center of mass to find the voxel center. However, the user can also input the voxel center as an argument.
Add folder structure
Add folder structure
Added spm152.nii template with per manual upload
[FEATURE] - Update Segmentation for BIDS and Overlay - OspreySeg - Helge Zoellner
Fix bug in the continuous integration pipeline related to BIDS segmentation
Fix continuous integration
Add example data for MM fitting in Osprey
Add new example data
Add the SPM152 BB and vx manually to make it less susceptible to wrong path set up
Add BB and vx manually
…i - Koen Cuypers - Once again fieldtrip is using MATLAB internal function names that break Osprey/MATLAB. Added a conditional statement to remove the fieldtrip function. - The user could also avoid this by including SPM12 without sufolders
[BUG FIX] - fieldtrip interferes with MATLAB finv - regression_line_c…
Add version number
Prepare Release v.2.4.0
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Bring all changes to the master branch