Release Osprey v2.6.0 #753
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- added LCModel binaries for linux for the compiled ubuntu version of Osprey.
LCModel integration Ubuntu
Merge pull request #613 from schorschinho/develop
Add dummy software if it is unknown in the DICOM Siemens files.
Add dummy software
[BUG FIX] - Update Matlab version requirement for GUI in Osprey docs - Osprey Docs - Carl #617
See https://forum.mrshub.org/t/error-from-io-lcmbasis-function/1389/12 Previous version incorrectly interprets METABO_CONTAM and METABO_SINGLET tags present in some basis sets as metabolite names, then may fail in eval'd code with error "Character vector is not terminated properly"
Bugfix, io_readlcmraw_basis METABO_* tags
…lone - Added more elaborate decisions during the compilation process. New flags to compile HBCD, CMD, or GUI as well as an additional flag for the installer packaging for easier runtime management.
[BUG FIX] - Can't compile Osprey CLI for Ubuntu - CompileOspreyStanda…
… io_loadspecniimrs - Steve Hui Account for phasing in Philips ISHTMUS data. Similar approach as in Gannet with a multiplication by the first point ratio of conj and abs of the fid.
[FEATURE REQUEST] - Account for ADC phase shift in Philips nii data -…
Add a line that ensures that Osprey carries over metabolites that are listed as 'chomit' in a template LCModel control file. This was previously not done correctly, resulting in 'chomit' metabolites erroneously included in the LCModel fit.
- Added Thalamus overlap calculations to HTML report - corrected Philips phasing issue with ISHTMUS data
HBCD reports update
- added voxel dimensions to HTML report
Add voxel dims
- Added a cellfun to remove leading or trailing whitespaces for filenames
[BUG FIX] - leading or trailing whitespaces
- catches empty position entries in DICOM header
[BUG FIX] - empty position entry in DICOM header
CreateOspryJob_app uses spm_select to choose files, which returns filenames as a (square) character array -- possibly padded with spaces. Added `cellstr` calls to trim those spaces. This is complementary to commit 985ad44 (which addresses a symptom of this same problem, and would additionally handle the case where a user-generated list has trailing spaces) Also includes a minor (unrelated) fix for compatibility with pre-2020b Matlab.
Avoid trailing whitespace in generated file lists
…trict - Steve Hui - this was related to wrong initialization of the frequency range for HERCULES data
[BUG FIX] - frequency-restricted specreg crashing - op_SpecRegFreqRes…
- some modifications to the Tarquin importer
Partial fix #730: mixed types for basisSetFile
Range check/adjustment of frequency limits failed due to incorrect variable name
Adaptable referencing for phantoms which may not include the typical reference singlets, and may include a 0 ppm reference.
Adaptable frequency referencing for phantoms
Add XA50 for io_loadspec_twix.m
…antomReferencing - added correct ref flags during coil combination - fixed function call for referencing of phantom data
[BUG FIX] - Load/Process crash for phantom data - osp_combineCoils/osp_Ph…
…x Gusseew - added more flexibility to the io_loadspec_twix function to support various XA software versions
[BUG FIX] - MEGA-PRESS XA31 files extra dim issues - OspreyLoad - Ale…
… a separate data file - osp_saveNII - support multiple-water references in a single P-file for GE
[BUG FIX] - osp_saveNII fails if water signal does not originate from…
Modified code to directly store version in string variable without modifying the twix_obj.
[BUG FIX] - twix_object read only - io_loadspec_twix - Alex Gussew
Adding a new dimension definition to hold metabolite cycling data in NIfTI-MRS (v0.9). Bringing in line with 3c16942 (wtclarke/mrs_nifti_standard@3c16942).
Encountered a VD13 Siemens product sequence that had the transients dimension in the `Set` flag, not in `Ave`.
…h Abbasi-Rad - correctly apply calculated corrections to the transients shown in the plot.
[BUG FIX] - Post-alignment plot incorrect - osp_plotProcess - Shahrok…
osp_Toolbox_Check would indiscriminately attempt to enable every toolbox available on the system. This patch selectively enables only the necessary ones.
Cleanup osp_Toolbox_Check
… Several reports - New PreservePolarity flag was not implemented correctly. Therefore, not all datasets were polarity corrected before the spectral alignment.
[BUG FIX] - 180 flip not corrected before alignment - OspreyProcess -…
Preparation for release
Prepare release v.2.6.0
HJZollner
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Jul 15, 2024
Merge pull request #753 from schorschinho/develop
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New release version v2.6.0