Osprey v2.5.0

What's new?

• This new release includes fully compiled versions of the OspreyGUI for MacOS, Windows, and Ubuntu. The installer includes the correct MATLAB runtime for each OS. This will allow the user to run Osprey without a MATLAB license. The compiled version also includes the matching binaries of LCModel if Osprey is used as a wrapper for analyzing conventional MRS with LCModel.

What's Changed (detailed)

• Fixes #498 by @CWDAVIESJENKINS in #499
• [FEATURE REQUEST] -Manually overwrite subspectra order - OspreyProces… by @HJZollner in #501
• [FEATURE] - XA30 loader Siemens WIP MEGA - load_twix - gunziyhu by @HJZollner in #503
• [BUG] - GUI crash for user defined metabs- OspreyJob - Bethany Stennett by @HJZollner in #505
• [BUG FIX] - Segmentation fails for DCM spec files - OspreyCoreg Ospre… by @HJZollner in #508
• Minor Bug fixes in various functions by @HJZollner in #509
• [FEATURE] - Add visual LB and Zoom - plot_OspreyFit - Richard Edden by @HJZollner in #510
• [FEATURE] - Add visual LB and Zoom - plot_OspreyFit - Richard Edden by @HJZollner in #511
• [FEATURE] - Adaptions for Compilation by @HJZollner in #513
• Prepare Windows compilation by @HJZollner in #514
• Reduce basisset filesize by @HJZollner in #515
• Some more prep for compilation by @HJZollner in #516
• Fix #517 by @CWDAVIESJENKINS in #518
• Fix #519 by @CWDAVIESJENKINS in #520
• [BUG FIX] - GUI quantify crash LCModel wrapper - Meredith Reid by @HJZollner in #522
• [BUG FIX] - Philips loader crashes on LINUX system - philipsLoad.m - … by @HJZollner in #524
• Update OspreyHTMLReport by @HJZollner in #528
• [BUG FIX] - External segmentation and json by @HJZollner in #530
• Update OspreySeg by @HJZollner in #531
• [BUG FIX] - OspreySeg not working for .nii.gz files - OspreyCoreg - … by @HJZollner in #534
• OspreyGUI fixes by @HJZollner in #535
• Update osp_fitInitialise.m by @HJZollner in #536
• Exporting fitting parameters by @JohnLaMaster in #525
• [FEATURE REQUEST] - Basis set resolution smaller than data resolution… by @HJZollner in #539
• Osprey docs update by @CWDAVIESJENKINS in #540
• [BUG] - Crash when loading MEGA-PRESS rda - io_loadspec_rda - Mary Ad… by @HJZollner in #542
• Update fit_createSoftConstrOsprey.m by @HJZollner in #543
• Prepare series analysis by @HJZollner in #544
• [BUG FIX] - SpectroFrequency nii-mrs header extension issue - io_writeniimrs - Helge by @HJZollner in #549
• [Feature Request] - Defacing of structural images - OspreyCoreg/Seg -… by @HJZollner in #552
• Add alpha correction for Glx and fix 1to1GABA concentrations by @HJZollner in #556
• [BUG FIX] - Incorrect coreg if multiple files per subjects - OspreyCo… by @HJZollner in #561
• OspreyLoad by @HJZollner in #562
• [FEATURE REQUEST] - Integer labels only for XAxis - all plot function… by @HJZollner in #563
• Update osp_plotFit by @HJZollner in #564
• Update osp_plotFit by @HJZollner in #565
• Better handle definition for plots by @HJZollner in #566
• Fixes #567 by @CWDAVIESJENKINS in #568
• [BUG FIX] - GUI Job generator has wrong tool tip - CreateOspreyJob_ap… by @HJZollner in #571
• [BUG FIX] - Overlap map not cerated - OspreySeg - Meredith Reid & Men… by @HJZollner in #575
• Addition to #571 by @HJZollner in #578
• [BUG FIX] - XA 30 data not correctly loaded - io_loadspec_twix - Helg… by @HJZollner in #581
• [BUG FIX] - Unable to pick GE DICOM through GUI - CreateOspreyJob - J… by @HJZollner in #582
• [FEATURE] - Allow NOBASE = T in LCModel wrapper - osp_fitUnEdited - H… by @HJZollner in #583
• [FEATURE] - NIfTI-MRS provenance integration - Helge Zöllner by @HJZollner in #584
• [FEATURE] - add diff3 GAP by @HJZollner in #586
• [FEATURE REQUEST] - GABA-GSH-EtOH HERMES - Mark Britton by @HJZollner in #587
• MRSI support in osp_exportParams by @JohnLaMaster in #572
• [FEATURE REQUEST] - Tissues alpha correction Glu - shaokunzhao by @HJZollner in #591
• [BUG FIX] - whitesapcePattern function not known - OspreyJob - Dina S… by @HJZollner in #594
• [BUG FIX] - Can not import basis set form LCModel correctly - shaokun… by @HJZollner in #597
• Finalizing osp_exportParams by @JohnLaMaster in #598
• BUG FIX - Missing End in OspreyJob by @HJZollner in #600
• BUG OspreyOverview by @HJZollner in #601
• BUG OspreyOverview by @HJZollner in #602
• BUG OspreyJob .m defaults by @HJZollner in #603
• BUG default options .m file by @HJZollner in #604
• [BUG FIX] - OspreyQuanitfy crash for limited basis - OspreyQuantify -… by @HJZollner in #606
• [BUG FIX] - Unrecognized field in basis set - OspreyFit - Mingrun Shi by @HJZollner in #608
• Preparation release v.2.5.0 by @HJZollner in #609
• Release v.2.5.0 by @HJZollner in #610
• Trigger CI by @HJZollner in #611
• [BUG] - LCModel Glu_Gln label crashes alpha correction by @HJZollner in #612
• LCModel label bug by @HJZollner in #613

New Contributors

• @JohnLaMaster made their first contribution in #525

Full Changelog: v.2.4.0...v.2.5.0

Osprey v2.4.0

What's Changed

• [FEATURE REQUEST] - Update description plotProcess and plotFit - Maari13 by @HJZollner in #455
• [BUG FIX] - GUI crashes during load plot - osp_plotLoad - Gaelle Doucet by @HJZollner in #457
• [BUG FIX] - plotPDF crashes for ref/water scan - osp_plotModule - Mikkelsen/Hupfeld/Mullins by @HJZollner in #459
• [NEW FEATURE] - Process 'any' water scan as water reference - various… by @HJZollner in #461
• [FEATURE REQUEST] - Import Siemens XA (31) data - OspreyLoad - Karl K… by @HJZollner in #462
• [BUG FIX] - Issue with Special Flag - osp_combineCoils - marilenad by @HJZollner in #464
• [FEATURE] - Add basis and remove noise scan - Gaelle Doucet by @HJZollner in #468
• [BUG FIX] - GE MRS & nifti anatomical LR flip - coreg_ge_nifti - Simm… by @HJZollner in #470
• [BUG FIX] - remove uncombined raw - OspreyLoad - Helge by @HJZollner in #472
• [BUG FIX] - crash during osp_plotModule - osp_plotModule - Gaelle Doucet by @HJZollner in #474
• [BUG FIX] - OspreyJobGUI not showing 1. header - CreateOspreyJob_app … by @HJZollner in #477
• [BUG FIX] - pars all sub options in OspreyJob - OspreyJob - Helge Zoe… by @HJZollner in #483
• [BUG FIX] - FID-A functions for multi-dim data - op_ppmref/op_autopha… by @HJZollner in #484
• [BUG FIX] - pre_referencing unreliable - op_preref - Helge Zoellner by @HJZollner in #485
• [BUG FIX] - non-integer spectral width - GUI functions - Helge Zoellner by @HJZollner in #486
• [BUG FIX] - file_w not loaded when file_ref is supplied - osp_CoilCo… by @HJZollner in #487
• [BUG FIX] - GUI crash during Load window - ? - Koen Cuypers by @HJZollner in #489
• [FEATURE] - Autodetect Same Name Masks - OspreyCoreg - Helge Zoellner by @HJZollner in #490
• [FEATURE] - Update Segmentation for BIDS and Overlay - OspreySeg - Helge Zoellner by @HJZollner in #491
• Fix continuous integration by @HJZollner in #492
• Add new example data by @HJZollner in #493
• Add BB and vx manually by @HJZollner in #494
• [BUG FIX] - fieldtrip interferes with MATLAB finv - regression_line_c… by @HJZollner in #495
• Prepare Release v.2.4.0 by @HJZollner in #496
• Release Push v.2.4.0 by @HJZollner in #497

Full Changelog: v.2.3.0...v.2.4.0

Osprey v2.3.0

What's Changed

• SPECIAL support by @schorschinho in #430
• HBCD - external segmentation not finished case - Erik Lee by @HJZollner in #431
• Add PRESS 97 ms - Todd Parrish by @HJZollner in #432
• Integrate Cystat - Todd Parrish by @HJZollner in #433
• Integrate Cystat - Todd Parrish by @HJZollner in #434
• Integrate Cystat - Todd Parrish by @HJZollner in #435
• [BUG FIX] - Osprey crash for non-integer spectralwidth - McNabb by @HJZollner in #437
• [BUG FIX] - Added 7T PE relaxation times for 7T- CWDJ #438 by @CWDAVIESJENKINS in #439
• [BUG FIX] - Fix issue parsing certain LCModel control file parameters & associated error reporting - #440 by @CWDAVIESJENKINS in #441
• [BUG FIX] - Osprey GUI crash - Model/Coreg button - Lewis Crawford by @HJZollner in #443
• [BUG FIX] - hermes fit crash - fit_sortBasisSet - Kathleen Hupfeld by @HJZollner in #445
• BUG FIX - MM3co scaling - fit functions - Kathleen Hupfeld by @HJZollner in #448
• [BUG FIX] - duplicate .ni.gz removal - osp_plotCoreg.m - Erik Lee by @HJZollner in #449
• [BUG FIX] - Osprey GUI - Crash for MEGA data - Gaelle Doucet by @HJZollner in #451
• Prepare v2.3.0 release by @HJZollner in #452

Full Changelog: v.2.2.0...v.2.3.0

Osprey v2.2.0

What's Changed

• [BUG] - Remove unwanted warnings and windows from Osprey GUI - Helge by @HJZollner in #402
• [BUG] - Multi-dataset errors and preparation of series - Helge by @HJZollner in #403
• Integrate json jobFiles by @HJZollner in #405
• Create OspreyHTMLReport.m by @HJZollner in #406
• Added description to HTML report by @HJZollner in #407
• Create RunOspreyJob by @HJZollner in #408
• [FEATURE REQUEST] - Add external segmentation results - OspreySeg - H… by @HJZollner in #409
• Prepare Osprey compilation - Helge by @HJZollner in #410
• Update T1w colormap - Resolve scaling issue - Richard Edden by @HJZollner in #412
• [BUG Fix] - OspreyFit crashing - Yulu Song by @HJZollner in #414
• [FEATURE REQUEST] - Single file external segmentation - HBCD by @HJZollner in #415
• [FEATURE REQUEST] - Add pre/post alignment - Eric Porges by @HJZollner in #417
• [BUG] - Keypress GUI - Yulu Song by @HJZollner in #419
• Upload basis sets for HBCD by @HJZollner in #420
• Update OspreyProc by @HJZollner in #421
• Add GE HERCULES basis set by @HJZollner in #422
• Remove SPMpath.mat - osp_Toolbox_Check - Helge Zöllner by @HJZollner in #423
• HBCD changes - [FEATURE REQUEST] - multiple functions - Helge Zöllner by @HJZollner in #424
• [BUG FIX] - example jobfiles - Helge Zöllner by @HJZollner in #425
• Add version number by @HJZollner in #426
• Prepare v.2.2.0 release by @HJZollner in #427
• fix MEGA fit by @HJZollner in #428
• Fix release v.2.0.0 by @HJZollner in #429

Full Changelog: v.2.1.0...v.2.2.0

Osprey v2.1.0

What's Changed Summary

• Edit ReadMe.md by @richardedden in #387
• Update io_loadspec_twix by @HJZollner in #390
• Bug fixes by @HJZollner in #391
• Update OspreyMinReport by @HJZollner in #392
• Integrate NIfTI MRS read/write/coreg implementaion by @CWDAVIESJENKINS in #398
• Prepare release v2.1.0 by @HJZollner in #399

Features

• Integration of coregistration and segmentation of NIfTI-MRS datasets
• Export function for edited/multi-subspectra NIfTI-MRS format
• Renamed Ins to mI for Myo-Inositol & Scyllo to sI. This has been passed to all basis sets, the default metabolite list, and example files. HOWEVER, if you are manually passing a metabolite list with the old naming convention the basis set will not be properly defined.

Bug fixes

• Full integration of SPM12 and GUI for MATLAB 2021a and newer
• Bug fix for failing coil combination for TWIX data if no water reference is supplied
• Write rda datapoint re-ordering fixed
• Fix for multi IMA DICOM loader
• Removed warning output from plots

Full Changelog: v.2.0.0...v.2.1.0

Osprey v.2.0.0

Features

• In case metabolite suppressed data is supplied, OspreyFit has been updated to perform three separate linear-combination modeling runs.: 1) Using parameterized MM basis functions (standard approach with Gaussian functions); 2) Include the cleaned measured MM spectrum (denoised by using a spline function) in the LCM; 3) If multiple subjects are supplied a mean MM spectrum across all subjects is created and included in the last run.
• Analysis of metabolite-suppressed data from edited and multiplexed spectra is now supported.
• Add multiple MRS experiments to a single subject by adding another dimension to your input cell arrays. Osprey will load and process all spectra and concatenate them along the extra dimension. In the current release, the extra dimension is not incorporated into the OspreyFit, OspreyQuantify or OspreyQuantify module. This will be part of a future release. However, this can be used if for example, multiple MRS experiments need to be averaged e.g. two separate scans from the same voxel (See example jobSDAT_MEGA_Multidataset.m). After processing you have to call osp_AverageAllDatasetsAlongExtras to average the acquisitions.

Changes

• The MRSCont struct has been completely restructured. Therefore the files from older versions are not compatible, please re-run the analysis or use an older release version.

Osprey v1.2.0

Features

• Added CRLBs and h2oarea as csv files to the LCModel fit in Osprey
• ProbSpecReg for multiplexed and MEGA data
• Tabular outputs are now .tsv, rather than .csv, and accompanying .json files are produced. File naming conventions for structural outputs are also reviewed.

Bug fix

• More information to the OspreyProcess Module in the ops_plotModule and updated the wrong calcualtion of FWHM in ppm. This was done to match the GUI and print output. Thank you Deborah Barany for reporting this issue.
• updated the nii viewer function to work for all kind of combinations of .nii and .nii.gz files
• close the opts.PDF generated plots
• MRShub.org report from Cristian Guerrero about 'Concatented' fitting not creating MRSinMRS.md
• Siemens DCM loader bug for older spectra fixed (reported by Jill Naaijen)
• Siemens HERMES/HERCULES coil combination not working when 4 averages are acquired in the water reference scan
• Bug fix for Siemens TWIX PRESS data acquired on Connectom Scanner with VD software version
• Single average RDA MEGA-PRESS data not being processed correctly

Osprey v1.1.0

New functionalities

• Automated LCModel integration from within the Osprey pipeline for unedited data. Osprey automatically creates the needed control files and calls LCModel from within MATLAB. The results are imported back into Osprey to be used in the downstream modules. You can also provide your own control files and .BASIS files. You need to add compiled LCModel binaries into the libraries/LCModel folder (visit for instructions). Currently, Osprey is shipped with compiled binaries for Windows 10 and macos catalina.
• Nifti MRS loader and export functions

Updates & Bugfixes

• Reduced file size by removing redundant basis set from the MRS container
• Issues related to the deletion of user supplied strucutral images

Other changes

• automated OS identifier and font picker

Osprey v1.0.2.1

Version check bug fix

Osprey v1.0.2

New functionalities

• updates to the MRSI module to process three slice edited MRSI data (loading & MoCo)
• GE nifti files accepted
• MRSinMRS markdown function
• 7 T relaxation time lookup table for quantification
• Improved functionality to run Osprey on the server
• Added co-edited MM model to HERCULES modeling
• OspreyOverview can be called after OspreyProcess to generate overview plots without fitting

Updates & Bugfixes

• Preliminary fit picks metabolites based on the supplied basis set (e.g. Cho containing compounds instead of Cho)
• FitQA definitions updated to match the original paper
• AllPDF bug fixes
• Updated GE load function
• Updated Siemens DICOM loader
• Updated all example jobFiles to reflect the current functionalities of Osprey and to reflect BIDS structured automated processing
• Updated version numbering and check function to give soft warnings only

Other changes

• Prior module check function