QMRTools - Release 4.3.9

Bugfixes and new networks: - EPG fit bug fix - segmentation network updates - ApplySegmentation fix

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling 6 months ago

QMRTools - Release 4.3.8

CSI recon performance update - Revmove batch/sh scripts from elastix call

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling 6 months ago

QMRTools - Release 4.3.7

Bugfixes in: - MuscleBidsTools - ReconstrucionTools - SpectroTools

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling 6 months ago

QMRTools - Release 4.3.6

update Max dcm2nii

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling 7 months ago

QMRTools - Release 4.3.4

• Bisds restructure settings
• bug fixes
• bidds features added

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling 7 months ago

QMRTools - Release 4.3.3

• Bisds restructure settings
• bug fixes
• bidds features added

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling 7 months ago

QMRTools - Release 4.3.2

• Bisds restructure settings
• bug fix segment
• bug fix elastix

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling 7 months ago

QMRTools - Release 4.3.0

• MuscleBids and segmentation update
• check for bvalvec in muscle bids conversion
• added mono exponential T2 fitting to T2Bids
• allow custom segmentation files in SegmentData
• added ViewProtocolNames

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling 8 months ago

QMRTools - Release 4.2.10

• MuscleBids update
• Volumes added
• bids naming corrections

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling 8 months ago

QMRTools - Release 4.2.9

• Elastix subfoder change
• added extra pulse profiles
• increased depth of classify networks

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling 8 months ago

QMRTools - Release 4.2.8

• update neural networks for segmenations

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling 9 months ago

QMRTools - Release 4.2.7

• Adding segmentation location
• small bug fixes

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling 9 months ago

QMRTools - Release 4.2.6

• small bug fixes

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling 10 months ago

QMRTools - Release 4.2.5

• BIDS EPG fitting update

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling 10 months ago

QMRTools - Release 4.2.4

• fix Loess plot
• small optimization of CSI recon

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling 10 months ago

QMRTools - Release 4.2.3

• new tensor denoising methods
• Update on how bids processes tensors
• added LOESS regression
• added RBPM fitting

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling 11 months ago

QMRTools - Release 4.2.1

• muscle bids update
• included tensor with gradient correction
• EPG T2 with siemens profile

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling 11 months ago

QMRTools - Release 4.2.0

• tractography updates
• gradient nonlinearity correction
• Helmholtz-Hodge tract denoising

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling 11 months ago

QMRTools - Release 4.1.5

• Performance updates
• Bids updates

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling 12 months ago

QMRTools - Release 4.1.3

• Segmentaion tools update

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling about 1 year ago

QMRTools - Release 4.1.2

• bug fixes in bids

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling about 1 year ago

QMRTools - Release 4.1.1

• bug fixes

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling about 1 year ago

QMRTools - Release 4.1.0

• performance update

• rebuild of documentation

• optimization of tensor fitting

• optimization of dixon fitting

• optimization of tractography

• Finetune MuscleBids tools

• bug fixes

• started on removing typos in functions and help

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling about 1 year ago

QMRTools - Release 4.0.5

• Update of tractograph

• small fixes in seed and handeling RK4

• optimization of tractograph method

• added parallelization for tracto

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling over 1 year ago

QMRTools - Release 4.0.3

• Muscle Bids analysis

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling over 1 year ago

QMRTools - Release 4.0

• finalized segmentation tools
• finalized CNN training framework
• many function optimizations
• full rebuild of docs and htmls docs
• fully tested for 14.1

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling over 1 year ago

QMRTools - Updated Segmentation tools

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling over 1 year ago

QMRTools - new build for 14.1

• updated elastix and dcm2niix
• small updates in trainsegmentationnetwork

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling over 1 year ago

QMRTools - Performance updates segmentation analysis

• new trained networks
• optimization of distance functions and loss layers
• training monitoring
• performance updates masking and segmentation analysis

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling over 1 year ago

QMRTools - Changing segment networks to U2Net

• code fixes to allow U2Net
• Optimization of mean surface distance calculation.

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling over 1 year ago

QMRTools - Large update muscle segmentation

• Added segmentations scripts
• new network versions
• new UNET functions
• new muscle bids functions

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling over 1 year ago

QMRTools - Small bug fixes

typos etc.

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling about 2 years ago

QMRTools - Rebuild for Release 14.0

Changes: - multiple small bugfixes - Introduction of world and voxel coordinates for tracto and surface plots

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling about 2 years ago

QMRTools - Cleanup and full documentation rebuild

Changes: - multiple small bugfixes - scientific color data to 8.0.1 - Clearup op Segmentation tools - Finisch documentation of Segmentation tools

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling about 2 years ago

QMRTools - Bugfixes and documentation update

Changes: - multiple small bugfixes - Dixon optimization - Documentation update

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling about 2 years ago

QMRTools - Dixon rebuild

Changes: - update to segmentation - rewrite off dixon reconstruction

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling over 2 years ago

QMRTools - Documentation update

Changes: - added new doc files - small bug fixes - code cleanup

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling over 2 years ago

QMRTools - Improvements of NN segmentation

Changes: - Updated trained neural nets - Optimization to many of the segmentation functions - Added many new functions for NN segmentation

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling over 2 years ago

QMRTools - Neural net segmentation

Changes: - Added Framework for UNET based muscle segmentation - Optimization to many of the segmentation functions - Performance optimization for many core functions

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling over 2 years ago

QMRTools - Tract based data evaluation

Changes: - Added Framework for tract based data analysis using GetTractValues and GetTractMeans - Optimization of GetMaskData - Cleanup of PlottingTools - Update of SelectValidCoors

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling over 2 years ago

QMRTools - Code cleanup

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling over 2 years ago

QMRTools - rebuild for 13.3

performance and functionality of tractography

rebuild of documentation.

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling over 2 years ago

QMRTools - tractography updates

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling over 2 years ago

QMRTools - finalize bids process for DTI, Dixon and T2mapping

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling almost 3 years ago

QMRTools - demonstration update

small bug fixes and alignment of demonstration notebook with code updates

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling almost 3 years ago

QMRTools - final muscle bids v1

completed muscle bids functionality for motion study

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling almost 3 years ago

QMRTools - Muscle Bids and Dixon

major changes to dixon and optimization of muscle bids.

needs documentation update!

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling almost 3 years ago

QMRTools - Introduction of Muscle-Bids

Update to include Muscle-Bids support, Extended logging for scripting and imporved tractography methods.

Full rebuild of 750 documentation pages.

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling about 3 years ago

QMRTools - FasculationTools

Added functions for Fasculation analysis of muscle DTI data

Update of documentation.

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling about 3 years ago

QMRTools - dixon and registration fixes

bugfixes and cleanup of registration functions. masking optimization restructure of internal toolboox demo data and files denoise updates dixon updates

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling over 3 years ago

QMRTools - Dixon upgrade

Dixon reconstruction update and performance improvements

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling over 3 years ago

QMRTools - tractography and cleanup

Full Changelog: https://github.com/mfroeling/QMRITools/compare/2.8.1...2.9.3

Finally full tractography functionality is in the toolbox

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling over 3 years ago

QMRTools - update paclet

update dixon recon and added NN denoising

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling almost 4 years ago

QMRTools - paclet loading

update to new packet format Mathematica 13+

still issues with documentation for release 13.0

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling about 4 years ago

QMRTools - tagging and recon

update to reconfiles and tagging tools

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling about 4 years ago

QMRTools - perfromance update

some small performance upgrades.

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling about 4 years ago

QMRTools - dixon bipolar

added fitting of bipolar dixon data and some small bug fixes

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling over 4 years ago

QMRTools - update functions documentation

Full Changelog: https://github.com/mfroeling/QMRITools/compare/2.5.0...2.6.0

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling over 4 years ago

QMRTools - 12.3 PlotData optimization

performance increase of PlotData fiber tractography bugfix in Unwarp resulting in water fat swaps in dixon reconstruction.

rebuild of the documentation (online and building).

optimized initialization of the toolbox.

fixed .paclet installation file errors.

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling over 4 years ago

QMRTools - tractography

add fiber tractography tools

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling over 4 years ago

QMRTools - Update of spar/sdat export

bug fix in NNLLS changes in jcoupling and spectra tools.

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling over 5 years ago

QMRTools - Bugfix in spectra tools

fixed some issues with the CSI plotting in CSI interface

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling over 5 years ago

QMRTools - Performance updates

updates to denoise and spectra tools. updated help index

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling over 5 years ago

QMRTools - added CSI interface

Added a GUI for CSI processing and plotting.

minor performance updates.

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling almost 6 years ago

QMRTools - Added reconstruction and spectro toolboxes

SpectroTools - Fitting spectra using a set of basis functions. - Phase correction and line-width optimization. - Basic plotting and visualization. - Automatic 0th and 1st order phase correction using Henkel matrix SVD. - baseline correction - CSI data visualization.

Reconstruction Tools - Basic algorithms for complex coil combination for spectra data including RSS, Roemer, WSVD. - Simple Image reconstruction (MS-2D and 3D reconstruction) - CSI data reconstruction - reading Philips *.list and *.data files. - Hamming filtering.

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling almost 6 years ago

QMRTools - Perfomance updates and bug fixes

• performance update tensor Calc
• update Jcoupling sim, added variable te for TSE sym
• added NormalizeOverlap for JoinSets
• changes to dixon fitting
• improvements in T2EPG to include water component (WIP)

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling over 6 years ago

QMRTools - cross platform compatibility and new documentation

Update to Wolfram mathematica version 12.0.

A full rewrite of file handling and external dependencies to allow better cross platform compatibility (Mac, Unix, and Windows).

Included more and new testing and demo data and examples.

Updated the package loader to allow monitoring of package loading and prevent pollution of the Global environment.

Updated the EPG fitting framework.

Added online documentation and website https://mfroeling.github.io/QMRITools/.

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling almost 7 years ago

QMRTools - Release of version 2.0 of QMRITools

A full refactor of the DTITools toolbox.

Now includes test and demo data.

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling about 7 years ago

QMRTools - many changes and new features

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling over 7 years ago

QMRTools -

Added functionality for nii import and export. New simulation tools. Added dixon and T2 fitting

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling over 8 years ago

QMRTools - DTITools

Scientific Software - Peer-reviewed - Mathematica
Published by mfroeling over 9 years ago