Release note

0.8.0 (commmit master)

Release date:

GUI related

• New layout for input/output panel for data selection
• New pipeline configuration file (sepia_config.m), log file (run_sepia.log) and error message file (run_sepia.error)
• New feature to load parameters in a pipeline configuration file (sepia_config.m) to the GUI
• New option to save unwrapped echo phase
• New option to exlcude unreliable voxels
• New option to select reference tissue for QSM normalisation/referencing
• New option to remove residual B1 field in local field using spherical harmonic function with adjustable order of the fitting

Toolbox related

• Support the lastest version of MEDI toolbox (Jan 15, 2020)
• Support extra brain extraction (FSL’s BET) parameters from MEDI toolbox
• New ‘percentage’ option for MEDI+0 algorithm
• Support the lastest version of FANSI toolbox (commit dc68c306)
• New option to use weak harmonic regularisation with FANSI

Backend related (advanced user)

• Support developers adding a third-party method as an addon
• Introduce tutorial scripts to guide developers on how to adding third-party method in SEPIA
• Introduce functions to simplify the workflow of creating new method panel
• The order of removal of residual B1 field and mask erosion is interchanged to produce better a fitting result

Bug fix

• Bug fix: running SEPIA without parrallel computing toolbox
• Bug fix: running MEDI toolbox nonlinear fit echo phase combination with 2 echoes
• Bug fix: running MEDI method in SEPIA
• Bug fix: running single echo data with exclusion of unreliable voxels option enabled

Please update the MEDI toolbox (Jan 15, 2020) and FANSI toolbox (commit dc68c306) to the lastest version for the best performance.

0.7.3 (commmit 68c53bc)

Release date: 9 Nov 2019

• Support nonlinear dipole inversion (NDI) as external library
• Support SEGUE as external library

0.7.2 (commmit bf020ce)

Release date: 4 Jun 2019

• Support single-echo dataset
• Bug fix with odd-number matrix dimension by zero-padding
• Offload unuse variables to reduce memory usage
• Bug fix for reading NIfTI when the rescale slope and intercept are not 1 and 0

0.7.1 (commmit dc51fbe)

Release date: 9 May 2019

• Support simple susceptibility weighted imaging (SWI) and susceptibility map weighted imaging (SMWI) as part of the GUI
• resolved loading/saving NIfTI issue related to 0.7.0 update
• DICOM input is deprecated: the only possible input is NIfTI data
• fixed bug when running MEDI with CSF regularisation
• fixed bug for single echo SWI
• now support automatic magnitude and phase images detection with name containing string “mag” for magnitude image and “ph” for phase image
• fixed global phase offset with graph-cut phase unwrapping

0.7.0 (commmit e66d8e4)

Release date: 12 Apr 2019

• redesigned log file format; the algorithms and parameters being used are much clearer and neat than before (previous log file cannot work in this version)
• resolved ‘.nii.nii’ issue when using STI suite algorithms
• resolved no. of iterations with FANSI does not change issue
• resolved problematic QSM results with FANSI when an input matrix is an odd number
• resolved excluded unreliable voxels issue when 3D best path algorithm doesn’t work
• improved build-in VSHARP results when there are masked voxels on the image edges
• added image erosion function for background field removal algorithms
• get header function is now compatible with the JSON files generated by dcm2niix and dicm2nii

0.6.0 (commmit 1c27dc4)

Release date: 1 Sep 2018

• updated diretcory structure
• added options to select individual files