Update to v1.7

- Initial support for structural connectivity analysis

Changelog.md

@@ -0,0 +1,59 @@
+New in this version [1.7]:
+- Initial support for calculating structural connectivity (based on tools from EDTI)
+
+Update 11-12-2024:
+- Bug fixes 
+- Updated compatibility to the latest version of WhiteMatterAnalysis
+- Initial support for tractography with Scilpy tools
+
+Update 17-02-2023:
+- This is the last stable release before a major change in structure. From the next release, all main functionalities will be come available as standalone commands and be designed to fully rely on Niftis only.
+- Fixes to the handling of Nifti headers
+- Automated brain extraction using image registration
+- added new class MRT_Library that will collect all own methods currently in MRTTrack and MRTQuant (transition in progress). This will clean MRTTrack and MRTQuant which are meant as documented interfaces.
+- Dramatic speed up of GRL and mFOD (major revision of MRTTrack.PerformDeconv)
+- Changes to MRTQuant.LoadNifti and SaveNifti, which now allows to preserve the original header of NIFTIs (if required). In future releases, no modifications of the headers will be required.
+- Update of Neuro.m to support the latest version of Elastix
+- Compressed niftis are now (un)compressed in a temporary folder
+- Added functions to track multiple FODs simultaneously
+- Changes to the automatic handling of Q-S form of NIFTIs
+- New mFOD fiber tracking
+- New TerminateTractsWithFraction approach with 1 voxel tolerance
+- Moved Trackers to aanother location
+- Fixes to SHPrecomp
+- Fixes to MRIToolkitInit
+- Tractography can now use parallel computing
+- Handling of NIFTI scaling factors
+- Failsafe mode for registration
+- Support for FSL Eddy
+- Support for FOD normalization
+- One call command to run GRL
+- Fix for MSCSD (probably still needs amendment on the detection of data shells)
+- Fix fot CAT12 processing
+- command line fixes
+- standardized preproc includes conformation
+- fixes to conformation
+- support for offset in DKI for GRL
+- fixes to DKI export
+
+
+Update 09-2021:
+- [NEW] Checkout the [tutorial](https://github.com/delucaal/MRIToolkit/tree/master/GettingStarted/Diffusion/7_WMA) on how to install/use automated tractography clustering (WMA) algorithm with CSD/GRL/mFOD
+- Fixes to MSCSD-related functions
+- Fixes to WM automated clustering
+- Support for Q-form in MRTTrack.ConformSpatialDimensions() 
+- New FOD scaling mode for GRL/mFOD
+- Renaming of some command line functions
+- Added an option to customise the number of dRL iterations
+- New functions to estimate SNR from b=0s/mm2 images (MRTQuant)
+
+
+Update 17-02-2021:
+- Run the CAT12 automatic pipeline for T1 images
+- Code re-organization into two main classes: MRTQuant (preprocessing/DTI/DKI) and MRTrack (Tractography related)
+- Support for automatic fiber clustering (see below for reference)
+- Early support for integration with Python (needed for the point above)
+- Support for VTK poly data 4.2 and 5.1 (also needed for the clustering)
+- Added a robust option to GRL/mFOD deconvolution
+- Initial support for storing the NIFTI Q/S form (to improve interoperability with other tools, not implemented yet)
+- Integration with CAT12

Core/MRT_Library.m

@@ -2065,6 +2065,20 @@ function WriteElastixParameters(fout,pars)
             end
         end
 
+        % Make an atlas file EDTI compatible
+        function AdaptAtlasEDTIStyle(parc_file,labels,ids,output)
+            pf = MRTQuant.LoadNifti(parc_file);
+            pf_new = pf;
+            pf_new.img = zeros(size(pf_new.img));
+            labels_txt = fopen([output '_labels.txt'],'wt');
+            for ij=1:length(ids)
+                pf_new.img(pf.img == ids(ij)) = ij;
+                fprintf(labels_txt,'1 %s%s',strrep(labels{ij},' ','_'),newline);
+            end
+            fclose(labels_txt);
+            MRTQuant.WriteNifti(pf_new,[output '_atlas.nii']);
+        end
+
         % To be completed
         function fs_lut = FreeSurferLabelsInParcFile(parc_file)
             fs_lut = [];

Core/mk_init.m

@@ -10,8 +10,9 @@
 % 24/10/2020: creation - v1.1
 % 01/01/2021: update v1.2
 % 12/01/2024: update v1.3
+% 18/12/2024: update v1.4
 global MRIToolkit;
-MRIToolkit.core_version = 1.3;
+MRIToolkit.core_version = 1.4;
 
 addpath(get_executed_file_path())
 addpath(fullfile(get_executed_file_path(),'Trackers'))