The UFA toolbox is a MATLAB toolbox running on the Ubuntu system, which calls the Linux shell scripts and Python scripts to complete the whole analysis pipeline. It was developed by Gaoxing Zheng. We are very grateful to Prof. He Wang for his technical guidance in multi-modal MRI preprocessing and post-processing. We also thank Prof. Xin Wang and Prof. Jing Ding for providing a good hardware and software platform as well as clinical resources.
The UFA toolbox is designed for multimodal magnetic resonance imaging (MRI) analysis of brain white matter diseases. It enables the automatic extraction of WMHs and establishes an automatic tracking and quantification scheme for superficial U-fibers, helping clinicians combine the T2 FLAIR image and DWI information to understand the white matter lesions with different etiologies. It may help clinicians to identify early white matter damage that is not visible to the naked eye on T2 FLAIR images.
The following table lists the open-source tools that need to be installed in advance to successfully use the UFA toolbox (Table 1). We have detailed instructions on how to successfully install the required open-source tools and how to successfully use the UFA toolbox in the ‘UFA_toolbox_tutorial.pdf’ file.
Table 1 | A list of neuroimaging tools required for successful use of the UFA toolbox.
| Toolbox | Website | Platform | Usage |
|---|---|---|---|
| CNS | https://github.com/cheba-nil/CNS | Matlab | WMH extraction |
| SPM12 | https://www.fil.ion.ucl.ac.uk/spm/software/spm12/ | Matlab | Required by CNS toolbox |
| FSL | https://fsl.fmrib.ox.ac.uk/fsl/fslwiki | / | Registration module in FSL ‘flirt’ |
| ANTs | http://stnava.github.io/ANTs/ | / | N4 bias field correction in ANTs are needed |
| FastSurfer | https://github.com/Deep-MI/FastSurfer | Python | T1 cortical segmentation |
| WMA | https://github.com/SlicerDMRI/whitematteranalysis | Python | White matter fiber clustering |
| 3D Slicer | https://www.slicer.org/ | Linux version | Required by WMA tool |
| FreeSurfer | https://surfer.nmr.mgh.harvard.edu/ | / | T1 cortical segmentation |
| MRtrix3 | https://www.mrtrix.org/ | Linux version | dMRI tractography |
The recommended computer configurations are listed below (Table 2).
Table 2 | Software and hardware configurations are required for the accelerated calculation. Abbreviations: HDD -- Hard disk drive.
For detailed step-by-step tutorials, please see the "UFA_toolbox_tutorial.pdf" to correctly use our UFA toolbox! Please cite our paper (https://dx.doi.org/10.21037/qims-23-847) if these codes are helpful in your study!
If you have any questions, please send the email to zheng_gao_xing@163.com.
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