We also provide some tools that may be useful while processing anatomical and diffusion scans with BrainSuite. Note that, while we try to make sure that they work as described, these files come from research code and are provided without technical support, so use at your own risk.
- Data Processing (Matlab): A collection of Matlab functions for processing data generated by BrainSuite and SVReg.
- BFC Correction Tool: This tool allows for manual bias-field correction. It is meant to be used in conjunction with BrainSuite’s bias-field correction, if additional correction is required, and uses the tissue classfication file generated by BrainSuite.
- BDP Addons: Tools for processing data generated using BrainSuite and BDP. It also includes a general purpose affine registration tool.
- IPEDcorrect: Distortion correction of diffusion weighted MRI images using interlaced q-space sampling.
- Prepare Fieldmap:
prepare_fieldmapis a command line tool for converting scanner saved fieldmap to units of radians/sec. As of now it only works with fieldmap saved with Siemens sequence ‘gre_field_mapping’.
- ReadDFS.m: This scripts allows you to load DFS files (surface files) into MATLAB for further processing (as described here).
- Add s-form matrix to NIfTI-1 files: This tool adds the s-form matrix to NIfTI headers, if absent. Try this if BDP is giving you an error regarding the lack of an s-form matrix.
- Joint Denoising of Diffusion MRI Magnitude Images: This tool implements a penalized maximum likelihood estimation method for reducing noise in diffusion MRI magnitude images.
- Eigen file (.eig) to NiFTI converter: Matlab script to convert .eig.nii.gz files saved by BDP to six NiFTI files (one 3D file for each eigenvalue and one 4D file for each eigenvector)
- Cortical Delineation Protocol: Description of cortical delineation protocol used for cortical registration.
- TractConnect: Diffusion fiber tract analysis tool for BrainSuite.
These are the files used in the tutorials. They can also be useful in ensuring that the software is set up correctly if you have any issues.
- BrainSuiteTutorialCSE_Sept16.zip: structural scan
- BrainSuiteTutorialSVReg_Sept16.zip: results of running BrainSuite’s Cortical Surface Extraction Sequence on structural scan
- DWI_Feb15.zip: diffusion scan and parameter files
- BrainSuiteTutorialDWI_Sept16.zip: all files (structural scan, BrainSuite output, SVReg output, and diffusion scan and parameter files)