Table 2 List of preprocessing steps applied to the DW images, together with web links to relevant software and, if available, brainlife.io Apps.

Preprocessing step	Software/Tool	Software website/App
1. DICOM conversion	dcm2niix	http://people.cas.sc.edu/rorden/mricron/dcm2nii.html
2. Denoising	MRtrix 3.0/dwidenoise	https://www.mrtrix.org
2. Denoising	MRtrix 3.0/dwidenoise	https://doi.org/10.25663/bl.app.68125
3. Removal of Gibbs ringing	MRtrix 3.0/mrdegibbs	https://www.mrtrix.org
3. Removal of Gibbs ringing	MRtrix 3.0/mrdegibbs	https://doi.org/10.25663/bl.app.68¹²⁵
4. Geometrical distortions corrections	FSL/topup	https://fsl.fmrib.ox.ac.uk/fsl/fslwiki
4. Geometrical distortions corrections	FSL/topup	https://doi.org/10.25663/bl.app.68¹²⁵
5. Eddy currents distortions corrections	FSL / eddy	https://fsl.fmrib.ox.ac.uk/fsl/fslwiki
5. Eddy currents distortions corrections	FSL / eddy	https://doi.org/10.25663/bl.app.68¹²⁵
6. Correction for head motion	FSL/eddy	https://fsl.fmrib.ox.ac.uk/fsl/fslwiki
6. Correction for head motion	FSL/eddy	https://doi.org/10.25663/bl.app.68¹²⁵
7. Correction for bias field	MRtrix 3.0/dwibiascorrect	https://www.mrtrix.org
7. Correction for bias field	MRtrix 3.0/dwibiascorrect	https://doi.org/10.25663/bl.app.68¹²⁵
8. Correction for gradient nonlinearities	gradunwarp/gradunwarp	https://github.com/Washington-University/gradunwarp
9. Coregistration to T1w image & Rotation of b-vectors	FSL/epi_reg & flirt MRtrix/mrresize HCP Pipelines/rotate_bvecs	https://fsl.fmrib.ox.ac.uk/fsl/fslwiki
		https://www.mrtrix.org
		https://github.com/Washington-University/HCPpipelines/blob/master/global/scripts/Rotate_bvecs.sh

Web services used to process that are available for reuse on https://brainlife.io/apps.

Quick links

Search