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Hi Freesurfer experts,

Follow up on the last question and correct me if I am wrong, the difference between dlabel/diff/lowb_brain_mask.nii.gz and dmri/nodif_brain_mask.nii.gz is that:

> the dlabel/diff/lowb_brain_mask.nii.gz is generated from "bet" (brain extraction)

> and dmri/nodif_brain_mask.nii is derived from aparc+aseg_mask.nii.gz which contains T1 information.

Because in fsl, nodif_brain_mask is named for "bet binary brain mask".

Best,

On Fri, Apr 22, 2022 at 3:25 PM Zeng, Qi <qi.zeng@icahn.mssm.edu> wrote:

Hi experts,

Just want to check if dmri/dwi.nii.gz is the 4D dwi volumes after correction for B0 inhomogeneities, eddy current, and head motion? and dmri/nodif_brain_mask.nii.gz is the 3D ROI mask for the whole brain? and dmri/bvals and dmri/bvecs are rotated bvals and rotated bvecs?
Thank you!

Best,
Qi

Ph.D. candidate

Icahn School of Medicine at Mount Sinai