Hi Qi - nodif_brain_mask is just a symbolic link to the brain mask that's used by bedpostx. By default, that's the mask created from the anatomical segmentation and mapped to DWI space (aparc+aseg_mask) and not the one created from the DWIs with bet (lowb_brain_mask). You could change that behavior by setting the usemaskanat variable to 0.

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zeng, Qi <qi.zeng@icahn.mssm.edu>
Sent: Wednesday, April 27, 2022 1:25 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] meanings of trac-all outputs

External Email - Use Caution

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