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.

Anastasia. ________________________________ 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

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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, Qi

Best, Qi

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

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Ph.D. candidate Icahn School of Medicine at Mount Sinai