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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zeng, Qi
<qi.z...@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,
Qi
Best,
Qi
On Fri, Apr 22, 2022 at 3:25 PM Zeng, Qi
<qi.z...@icahn.mssm.edu<mailto:qi.z...@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
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