If you run mri_info on the output you should see that it is what we call a “surface-encoded volume”. That is, it is  a 1D volume that is essentially a list of the voxels that are in the surface and their values (1 in the mask and all 0 otherwise).  You could convert it to a true volume easily enough in matlab by loading whichever surface you want to use to put it in the volume (like white or pial), then for each value that is >0 in the mask set the voxel that the corresponding vertex (at the same index) in the surface occupies to 1. It is possible we have something to do this, or even to fill the ribbon, but I’m not sure. Do others know?

Cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of zhouleqing2022@bupt.edu.cn
Sent: Friday, February 17, 2023 10:14 PM
To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Some bugs in FreeSurfer 7.2.0

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Dear Sir,

I am using FreeSurfer to process my MRI data. I would like to locate the V1 area, as a nii file. But when I use mris_convert –label2mask, the output file is not the mask I expected. My command is as follow.

The nii file can not open in ITK_SNAP, because it is not a nifti file.

In freeview, It shows:

I wonder if it is a bug, or you can give me some advice. Thank you a lot!

                                                                        Sincerely

                                                                       Rosie Zhou