[Freesurfer] Issue related to converting .nii.gz file to .mgz using FreeSurfer's mri_convert

External Email - Use Caution Hello FreeSurfer Developers, I am using FastSurfer for this processing, but the issue is related to FreeSurfer's mri_convert function. I wanted to perform some manual segmentation edits on the "aparc.DKTatlas+aseg.deep.mgz" output file of FastSurfer.

[Freesurfer] error using mri_em_register

External Email - Use Caution It does not create the nu.mgz file. Error logs are attached. The result is that when running recon all it cannot find the LH and RH files and then collapses. Darwin Kernel Version 21.3.0 iMac-Pro 21.3.0 Root: xnu-8019.80.24~20/RELEASE_X86_64 x86_64

Re: [Freesurfer] error using mri_em_register

There is an error in your first 'recon-all -autorecon1 -noskullstrip' attempt: " \n ERROR! FOV=302.000 > 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. \n " You can't

Re: [Freesurfer] Issue related to converting .nii.gz file to .mgz using FreeSurfer's mri_convert

I'm trying to understand the issues related to mri_convert. It looks like you did the following: 1. mri_convert aparc.DKTatlas+aseg.deep.mgz aparc.DKTatlas+aseg.deep.nii.gz 2. saved the manually edited as aparc.DKTatlas+aseg.deep.edited.nii.gz 3. mri_convert aparc.DKTatlas+aseg.deep.edited.nii.gz