Freesurfer .mgz to nifti

1

Greetings,

I have a script that is part of my analysis and it expects aparc+aseg.nii.gz because it passes it to AFNI for resampling. The freesurfer output from fmriprep is in .mgz format(i.e. aparc+aseg.mgz). Is there a way to have fmriprep output this file as .nii.gz or does it need to be converted using a different software?

Thank you,
Yonatan

2

You can use mri_convert aparc+aseg.mgz aparc+aseg.nii.gz (mri_convert is a FreeSurfer command).

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3

Thank you very much Steven!

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4

you can also use AFNI’s “@SUMA_Make_Spec_FS” which runs mri_convert under the hood and does other things to prep FS voxel and surface outputs for AFNI analyses