At one point mri_convert had an error that caused it to compress all nifti files regardless of whether they had .gz extesion or not. Try converting explicitly to .gz and loading into afni.

Also, what version of afni are you using? The one prior to March 06 had problems (but should work with the most recent mri_convert).

doug

Michele Perry wrote:

Hi,
I am running FreeSurfer version 3.01 and am trying to convert some .mgz
files to *.nii format.
When I run

mri_convert in_vol.mgz out_vol.nii

or

mri_convert -ot nii in_vol.mgz out_vol.nii

mri_convert runs without errors but the resulting .nii file cannot be
opened by AFNI.
Do you know how I can create an nii file that will open in AFNI?

~Michele

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