There should already be two volumes (aparc+aseg.mgz and
aparc.a2009s+aseg.mgz) which you can simply convert to nifti with
mri_convert file.mgz file.nii.gz


On 1/15/19 2:14 PM, Stephanie Hare wrote:
>
>         External Email - Use Caution
>
> Good afternoon,
>
> I'm new to Freesurfer; my background is resting-state fMRI using SPM.
> Years back, left and right cortical thickness measures were calculated
> for our sample of schizophrenia patients using the Desikan-Killiany
> atlas and were input to an SPSS spreadsheet. In an exploratory
> analysis of the data, I found that behavioral performance on a skills
> assessment was correlated with thickness of lh_rostralmiddlefrontal
> and lh_parstriangularis regions.
>
> I'd like to perform a follow-up resting-state fMRI analysis, using
> these two surface-based parcellations ( lh_rostralmiddlefrontal and
> lh_parstriangularis) as seed regions and use those behavioral
> performance scores as a regressor.  Is there a simple way to convert
> these two 2D-surface-based atlas measurements to masks in nifti format
> in 3D-volumetric space? I was doing a quick google search and came
> across the mri_label2vol command. Would this be helpful? Sorry for
> my naiveté. I appreciate your time.
>
> Best,
>
> Stephanie Hare
> Postdoctoral Fellow
> Neuroimaging Research Program
> Maryland Psychiatric Research Center
>
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