Thanks Matthew!
To compare several groups results, I assume that I need to normalize the numbers of voxels of subcortex in different groups.
Any simple tool in FSL that counts activated voxels in subcortex only?
Best regards,
Ray
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Matthew Webster
Sent: Thursday, February 28, 2013 8:52 AM
To: [log in to unmask]
Subject: Re: [FSL] Subcortical voxel count in atlasquery
Hello Ray,
The probabilities should be averaged over the masked portion of the subcortical atlas.
Kind Regards
Matthew
> Hello FSLers
>
> When using atlasquery with mask, and "Harvard-Oxford Subcortical Atlas", are the probabilities averaged over the subcortical mask, or the mask for entire brain (both cortex and sub cortex)?
>
> Thanks,
>
> Ray
>
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