That seems to have worked!

Thanks a bunch! Best, Omar

On 08/29/2013 02:54 PM, Omar Singleton wrote:

...

Dear List,

I have a couple questions I need help with.

First, I am trying to constrain my subcortical (mni305) analysis with mri_glmfit to a certain ROI. Can I run mri_glmfit with the --mask flag and use a volume mask to constrain it to this space?

Yes.

...

Second, if so, then how do I create a mask from the subcortical activation map I have from my fsfast analysis. Is there a way like in tksurfer to add all voxels up to a certain threshold to a mask?

You can use mri_binarize. You can pick the threshold and sign you want to use for the mask doug

...

Thanks!

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