If it is in mni152 space, you can use $FREESURFER_HOME/average/mni152.register.dat doug

On 11/19/2012 12:12 PM, Eun Young Choi wrote:

Hi Doug,

It's in MNI space.

Thanks, Eun Young

On Mon, Nov 19, 2012 at 11:05 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

what space is the spmT volume in?

On 11/15/2012 04:58 PM, Eun Young Choi wrote:
> Hi all,
>
> I'd like to convert SPM2 spmT files to FreeSurfer space. I have a
> Colin template brain available to help with the conversion, as well.
> Has anyone done this before? Any suggestions on how to do this?
>
> Many thanks in advance,
> Eun Young
>
>
>
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On 11/19/2012 12:28 PM, angela.favaro@unipd.it wrote:

Dear list, I am quite new in the use of freesurfer and I have two doubts.

1. I am studying the visual areas of the brain, but I do not know how to

perform a vertex analysis within a ROI. I already know how to obtain thickness data on a ROI (either drawn by hand or labeled), but I would like to restrict the area of a vertex-analysis to my ROI (visual brain areas)

When you run mri_glmfit, you can pass it a label (--label) or mask (--mask) in which you specify only the areas you want to analyze. You will need to re-run the simulation for the correction for multiple comparisons since your search space has changed.

2. When performing a vertex-analysis, is it correct to include TIV (total

intracranial volume) as a nuisance variable?

It depends on what you are analyzing. I think for thickness, people are not doing a correction. For volume, they are. For surface, a correction is often done, but not with the raw TIV (maybe taking the 2/3 root to give it surface dimensions). doug

Thank you for any help

Angela

Angela Favaro, MD, PhD Psychiatric Clinic Department of Neurosciences via Giustiniani 3 35128 Padova Italy

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