Dear Bruce,

Thank you for your response.

So would you please guide me how I should register the image into MNI152 coordination? And is the cvs_avg35_inMNI152, the MNI152 template?

Best Regards, Mahtab.

On 3 June 2016 at 13:48, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Mahtab

we do all the analysis in native space and don't transform the data to a template (although we do compute mappings to various templates).

As for your other question, there are too many variables to control for (age, gender, scanner type, sequence) for us to distribute a normative database. You will probably need to scan some controls.

cheers Bruce

On Fri, 3 Jun 2016, Mahtab Farahbakhsh wrote:

Dear Freesurfer,

...

The data that I'm using as a part of my study contains only the patients' T1 images and we have not collected any control subjects yet. I want to compare the cortical thickness of these subjects with a template (instead of a control subject), but I'm confused which volume I need to choose. When I run recon-all, does it transform the slices based on the fsaverage? Is fsaverage based on Talairach template or MNI or something else?

Would you please guide me with the question and inform me what template volume is the best for me to use instead of my control subjects?

Best Regards, Mahtab.

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