1. Doing it on fsaverage is fine. 2. You can run mris_inflate -w 1 -scale 1 lh.white lh.inflated

and it will generate a snapshot every step of the integration so you can pick which one you want.

cheers Bruce On Mon, 2 Jun 2014, Zixuan Yang wrote:

Dear Freesurfer experts,

I would like to overlay the significance map and gamma.mgh map from cortical thickness GLM on a semi-inflated surface according to one previous post in the mailing list (shown as below) by using the command (shown) under the directory of fsaverage.

https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-November/012445 .html

mris_inflate -n <steps> lh.white lh.partially_inflated

My questions are:

1)      Is it right to generate semi-inflated surface under fsaverage file? Or, I need to generate a semi-inflated surface for each subject (n>500) and make an average surface? How?

2)      I tried different ‘n’, the new generated surface while n=5, 10 or 55 didn’t look different at all! Is this normal? It did look very different from lh.white though.

3)      Why the generated surface can only be open using tksurfer toolbox, but not a similar command like below?

tksurfer fsaverage lh inflated -overlay ./directory_path/gamma.mgh

Many thanks for your attention and looking forward to your answers.

Best regards,

Zixuan

--

Zixuan YANG

Ph.D candidate Centre for Healthy Brain Ageing (CHeBA)

School of Psychiatry, UNSW Medicine

NPI, Euroa Centre, Barker Street, Randwick

NSW  2031  AUSTRALIA

T: +61 (2) 9385 0427

W: www.cheba.unsw.edu.au

E: z.yang@student.unsw.edu.au

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