You don't need T2w to run FreeSurfer/recon-all. There is an option to add a T2, but it is not necessary. In any event, you will not be able to use an fMRI scan for this purpose.

On 8/30/16 7:50 AM, Dev vasu wrote:

Dear Sir,

In order to run my structural analysis pipeline , i require T2w images, but unfortunately we have not performed T2w scans , my colleague suggests we can use rfMRI instead T2w images Could you please let me know if i can use rfMRI image instead of T2w image?.

Thanks Vasudev

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