[Freesurfer] recommendation for T1 and T2-based sequences use with FreeSurfer

Hi everybody,

I’m endeavoring to help a researcher come up with a protocol which might be “optimal” (in some sense) for use with FreeSurfer. I’ve not really used FreeSurfer much hence my lack of familiarity with what the recommended sequences are for use with FreeSurfer.

Having searched around, I’ve found [1]. Do the recommendations in [1] still apply?

I’d like the researcher to get good pial surface estimate so would like to be able to recommend that he perform a T2 scan as well. Having read through [2], it makes mention of T2 and FLAIR images for improving pial surface estimation. Is the FLASH image recommended in [1] appropriate for use with the -T2 or -FLAIR args to recon-all?

We’ll be running these scans on a 3T Siemens Prisma running V11c software. Are there particular scans that you recommend for this particular scanner or again does [1] apply?

[1] https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki?action=AttachFile&a... [2] https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#UsingT2orFLAIRdatatoimpr...

Thanks in advance for you time,

Regards, -- Colm G. Connolly, PhD Dept of Biomedical Sciences Florida State University Tallahassee, FL 32306 Tel: +1-850-644-2105 https://www.researchgate.net/profile/Colm_Connolly2