I think the HCP CCF protocol is a good start:
http://protocols.humanconnectome.org/
Peace,
Matt.
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Colm Connolly
<cconno...@fsu.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, February 6, 2018 at 10:41 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] recommendation for T1 and T2-based sequences use with
FreeSurfer
Hi everybody,
I¹m endeavoring to help a researcher come up with a protocol which might be
³optimal² (in some sense) for use with FreeSurfer. I¹ve not really used
FreeSurfer much hence my lack of familiarity with what the recommended
sequences are for use with FreeSurfer.
Having searched around, I¹ve found [1]. Do the recommendations in [1] still
apply?
I¹d 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?
We¹ll 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
o=get=FreeSurfer_Suggested_Morphometry_Protocols.pdf
[2]
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#UsingT2orFLAIRdatatoimpr
ovepialsurfaces
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
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