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&d o=get&target=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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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