Hi Yun,

if it is for some reason impractical to use a beta version of FreeSurfer you can also try to follow the HiResRecon (http://freesurfer.net/fswiki/HiResRecon) I put together some time ago. This solves the issues related to high resolution data and will circumvent conformation to 1 mm^3.

However, if the subcortical segmentation is of interest or if you want to have a look at a future-proof processing pipeline you should aim for the beta version of FreeSurfer. Several improvements have been made to v6.0 so it's definitely worth checking out, especially for high resolution data.

Best, Falk

-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Samstag, 10. Oktober 2015 19:23 An: Freesurfer support list Cc: Kyoko Fujimoto Betreff: Re: [Freesurfer] high resolution data using recon-all

Hi Yun

you should probably get a beta version of 6.0 - it has much improved highres support. 7T can be hard though. Kyoko Fujimoto (ccd) put together a pipeline for 7T that worked pretty well. You might check in with her Bruce

On Sat, 10 Oct 2015, Yun Wang wrote:

Hi All,

I have 7T high resolution data 0.625mm. Is it appropriate to process the data using recon-all ? If not, any idea?

Thanks!

Yun Wang _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Hi Kevin,

yes, FS 6.0 will make my workaround redundant. Changes have been done to mri_normalize, mri_em_register and mri_watershed enabling high resolution processing without constraints. However, as 7T data is always a bit tricky to process it does not run as smoothly as the standard recon-all. At least as far as I can tell.

Best, Falk

P.S. Glad to hear the workaround is doing well! :)

Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Kevin Aquino Gesendet: Montag, 12. Oktober 2015 11:40 An: Freesurfer support list Cc: cloud87fan@gmail.com Betreff: Re: [Freesurfer] high resolution data using recon-all

Hi Falk,

Just to jump on this as well – does FS 6.0 make HiResRecon redundant?

– I've been using HiResRecon [working like a charm :) ] and wondering if FS 6.0 will cut the need for that workaround.

Cheers,

Dr Kevin Aquino Research fellow, Sir Peter Mansfield Magnetic Resonance Center, The University of Nottingham.

Honorary Research Fellow School of Physics, Faculty of Science, University of Sydney

E Kevin.aquino@nottingham.ac.ukmailto:Kevin.aquino@nottingham.ac.uk, aquino@physics.usyd.edu.aumailto:aquino@physics.usyd.edu.au | W www.physics.usyd.edu.au/~aquino/http://www.physics.usyd.edu.au/~aquino/

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On Mon, Oct 12, 2015 at 9:24 AM, Falk Lüsebrink <falk.luesebrink@ovgu.demailto:falk.luesebrink@ovgu.de> wrote: Hi Yun,

if it is for some reason impractical to use a beta version of FreeSurfer you can also try to follow the HiResRecon (http://freesurfer.net/fswiki/HiResRecon) I put together some time ago. This solves the issues related to high resolution data and will circumvent conformation to 1 mm^3.

However, if the subcortical segmentation is of interest or if you want to have a look at a future-proof processing pipeline you should aim for the beta version of FreeSurfer. Several improvements have been made to v6.0 so it's definitely worth checking out, especially for high resolution data.

Best, Falk

-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Samstag, 10. Oktober 2015 19:23 An: Freesurfer support list Cc: Kyoko Fujimoto Betreff: Re: [Freesurfer] high resolution data using recon-all

Hi Yun

you should probably get a beta version of 6.0 - it has much improved highres support. 7T can be hard though. Kyoko Fujimoto (ccd) put together a pipeline for 7T that worked pretty well. You might check in with her Bruce

On Sat, 10 Oct 2015, Yun Wang wrote:

Hi All,

I have 7T high resolution data 0.625mm. Is it appropriate to process the data using recon-all ? If not, any idea?

Thanks!

Yun Wang _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer