Hi Damien,

depending on what you want to do you are forced to use the stable release. The developmental version of FreeSurfer should be used for testing only, not publishing results.

Following the notes of the HiResRecon (https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon) you should be able to process your data with version 5.1 and above at native resolution. However, this affects the surfaces based processing only as the aseg.mgz is simply upsampled from previously downsampled data. There are also a few methods to make use of the native resolution which I haven't tested in recent past, e.g. using the surface of the downsampled data on the native data. Otherwise you will have to downsample you data to 1mm using v5.3.

Version 6 will be able to handle high resolution data at native resolution using the -hires flag, making the workaround of the HiResRecon obsolete. Having tested the developmental version (from mid September) on several high resolution 7T datasets it seems to work nicely and is less laborious than before. I haven't compared results between v5.3 and v6 though.

Best, Falk

-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Damien MARIE Gesendet: Donnerstag, 6. Oktober 2016 14:01 An: freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] Processing 7T data

Dear experts,

I plan to process some MRI 7T data, 0.6 mm^3 isotropic voxel size. The aim is to look a R1 maps.

I was wondering what was your opinion concerning the downsampling to 1 mm^3 (performed by the current FreeSurfer version if I am correct). What do you think would be the best: FreeSurfer 5.3 , FreeSurfer 5.3-HCP or FreeSurfer beta 6.0?

Thank You and Best,

Damien

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Hi Damien,

please be sure to check with our wiki page on there recommended way to run submillimeter recons with v6. https://surfer.nmr.mgh.harvard.edu/fswiki/SubmillimeterRecon https://surfer.nmr.mgh.harvard.edu/fswiki/SubmillimeterRecon It is still work in progress, and the described procedure may slightly change, so it’s worth checking with this page every now and then.

Good luck! Natalia

On 06 Oct 2016, at 14:01, Damien MARIE <damien.marie@unige.ch mailto:damien.marie@unige.ch> wrote:

Dear experts,

I plan to process some MRI 7T data, 0.6 mm^3 isotropic voxel size. The aim is to look a R1 maps.

I was wondering what was your opinion concerning the downsampling to 1 mm^3 (performed by the current FreeSurfer version if I am correct). What do you think would be the best: FreeSurfer 5.3 , FreeSurfer 5.3-HCP or FreeSurfer beta 6.0?

Thank You and Best,

Damien

---

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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.