Hi Joshua,

The version of the hippocampal subfield segmentation routines currently in FreeSurfer will only work out of the box on the usual FreeSurfer-resampled 1mm isotropic data. If you are technically skilled, it should be possible to tweak things to make it work on other data (we don't assume specific contrast properties and/or acquisition sequences in the actual subfield segmentation algorithm). We have a Matlab version of the code as well that might be a lot easier to play with - please let me know if you're interested in that.

Koen

On Fri, Oct 14, 2011 at 1:46 PM, Joshua Lee jkilee@ucdavis.edu wrote:

Dear Experts,

I've been collecting hi-res hippocampal scans with a 32 ch coil on a 3T Siemens Trio to manually segment hippocampal subfields. However, I wonder whether the protocol is appropriate for use with the new Freesurfer subfield segmentation tool.

Specifically, our hi-res scan does not capture the entire brain, rather it acquires slices perpendicular to the long axis just for the length of the long axis axis. Can this scan be used for the new subfield auto-segmentation? Or does it require a whole-brain acquisition?

We do acquire a 1 mm isotropic whole brain MPRage, but...

Thanks for any info, Joshua

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