Hi Pedro,

On Oct 7, 2011, at 9:02 , Pedro Paulo de Magalhães Oliveira Junior wrote:

I have data from 100 monkeys and I need to compare cortical thickness among two groups.

In the wiki page there is an entry MonkeyData that has a set of scripts which break-down the steps needed, unfortunately I'm having trouble with this scripts and FS 5.1

I was somewhat involved with these scripts in the past, I only used them with 4.5 so far, therefore I do not know what issues you encounter, care to elaborate what causes the trouble? (BTW the old monkey pipeline will fake the resolution information in the volume headers so Freesurfer sees 1mm isotropic and does not go and resamples the data to 1mm, at least for macaques and smaller monkeys that would throw away too much information in my opinion (don't know for apes...)). So if you use these scripts for morphometry keep in mind that all length measurements are off by 1/real_isotropic_voxel_size, area and volume are therefore off as well; but then this can be easily corrected for I think... Now, I hope some other monkey people can chime in and share their improved freesurfer pipeline :)

Best Sebastian

Are there an updated version of those procedures?

Thanks

PPJ

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