Hi Nic,

in part it depends on where in the brain you are interested. The biggest need for manual intervention in reprocessing is to remove dura. This is mostly a problem near entorhinal cortex where the tentorium is tangent to the pial surface, and extremely difficult to distinguish from gray matter. Most of the brain is pretty accurate though, so if you have limited time you might run them all through automatically and do visual inspection/correction on regions where you find an effect to make sure that the effect is real and not an artifact of the processing.

cheers, Bruce

On Tue, 31 Oct 2006, Nicolas Cherbuin wrote:

Hi,

I have to process more than 500 good quality scans (1mm isotropic) for an epidemiological study and have limited time resources. Initial processing of 20 scans seems promising but I am new to freesurfer and therefore I am not quite sure how significant small defects might be in the big picture (where they will be averaged over a large number of subjects).

I would be interested to hear the experience of others in using autoreconall for processing most scans and only reprocessing a small portion of scans with obvious substantial defects (mostly on the inflated surface).

With good quality scans would most people reprocess most scans?

Thanks for sharing your experiences.

Nic

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