did you check the talairach.xfm too see if it is reasonable? Is that what you were looking at in tkregister2? Check that and the skull stripping. You can also look at the volumes to see which one is the last one that is ok (orig.mgz, nu.mgz, T1.mgz, brain.mgz, norm.mgz, ...)

On Fri, 9 Sep 2011, Sita Kakunoori wrote:

Hi Christopher,

If you want to upload the dataset, I can take a look.

Sita.

On Fri, 9 Sep 2011, Christopher Luna wrote:

...

Hello,

After running an *.img file through autorecon1. Freesurfer says it finishes with errors, but I cannot find any error messages in the command line output. Checking the tkregister2 of the output shows that the "Target" is just a white box, while the "Moveable" stills eems like a typical image that I would find in any other output.

Are there some settings I need to alter for mri_convert? The IMG file looks fine before running autorecon1.

Thanks, Christopher Luna MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab, McGovern Institute for Brain Research MIT Archery Club Alpha Kappa Psi Colony at MIT

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