Dear Marko, dear Negar,
Well, fooling CAT should be easy. Adjust the threshold in cat_run_job.m line 77, e.g. >6. You might run into some more errors then still, thus possibly, you would have to alter the thresholds in line 91 as well. Another solution would be to keep scripts as they are and instead, resample the data with thinner slice thickness.
However, I agree with Marko that you should be very careful when working with "atpyical" data. Even if you are able to run the segmentation the quality of the output might be poor, and it might be more reliable to just go with the old normalisation (warping onto a template image without any segmentation) in your case (but this depends on your exact purpose of course).
Best
Helmut
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