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I finally was able to run recon-all-clinical.sh without errors!
There is a file in the development fork on Github called *colortable_BA_thresh.txt* in the *average* directory that is not present in the 7.4.1 release. When I downloaded this and put it into the 7.4.1 release, the replacement recon-all-clinical.sh ran without any errors.
I also solved the mystery of the missing lateral ventricles. The file mri/brainmsk.mgz in the clinical version is a synthetic file that doesn't contain any ventricles. The equivalent to brainmsk.mgz in the clinical version is synthSR.mgz. This has the missing ventricles and indeed all the other brain components like the cerebellum etc.
Alas, despite running error free, there is still no stats/aseg.stats file. I hope that this is on the TODO list for the developers. In the meantime I will write a matlab function to extract the aseg stats from mri/aseg.mgz, which seems to have all the necessary data. If anyone wants a copy of this please email me.
Michael McLaughlin,