Wayne,

I'm not sure how it came to be that the aseg.auto.mgz file contained the CC segmentation data, but the v4.0.1 recon-all script's handling of the aseg unfortunately allows for unusual scenarios in creating/handling aseg.mgz, aseg.auto.mgz and aseg.auto_CCseg.mgz (an intermediate file), which are not always handled properly by recon-all on subsequent runs.

Your best bet is to use the -noccseg flag with subjects that encounter this, but only use it if you see the message ".../mri/aseg.auto.mgz already has CC in it".

Nick

On Tue, 2008-03-18 at 10:00 -0700, Wayne Su wrote:

I have a couple of scans which were failed during mri_cc (corpus callosum segmentation). Log file is attached here.

#@# CC Seg Mon Mar 17 11:21:32 PDT 2008 \n mri_cc -aseg aseg.auto.mgz -o aseg.auto_CCseg.mgz ERP_3000_Month1L \n reading input aseg from aseg.auto.mgz writing aseg with cc labels to aseg.auto_CCseg.mgz mri_cc: volume /Applications/freesurfer/subjects/ERP_3000_Month1L/mri/aseg.auto.mgz already has CC in it reading aseg from /Applications/freesurfer/subjects/ERP_3000_Month1L/mri/aseg.auto.mgz Darwin centaurs.vchri.med.ubc.ca 8.11.1 Darwin Kernel Version 8.11.1: Wed Oct 10 18:23:28 PDT 2007; root:xnu-792.25.20~1/RELEASE_I386 i386 i386

recon-all exited with ERRORS at Mon Mar 17 11:21:35 PDT 2008

I am using version 4.0.1. Could anyone point out what's the problem? Thanks.

Wayne

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