hi Oleg-

make sure you're using the MNI talairach coordinates. to view them in tkmedit go to View->Information->MNI Coordinates

if you can't view MNI Coords: -------------------------------- you will need a talairach transform to view these coordinates. it can be generated(if it's not already) with the command: recon-all -talairach -subjid <subject_name>

you will also need the xform line in your COR-.info file. if it's not there, you can add it. the format is: xform /path/to/talairach.xfm --------------------------------

if you can view MNI Coords: -------------------------------- specify the points you select in the wm volume on the command line: recon-all -stage2 -cc-xyz <MNI tal coords> -pons-xyz <MNI tal coords> -subjid <subject_name> --------------------------------

good luck, brian t. quinn

On Tue, 2 Nov 2004 aleontie@meded-mail.ucsd.edu wrote:

Hello,

I am new to the world of free surfer and just started processing my first set of data. I was able to perform volume processing without any error messages. However, during the second stage of surface processing, an error message showed up saying, Images(filled): /apps/freesurfer/freesurfer/subjects/oleg-practice/mri/filled/COR-001....   not found ...wmfill first

Inside my filled directory, there is only COR-.info file for this subject.

Additionally, the log file complains that 'mri_fill could not find the corpus callosum seed point not in structure! Searching neighborhood...'

I attempted to manually define a corpus callosum cutting plane and a pontine cutting plane but got the same error message.  What should I do at this point?

Thank you.

Oleg Leontiev