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