Just to clarify, I ran autorecon1 and autorecon2 on this subject. When examining the surfaces in tkmedit, the left temporal pole is not included in the pial surface. Is there a way to force freesurfer to recognise this as valid brain tissue, bearing in mind that there is no visible white matter underneath (and therefore the option of adding control points is not possible).

Olivier

On 13/05/2009, at 12:57, Olivier Piguet wrote:

Hi there,
I've run autorecon2 on a subject who has significant unilateral atrophy in the anterior temporal region. In the last few slices anteriorly, the pial surface does not include what is clearly atrophied cortical tissue without underlying white matter. What is the method to correct for this? Looking at previous queries, all of them refer to spots where one can manipulate the segmentation by adding control points in the neighbouring white matter, which is not present in this instance.
Any suggestion appreciated.
Olivier

~~~~~~~~~~~~~~~~~~~~~
Olivier Piguet Ph.D.
NHMRC Fellow (Clinical Career Development Award)
Conjoint Senior Lecturer UNSW
Prince of Wales Medical Research Institute
Barker St
Randwick NSW 2031
Australia

Voice: +61 2 9399 1113
Fax: +61 2 9399 1047
E-mail: o.piguet@powmri.edu.au

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