Dear all

Actually I would like to perform automated reconstruction for my T1 image and then obtain anatomical labels after cortical parcellation. I have done fully automated reconstruction using recon-all. But for my case, the white and grey matter segmentation appears to be weird. The green line seems laying on the pial surface rather than on the white surface, and the red line seems including some non-brain structures (including small portion of CSF and skull). Thus, the resultant cortical thickness appears to be very thin after the segmentation. I just doubt if anything was going wrong during the procedure. Or need any preprocessing to enhance the segmentation quality before performing the reconstruction? If you have had similar situation as mine, please let me know how to tackle the problem.

Attached please find the images for better illustration.

fs_image_brain.tiff - use brain.mgz as aux volume
fs_image_norm.tiff - use norm.mgz as aux volume
fs_image_brainmask.tiff - use brainmask.mgz as aux volume and load segmentation file aseg.mgz
 
Thanks
Angel