eek, that looks pretty bad. Can you tell us what the acquisition parameters are? On Thu, 8 Oct 2009, Angel Wong wrote:
> 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 > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
