I see. Your TR is quite short and your TE relatively long, so this is probably pretty poor CNR between gray and white. If you send me the orig.mgz I'll take a look and see if it's fixable On Thu, 8 Oct 2009, Angel Wong wrote:
> Hi Bruce > > Attached please find the parameters for acquiring the T1 image. > > Thank you for your help. > > Angel > > 2009/10/8 Bruce Fischl <fis...@nmr.mgh.harvard.edu> > >> 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
