Hi Angel,
I'm just about done running the dataset and the results actually look ok (see attached tif). I didn't intervene at all, although you would want to to get rid of some non-brain tissue that the pial surface is grabbing, but that's pretty easy. Did you minimize your TE? I don't know what your gradient set is, but usually you can get your TE down a bit more than that. You also might be better off sacrificing a bit of resolution and lengthening your TR cheers, Bruce
On Thu, 8 Oct 2009, Angel Wong wrote:
Thanks a lot with your help. This is because we want to perform quite a number of functional runs on the same subject at the same session. So we tried to shorten the T1 scan time to minimize the motion artifacts come from the subject.
Attached please find the orig.mgz for your information.
2009/10/8 Bruce Fischl fischl@nmr.mgh.harvard.edu
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 fischl@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