eek, that's terrible! SO it's a standard FLASH scan? The TE is a bit long, but not terribly so. If you upload one of the subjects that did poorly I'll take a look. We try hard to be agnositc to many things, but if you know the sequence is fixed you can specifiy some of the contrast parameters once for the whole study and improve this a ton. I'm not sure I've ever seen one quite this bad though. What are the voxel dimensions?
cheers Bruce
On Fri, 25 Mar 2016, Dr. Benson wrote:
Good. Thanks.
On Fri, Mar 25, 2016 at 9:59 PM, Ramtilak Gattu ramtilak.gattu@wayne.edu wrote:
Hello all, We have run recon -all on some healthy control subjects T1 images but we found out that the gray-white segmentation on half our subjects is bad and it leads to increased white matter volumes and decreased gray matter volumes. I have included a snap shot showing the difference in segmentation from bad to good for 3 caseshttps://waynestateprod-my.sharepoint.com/personal/ao3080_wayne_edu/_layouts /15/guestaccess.aspx?guestaccesstoken=ajPIRobFq548RyhRJWPQ9q70vAXUGIJ9h5WPD E1klUw%3d&docid=0dd4546a8004f46578b7a2177b192806a
. The parameter in the sequence are TE=4.92 ms, TR=19 ms, Flip angle =20 degrees. and use a snapshot one slice to show the good CNR. We are using Freesurfer version 5.3. Thanks Regards Tilak.
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