Re: [Freesurfer] improving white/grey segmentation in recon -all for better volume estmation

Hey Bruce,

The scans are done on 3T Siemens TRIO and 8 Channel head coil with a GRAPPA of 2.

Here is the screen shot of protocol used.

https://waynestateprod-my.sharepoint.com/personal/ao3080_wayne_edu/_layouts/...

Thanks

Regards Tilak

________________________________ From: Ramtilak Gattu Sent: Saturday, March 26, 2016 6:59 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: improving white/grey segmentation in recon -all for better volume estmation

Hey Bruce,

Thanks for the quick reply.

I have uploaded the cases in

https://waynestateprod-my.sharepoint.com/personal/ao3080_wayne_edu/_layouts/...

The voxel dimensions are 1x1x1 mm.

Thanks

Regards

Tilak

________________________________ From: Ramtilak Gattu Sent: Friday, March 25, 2016 9:59 PM To: freesurfer@nmr.mgh.harvard.edu Cc: tilakgattu@hotmail.com Subject: improving white/grey segmentation in recon -all for better volume estmation

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 cases

https://waynestateprod-my.sharepoint.com/personal/ao3080_wayne_edu/_layouts/...

. 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.