Re: [Freesurfer] Fwd: question about voxel size

Hi Dorsa I don't see any holes in the thalamus in your aseg, nor separated pieces. What voxel coords do you mean? Remember to look at the data in other orientations. Things that look like islands in one view may be peninsulas in anothers cheers Bruce On Wed, 20 Jul 2016, Dorsa Haji

Re: [Freesurfer] Fwd: question about voxel size

I mean the holes in the thalamus and also some parts that are labeled as thalamus but not attached to the rest of thalamus volume. On Wed, Jul 20, 2016 at 10:49 AM, Bruce Fischl wrote: > what missing parts do you mean? The segmentation seemed pretty reasonable, > but

Re: [Freesurfer] Fwd: question about voxel size

what missing parts do you mean? The segmentation seemed pretty reasonable, but the contrast wasn't good enough to say how accurate it was in some places On Wed, 20 Jul 2016, Dorsa Haji Ghaffari wrote: Yes it is taken at 3T. I have asked our team to provide these information about the MRIs

Re: [Freesurfer] Fwd: question about voxel size

Yes it is taken at 3T. I have asked our team to provide these information about the MRIs and will let you know when I hear back. I also wanted to ask if you know a good way to refine the thalamus and fill out the missing parts within the volume? Thank you Dorsa On Tue, Jul 19, 2016 at 5:10 PM,

Re: [Freesurfer] Fwd: question about voxel size

what is a "3TS" image? Do you mean it was acquired at 3T? What sequence and what parameters (TE/TR/TI/TD/flip angle)? cheers Bruce On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote: > Hi Bruce, > that is a 3TS T1 weighted image and is taken after the patients have taken > the contrast medium. I

Re: [Freesurfer] Fwd: question about voxel size

Hi Bruce, that is a 3TS T1 weighted image and is taken after the patients have taken the contrast medium. I have played with the intensities in Analyze and this is the best I could get. Do you have any suggestions for getting better contrast? Thank you Dorsa On Tue, Jul 19, 2016 at 4:29 PM,