Yes That is a possible and I am going to talk to my group about it. I have attached the brain segmentation and the aseg.stats. I'll be happy to hear any comments about the thalamus size.
Thank you
Dorsa
On Tue, Jul 19, 2016 at 2:08 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Dorsa
why not give the original 1mm scans to freesurfer, then upsample the segmented images? And no, I wouldn't venture a guess without seeing the data
Bruce
On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote:
Hi Bruce,
The original 3TS images have 1mm^3 resolution, but we resample and co-register them to our CT scans and the resulting image has a higher resolution. My problem now is that the volume of the left thalamus segmented out by Freesurfer is half of the volume of the thalamus traced manually by one of my labmates. Do you have any guesses on why is this happening?
Thank you
Dorsa
On Tue, Jul 19, 2016 at 1:49 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote: Hi Dorsa
are they really that highres? Sometimes people do zero-padding and Fourier interpolation on the scanner. 1/2mm cubic is pushing the resolution and if they are really that high res they will be either very noisy or very long scans (or both) cheers Bruce On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote: Hi, I have a T1 weighted MRI which I want to segment using Freesurfer. The voxel sizes are 0.48*0.48*0.48. I read that the ideal voxel size for freesurfer is 1mm^3. Is there any manual adjustments that I can make to get good results with my 0.48 voxel size images? Thank you Dorsa Ghaffari
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