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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