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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