Hi Dorsa

without the norm.mgz I have no way to evaluate the accuracy of the aseg.

cheers
Bruce
On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote:

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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