(sorry. I just clicked reply, and didn't send the screenshots to the list) You can see in the images (I'm using neurolens) the contraction of the left-right axis and the shift: the black space at the left and right sides is even originally but uneven in the converted data. In another slice (not included) you can see a little bit of the right ear appearing from the left side. There's also the problem with the rotation, the nose is originally pointing to the right but then it's pointing down, which is why the axial slices look coronal and vice-versa. Keeping that in mind, you can see that left and right hemispheres are swapped (look at the shape of the posterior horn of the ventricles, which is longer in the left hemisphere) thanks, roberto ---------- Forwarded message ---------- From: roberto toro <rtoro@snv.jussieu.fr> Date: Sep 27, 2007 4:23 PM Subject: Re: [Freesurfer] convert mnc->analyze->mgz To: Bruce Fischl <fischl@nmr.mgh.harvard.edu> On 9/27/07, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Roberto,
can you send us the command line and full screen output of the minc to
mgz step? It shouldn't change the aspect ratio.
thanks,
Bruce
hi Bruce, here's the command: roberto% mri_convert P.mnc P.mgz mri_convert P.mnc P.mgz reading from P.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to P.mgz... roberto% and I attach screenshots of the result (which is scaled and shifted). thank you, roberto
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