Jing, why are you running these commands by hand instead of just running recon-all? These are very complicated steps and don't lend themselves to running by hand.

doug

Huo, Jing wrote:

Hi,

I have a problem with using mri_normalize for intensity normalization for T1w+contrast 3D volumes.

What I ran: mri_convert t1.hdr t1.mgz mri_normalize -g 1 t1.mgz t1_norm.mgz mri_convert t1_norm.mgz t1_norm.hdr

(1) The first problem is that all volumes are 256*256*256 as output. Why are there dummy slices? Is there an automatic way to get rid of the dummy slices?

(2) For 1/3 of the 50 cases, I observed a spatial shift for some voxels. I was wondering whether this comes from the spatial registration, but it is wierd coz the rest 2/3 of the cases are pretty OK visually. Anyone has similar experience before? That would be very helpful. Thanks.

(3) For 4 cases, the brain white matter was normalized to 59 instead of 110. I dunno why...

Thanks! I will really appreciate if anyone could help here!

Best, Jing

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