MNI-coordinate Replication Issue

Questions about Anatomist manipulation

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Nick Buser
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Joined: Wed Nov 11, 2015 12:58 am

MNI-coordinate Replication Issue

Post by Nick Buser »


I've been using Brain Anatomist to replicate a DTI study done in 2008 (A diffusion tensor imaging tractography atlas for virtual in vivo dissections by Catani & Thiebaut de Schotten). We registered brains to MNI-space using FSL's FLIRT software then opened the brains in Brain Anatomist, loaded from header and changed the reference to Talraich-MNI Template-SPM. The coordinates seemed to be correct (e.g. origin was at the anterior commissure).

Where I ran into trouble was using the MNI-coordinates described in the paper to define regions. The coordinates seemed to be misaligned by as much as 7 mm. I wanted to ask if there have been any changes to the software or the registration process since the paper was published that might explain some of this discrepancy. The authors used Brainvisa 3.02 for registration and SPM5 for normalization.

I would greatly appreciate any suggestions. We've hit a bit of a dead end now and aren't sure where to go from there so any thoughts or ideas would help tremendously.


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Re: MNI-coordinate Replication Issue

Post by riviere »

I don't remember of fundamental changes in referentials and coordinates transformations in Anatomist. But 3.02 is a very old version.
If registration has been performed by FSL and/or SPM, Anatomist and Brainvisa should not interfere with coordinates in MNI space (as long as the transforms to the MNI space are correctly interpreted).
You could try loading them in the SPM viewer, for instance, to see if images match in MNI space also.
Otherwise I don't have clear ideas of what is going on...
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