[FieldTrip] MNI coordinates of the individual 15684p mesh

Schoffelen, J.M. (Jan Mathijs) jan.schoffelen at donders.ru.nl
Thu Dec 19 10:17:15 CET 2019

Dear Paolo,

Just as a quick correction: spherical topologies can never be in MNI coordinates, since a sphere is a deformed surface. I don’t know for sure why the spheres have ‘MNI” in their names, this has probably been decided by the wisdom of the people who implemented the original pipeline procedure and code, which I adjusted to create the postfreesurferscript.

I don’t know what the exact motivation would be for you to get the MNI coordinates, but if you want to do this in a rigorous and correct way, you probably want to check out the original post freesurfer processing script that is used in the structural processing pipeline of the HCP. I used a(n older) version of the code that can be found here: https://github.com/Washington-University/HCPpipelines/blob/master/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh

Alternatively, if you are looking for an approximation, you could estimate the normalisation parameters from a call to ft_volumenormalise, with the subject’s anatomical MRI in the input (ensuring it to be in the same coordinate space as your meshes, and both probably in ‘mm’ (ft_convert_units) ), and use ft_warp_apply on the mesh.pos to get the ‘MNI coordinates’.

Best wishes,

On 18 Dec 2019, at 17:42, Paolo Belardinelli <paolo.belardinelli at gmail.com<mailto:paolo.belardinelli at gmail.com>> wrote:

Dear FieldTrippers,

I am using Jan Mathijs's procedure for the mesh sourcemodel and I would like to get MNI coordinates of each single subject. As far as I understand, only the sphere files contained in the folder workbench/fsaverage are in MNI coordinates. However, these are generated only for the 164K p meshes by the ft_postfreesurfer script of Jan Mathijs. Should one modify this to get the Sphere files in MNI coordinates for the 8K files of the two hemispheres involved in the 16K procedure?

Thanks and best wishes,


Paolo Belardinelli, PhD
Neurology Department
University Hospital Tuebingen
Eberhard Karls University Tuebingen
Hoppe-Seyler Str. 3
D-72076 Tuebingen
Tel: +49 7071 / 29 80478

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