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<span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);" class="">Dear Paolo,</span>
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<div class="" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);">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. </div>
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<div class="" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);">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: <a href="https://github.com/Washington-University/HCPpipelines/blob/master/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh" class="">https://github.com/Washington-University/HCPpipelines/blob/master/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh</a></div>
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<div class="" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);">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’.</div>
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<div class="" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);">Best wishes,</div>
<div class="" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);">Jan-Mathijs</div>
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<div class="">On 18 Dec 2019, at 17:42, Paolo Belardinelli <<a href="mailto:paolo.belardinelli@gmail.com" class="">paolo.belardinelli@gmail.com</a>> wrote:</div>
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<div class="gmail_default" style="font-size:large">Dear FieldTrippers,</div>
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<div class="gmail_default" style="font-size:large">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?</div>
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<div class="gmail_default" style="font-size:large">Thanks and best wishes,</div>
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<div class="gmail_default" style="font-size:large">Paolo</div>
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-- <br class="">
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<div class="">--<br class="">
Paolo Belardinelli, PhD<br class="">
Neurology Department<br class="">
University Hospital Tuebingen<br class="">
Eberhard Karls University Tuebingen<br class="">
Hoppe-Seyler Str. 3<br class="">
D-72076 Tuebingen<br class="">
Tel: <a value="+4970712985894" class="">+49 7071 / 29 80478</a><br class="">
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