[FieldTrip] Small Issues with the 15684 Mesh Creation Procedure

Schoffelen, J.M. (Jan Mathijs) jan.schoffelen at donders.ru.nl
Mon Oct 7 14:33:27 CEST 2019

Dear Paolo,

@1: I have not encountered the issue you describe. Probably it is the consequence of the fact that the anatomical images you use are different as compared to ours, e.g. in terms of voxel sizes, field-of-view, acquisition sequence. I am no expert in mri_convert, but this function has some options that might tweak its behavior such that it does justice to your anatomical images.

@2: If you run the post processing script (which relies on hcp-workbench) the meshes will be surface-registered to a template, which allows for direct vertex-wise comparison across subjects (as well as across hemispheres).


On 2 Oct 2019, at 11:35, Paolo Belardinelli <paolo.belardinelli at gmail.com<mailto:paolo.belardinelli at gmail.com>> wrote:

Dear all,
I would first like to thank Jan-Mathijs for the massive work on the mesh sourcemodel.
I encountered a couple of minor issues while implementing the whole process:

1. In some subjects, after saving the .mgz file with Fieldtrip (including acpc coordinates and reference point), the image is slightly shifted towards the superior side of the frame by mriconvert (mri_convert -c -oc 0 0 0 $SUBJECTNAME.mgz orig.mgz). This implies that the upper part of the brain is being chopped and the further segmentation process with recon -all makes no sense anymore. Has anyone the same issue?

2. As far as I understand, an average, atlas-mapped mesh where to visualize pooled results is not generated. What would be a straightforward way of visualizing group results in standard coordinates?

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

fieldtrip mailing list

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20191007/f4a2f10b/attachment.html>

More information about the fieldtrip mailing list