Importing FreeSurfer results: Atlases, "dimensions of the two volumes don’t match"

Discussions
4

This is not related to importing the data, but to the MRI data itself. As FreeSurfer results do not have the scalp surface, this one is computed by Brainstorm from the MRI, using default parameters.

Can you share a screenshot of the scalp surface you got?

You can try:

  1. Tune-up the parameters to improve the scalp surface.
    Right-click on the MRI (once everything is imported), then MRI segmentation > Generate head surface

    The default parameters are:

    • Number of vertices: 10 000
    • Erode factor: 0
    • Fill holes factor: 2
    • Background threshold: This is guessed from the MRI data

  2. Compute the BEM surfaces using FieldTrip method.
    Right-click on the MRI (once everything is imported), then MRI segmentation > Generate BEM surfaces > FieldTrip

    :light_bulb: Please update your Brainstorm instance to 20-Nov-2025, as there was a bug with the interaction of FieldTrip and SPM plugins, that blocked the computation of BEM surfaces with FieldTrip

That depends on what do you mean with "done the MEG data analysis".

Processing that do not depend on the position of the MEG with respect to the head are ok:

  • ICA and SSP
  • Frequency filters
  • Event detection

Processing that depend on the position of the MEG with respect to the head must be redone:

  • MRI-registration (of course)
  • Computation of head model, and consequently
  • Source estimation and their analysis

Does your data have digitized points for the head shape?
https://neuroimage.usc.edu/brainstorm/Tutorials/ChannelFile#Automatic_registration

:light_bulb: If you have digitized points for the head shape, you need first to compute an accurate head (scalp) surface