Import Infant freesurfer anatomy folder

Requests
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1

Hello,

I am working on some infant data for whom I have the anatomy folder calculated through "Infant freesufer" (recon-all).
When I import the anatomy folder (as a "freesurfer" folder), the MRI and surfaces are not coregistered. I think that brainstorm applies a Freesurfer-->Brainstorm transformation to the MRI which may be the problem. (The anatomical labels of the MRI are wrong after the import in Brainstorm, while they are fine on the original file)

Do you have a solution for this? Is there any way to import a Freesurfer anatomy folder without applying that transformation?

Thank you very much!

2

I don't know, I had never heard of infant_recon_all before...
Could you please share an example dataset?

@christianoreilly Have you been using this?

3

Yes, this is the command that comes with the Infant version of the FreeSurfer pipeline. I don't know about this issue of MRI and surfaces not being co-registered put I did many post-processing steps beside using this command (e.g., extraction of the head surfaces) before trying to import my surfaces into Brainstorm so it is possible that I solved such an issue along the way. This notebooks contain all the manipulations I used: https://github.com/christian-oreilly/infant_template_paper/blob/master/process_infants_freesurfer.ipynb if it may be of any help...

4

Thanks Francois for your reply. I will de-anonymize a dataset and send (should I send it to you?).
By the way, If I upload MRI and surfaces separately, it works.
Yet, when I import the whole anatomy folder it does apply a transformation to the MRI, the anatomical labels get swapped and so does the co-registration with the surfaces.

I did not look into the codes that @christianoreilly shared. It's pretty lengthy and not sure where to find what I'm looking for.

5

Yes, please zip the output of one subject folder that is not imported correctly in Brainstorm, upload it somewhere and post the download link here.