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Dear Malte, thanks for your reply. I need to apply a deformable transform. I've been using ANTs (antsRegistrationSyN and ApplyTransformsToPoints) and I would like to update that part of the pipeline with mri_synthmorph. Do you think it will be possible in the near future?

Best,


Ezequiel



________________________________________
Hi Ezequiel,

Yes, this is supported by mri_label2label if you save the coordinates in a
.label file with vox2ras=3Dscanner in the header. These are simple text fil
es; you can find examples in the label subfolder of a FreeSurfer-processed
subject.

However, this currently only works for rigid or affine transforms, that is,
LTA files. What kind of transform are you looking to apply?

Best wishes,
Malte

________________________________________
From: Ezequiel Mikulan <emikulan@yahoo.com>
Sent: Monday, June 22, 2026 07:40
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] apply mri_synthmorph transform to a set of coordinates
        External Email - Use Caution

Hi, I would like to know whether it is possible to apply a transform estima
ted with mri_synthmorph to a set of coordinates (i have them in RAS space).
These are SEEG electrode positions, and the transform maps between a subje
ct's native space and the MNI152 template.

If this is not currently supported, is this something that might be added i=
n the future?

Thanks a lot for your tools.

Best,

Ezequiel