I can only find the transformations from each timepoint to base, and vice-versa in the base (<templateid>) mri/transforms directory. Those lta are used during long processing to transform input images to base space. I will confirm that and update the wiki accordingly.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Christine Farrugia
Sent: Wednesday, September 18, 2024 9:46 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Transforming aseg.mgz to native anatomical space - transform files absent

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Hi,

I'm trying to convert the aseg output of my longitudinal runs from FreeSurfer space back to native anatomical space by following the directions here:

https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat

However, I've noted that none of my subjects have a <tpid>_to_<tpid>.long.<baseid>.lta transformation in <tpid>.long.<baseid>/mri/transforms. The transformations from each of the longs to the base (and vice-versa) are in the mri/transforms folder of the <templateid> directory, but that's about it, despite the fact that recon-all finished without errors. I'm using FreeSurfer v7.4.1.

Is this a feature of FreeSurfer v7 or is something going wrong somewhere?

Thanks in advance,

Christine

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