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Hi Yujing,
Many thanks for your reply.
Is this a new feature of FreeSurfer v7, then? As v6 would generate the
<tpid>_to_<tpid>.long.<baseid>.lta files - we used that version before and I
checked the data repository for the transformations in question.
Could you kindly advise how best to transform the aseg back to native space in
the longitudinal case?
Christine
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From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Huang, Yujing
<yhuan...@mgh.harvard.edu>
Sent: 19 September 2024 15:09
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Transforming aseg.mgz to native anatomical space -
transform files absent
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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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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
External Email - Use Caution
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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