Hi Christine,

For the current version of Freesurfer, those transformations are in base directory. I don’t have access to longitudinal processing using Freesurfer v6. Not sure when things changed.

Here is the example provided in https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat to map segmentation aseg to the native space:

cd $SUBJECTS_DIR/<tpid>.long.<baseid>/mri

mri_convert -ait transforms/<tpid>_to_<tpid>.long.<baseid>.lta \

            -rl $SUBJCECTS_DIR/<tpid>/mri/rawavg.mgz \

            -rt nearest -odt uchar \

            aseg.mgz aseg-in-rawavg.mgz

Replace the first line with ‘-ait $SUBJCECTS_DIR/<baseid>/mri/transforms/<tpid>_to_<baseid>.lta’.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Christine Farrugia
Sent: Thursday, September 19, 2024 11:38 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Transforming aseg.mgz to native anatomical space - transform files absent

        External Email - Use Caution        

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

---

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@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

This email was sent to you by someone outside the University.

You should only click on links or attachments if you are certain that the email is genuine and the content is safe.

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

        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

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.