They're under $base/mri/transforms/*.lta.

From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Matthieu Vanhoutte [matthieuvanhoutte@gmail.com]
Sent: Friday, March 24, 2017 10:43 AM
To: Freesurfer support list
Subject: [Freesurfer] Longitudinal: obtain rigid registration matrix from cross to long subject

Dear Freesurfer's experts,

I would like to obtain the rigid registration matrix of the transformation between cross and long subject. Where could I find this (.dat or .lta file) ?

Best regards,

Matthieu