Hi Liz,

the registrations are stored in baseid/mri/transforms look for files baseid_to_tpNid.lta and the inverse tpNid_to_baseid.lta (which is the map you are looking for). These should align all your TPs to the base space.

Best, Martin

On Mon, 2009-08-03 at 16:19 -0400, Elizabeth Selgrade wrote:

Hello FreeSurfer Users,

I am using the longitudinal stream to look at four timepoints/subject, and I'd like to transform all of my timepoints to the base scan's unbiased space so that I can calculate ROI volume overlap. I have been using tkregister2 to calculate the transform from my scan.base.long/mri/aseg.mgz to base/mri/rawavg.mgz and then using mri_label2vol to apply the transform. When I do this for all of my scans, I expect to see that the brains are overlapping in the same space. But, I'm not getting that. Any suggestions for how to get all of these scans back in the base space?

Thank you! Liz Selgrade _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer