We don't have a replacement yet for tkregsiter2, but here is a work-around

cd $SUBJECTS_DIR/subject/mri/transforms

First, convert the xfm to an lta file

lta_convert --src ../orig.mgz --trg $FREESURFER_HOME/average/mni305.cor.mgz --inxfm talairach.xfm --outlta talairach.xfm2.lta --subject fsaverage --ltavox2vox

Next, check the registration with

tkregisterfv --mov ../orig.mgz --reg talairach.xfm2.lta

If everything is ok, then just exit out of freeview and move on. If you need to make changes, then save the changes back into talairach.xfm2.lta

Then convert the lta back to xfm:
lta_convert --inlta talairach.xfm2.lta --outmni talairach.xfm

On 6/28/2020 4:30 PM, Wakim, Kathryn-Mary wrote:

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Hi all,

I’m a new FreeSurfer user, so I’d like to thank you all in advance for your patience!

After running recon-all to completion, I reviewed the log file and found the warning "#@# Talairach Failure Detection.” I am assuming that this is a warning and not a hard failure, because it seems that recon-all has run to completion “without error” (according to the log file).

I attempted to follow these instructions to verify my Tal registstration output: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview#:~:text=FreeSurfer%20computes%20a%20linear%20Talairach,via%20%2Dnotal%2Dcheck) However, it seems based on archived Freesufer forum posts that the GUI for tkregister2 is no longer compatible with the current Mac OS, and I was therefore unable to use this tool.

I’m wondering if someone can provide me with some alternate instructions for how to view the output of the Tal registration so that I can verify whether or not there has been a registration error.

Warm regards,

Kamy Wakim
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