The .lta file will not be changed in that command line (only the reg), you need to add --ltaout talairach.lta If you re-run, remove the --lta and it will load the --reg which you can then save back to talaairach.lta with the --ltaout flag.

Having said that, recon-all will actually overwrite your lta. To avoid this, run with -nogcareg as the last argument (but make a copy first!). I don't think we anticipated that that lta would be modified manually.

doug

On 02/21/2014 07:06 PM, Mark Plantz wrote:

Hello freesurfers,

I recently attempted to fix the talairach.lta file from a bad 

recon-all run for one of my subjects. I originally thought that the second pass of recon-all would automatically load this talairach file. However, it looks like the talairach alignment keeps restarting each time recon-all is run. I couldn't seem to find a recon-all flag to manually send the program this new talairach.lta.reg.dat file. Has anyone else encountered this type of problem?

My command line is as follows:

tkregister2 --mov /Applications/freesurfer/subjects/CMH-9018/mri/brainmask.mgz --targ /Applications/freesurfer/subjects/fsaverage/mri/brainmask.mgz --lta /Applications/freesurfer/subjects/CMH-9018/mri/transforms/talairach.lta --reg /Applications/freesurfer/subjects/CMH-9018/mri/transforms/talairach.lta.reg.dat --s CMH-9018

Thanks in advance!

• Mark

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