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