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|You may discover that the alignment is very poor, despite the fact that the tal-check passed. [[FsTutorial/Talairach|Manual registration]] is the only option failing these two workarounds.||You may discover that the alignment is very poor, despite the fact that the tal-check passed. [[FsTutorial/ManualRegistration|Manual registration]] is the only option failing these two workarounds.|
Talairach Failures in FS v5.1
Freesurfer v5.1 introduced a modification to the Talairach alignment stage which seems to have resulted in poor Talairach alignment results compared to prior versions of Freesurfer in some subjects. The change was to move the Talairach stage to run before the NU bias-correct stage (instead of after it which was the case in versions prior to v5.1). The change was made in order for the NU correct stage to make use of coarse Tal coords to refine the normalization. Testing of running the Tal stage with the non-bias-corrected input (orig.mgz) did not reveal problems in our data set. However, it seems that the Tal stage runs optimally when using the bias-corrected input (nu.mgz) as was the case in versions prior to v5.1. Therefore, in release v5.2, the input will again be bias-corrected by NU correct prior to input to the Tal stage.
There are two work-arounds for users of v5.1:
Run these commands:
cd $SUBJECTS_DIR/subjid/mri mri_nu_correct.mni --i orig.mgz --o orig.mgz --n 1 recon-all -s subjid -talairach -clean-tal -tal-check
This runs the NU bias correction on the input 'orig.mgz' and saves the output to the same name 'orig.mgz', such that the subsequent recon-all command will use it as input to the talairach stage. Note that the '-clean-tal' flag is essential to delete the existing talairach.xfm file.
If this completes without failing the tal-checker (you can try increasing the iterations value --n X to add more bias-correction), then you should also confirm the registration manually:
tkregister2 --s subjid --fstal
If it looks fine, then you can run your recon-all commands any way you want, except do not include the -clean-tal flag or -clean flag. If you must use the -clean flag (for instance to delete a bad brainmask, however in that case you should use -clean-bm, which doesnt affect your saved talairach.xfm), then use -clean instead of -clean-tal in the recon-all -talairach command shown above. Your talairach.xfm will be retained unless this flag is included. Your talairach.xfm will not be overwritten even if the -talairach stage is run again.
An alternative Tal stage method is 'mritotal' which is an MNI tool. To use it, run this recon-all command:
recon-all -s subjid -talairach -use-mritotal -clean-tal -tal-check
Notice the '-clean-tal' is necessary to delete the existing tal file. If this completes without failing the tal-checker, then you should also confirm the registration manually:
tkregister2 --s subjid --fstal
You may discover that the alignment is very poor, despite the fact that the tal-check passed. Manual registration is the only option failing these two workarounds.