Hello Freesurfer Experts-

      We recently reran several subjects from scratch through the stable Freesurfer 5.0 pipeline who had previously been processed with the stable 4.5 pipeline. We used tkregister2 for QA of the 5.0 data and noticed that the talairach transform was off (misaligned) for the first 5 subjects we examined. All subjects passed the auto Talairach check, and their 4.5 data was not misaligned.

      Applying the talairach.xfm matrix from the 4.5 pipeline corrected the problem. Looking at the recon-all.cmd files from the different versions, it looks like the only difference for the tailairach_avi step was that the 4.5 version called for nu.mgz whereas the 5.0 version called for orig.mgz. I reran a couple of 5.0 subjects using

 talairach_avi --i nu.mgz –xfm transforms/talairach.auto.xfm

        Doing this fixed the transform and subsequent alignment problems (copied above to talairach.xfm and re-ran tkregister2).       

        I have read on the list that the talairach.xfm is not used in the majority of data streams (although table indicates otherwise). Our plans were to use the data for both cortical thickness analyses as well as MEG analyses (source mapping). I would appreciate it if someone could tell me:

1)      The best way to rerun the current data that has been run through 5.0. We have already run about 50 of 100 subjects through 5.0.

2)      The best way to fix our recon-all program for 5.0 so that the correct transform is generated for new subjects.

3)      In addition, we also observed the following error in the log file and could not find any information on what it may mean (all checked subjects had error)

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Computing MAP estimate using 3481 samples...

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IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH

ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR

GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA:

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 EM alignment process ...

 Computing final MAP estimate using 382743 samples.

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 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH

ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR

GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through

quasi-newton minimization...

Thanks for your time!

Andrew