Dear Clemens,

I am almost out of ideas, since the behaviour is contrary to my expectations.

I would expect that if you run your recon by

recon-all -s subject_id -all

the files you named

before_recon-all_talairach.xfm and after_recon-all_alairach.xfm

should be identical.

Could you assure that after tkregister2, you saved the transform file under name talairach.xfm and put into directory

/Volumes/PromisePegasus/HippocampusPreparedT1Data/subjects/x140214_b02_0917040_3_1_wipmp2rage0p8mmsenseV42_reOrient/mri/transforms ?

What freeSurfer version are you using? Could you post full recon-all output?


Antonin