Dear Antonin
Yes, that is the directory where - after failed recon-all - I opened, manually registered, then saved the talairach.xfm file. Before I re-ran recon-all, I reopened the modified talairach.xfm file with tkregister2 to verify that it was my manual registration, which was true.
I attached the recon-all log and error files and the talairach and talairach-avi log file.
Version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Clemens
-----freesurfer-bounces@nmr.mgh.harvard.edu schrieb: ----- An: freesurfer@nmr.mgh.harvard.edu Von: Antonin Skoch Gesendet von: freesurfer-bounces@nmr.mgh.harvard.edu Datum: 16.08.2017 12:23 Betreff: Re: [Freesurfer] Antwort: Re: use manually defined talairach.xfm
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
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