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

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.