To add to this thread, I have this same problem (upside-down display in tksurfer, with mismatch with the reported annotation labels in the Tools window) when using a CentOS 6.4 system, using both FS 5.1 and FS 5.3, but not when using a CentOS 5.5 system.

If there is an easy fix for this (environment or system variable of some sort?) that would be very helpful to know.

thanks,
-MH

-- 
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: mharms@wustl.edu

From: Doug Greve <greve@nmr.mgh.harvard.edu>
Date: Sunday, January 12, 2014 11:34 AM
To: "Schweren, LJS (med)" <l.j.s.schweren@umcg.nl>, free surfer <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] brain orientation in qdecDouglas N Greve


Sounds like it is some problem with the display libraries. I think someone else was having the same problem recently (ie, hemisphere displayed upside down in tksurfer). Does anyone remember? Zeke?
doug





On 1/12/14 5:03 AM, Schweren, LJS (med) wrote:
No, in Freeview I encountered no such problems. Also in tkmedit the brains appear in normal orientation. 
Also, the scale bars and titles are displayed upside down in tksurfer. 

Best, Lizanne



Does the same thing happen in freeview?

On 01/06/2014 04:45 AM, L. Schweren wrote:
>
> Dear experts,
>
> I ran recon-all with qcache. When loading the right hemisphere of 
> fsaverage (or any other surface reconstruction) into tksurfer (for 
> example command: tksurfer fsaverage rh white), the left hemisphere 
> surface is displayed, and it is upside down. When I import annotations 
> they load in the same orientation as the surface. However, the 
> coordinates and the labels, displayed in the Tksurfer Tools window, 
> are not. For example, when I move the cursor to the temporal lobe, the 
> label says it’s postcentral. I do not mind manually turning the 
> surfaces in tksurfer, but I do need to be sure I am looking at the 
> correct hemispheres, coordinates and labels.
>
> I hope you can help me solve this. Thank you in advance.
>
> Best wishes,
>
> Lizanne
>
>
>
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> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
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