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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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Hi Mike
what kind of mismatch do you mean? Bruce On Mon, 13 Jan 2014, Harms, Michael wrote:
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 a ppear 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The surface initially loads upside down, and if you load the annotations the ensuing parcellations are mapped to an upside down surface appropriately, but the label reported in the 'Tksurfer Tools' window appears to be based on a right-side-up brain. For example, if I position the cursor over the brown patch that is the "caudal middle frontal" region, the "Mouse" position says "middletemporal". If I then click at that location, the "Cursor" label changes to "middletemporal" as well, but the funny thing is that region that shows up outlined in yellow, and the position of the asterisk that gets placed on the surface is indeed the middle temporal region (i.e., at the top of the Tksurfer window since the brain is upside-down).
Does that make sense?
cheers, -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
On 1/13/14 12:51 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Mike
what kind of mismatch do you mean? Bruce On Mon, 13 Jan 2014, Harms, Michael wrote:
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 a ppear 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 it¹s 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
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.
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freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas Greve -
Harms, Michael