Hi Ruopeng,
When I try to open it, this is part of the error message that appears: freeview -v 2000_2/mri/T1.mgz 2000_2/mri/brainmask.mgz:colormap=heat:opacity=0.4 libGL error: No matching fbConfigs or visuals found libGL error: failed to load driver: swrast X Error: BadValue (integer parameter out of range for operation) 2 Extension: 150 (Uknown extension) Minor opcode: 3 (Unknown request) Resource id: 0x0 X Error: GLXBadContext 160 Extension: 150 (Uknown extension) Minor opcode: 5 (Unknown request) Resource id: 0x6000ba X Error: 0 0 Extension: 150 (Uknown extension) Minor opcode: 26 (Unknown request) Resource id: 0x0 X Error: GLXBadContext 160 Extension: 150 (Uknown extension) Minor opcode: 5 (Unknown request) Resource id: 0x6000ba X Error: 0 0 Extension: 150 (Uknown extension) Minor opcode: 26 (Unknown request) Resource id: 0x0 X Error: GLXBadContext 160 Extension: 150 (Uknown extension) Minor opcode: 5 (Unknown request) Resource id: 0x6000ba X Error: 0 0 Extension: 150 (Uknown extension) Minor opcode: 26 (Unknown request) Resource id: 0x0 X Error: GLXBadContext 160 Extension: 150 (Uknown extension) Minor opcode: 5 (Unknown request) Resource id: 0x6000ba X Error: 0 0 Extension: 150 (Uknown extension) Minor opcode: 26 (Unknown request) Resource id: 0x0 X Error: GLXBadContext 160 Extension: 150 (Uknown extension) Minor opcode: 5 (Unknown request) Resource id: 0x6000ba X Error: 0 0 Extension: 150 (Uknown extension) Minor opcode: 26 (Unknown request) Resource id: 0x0 X Error: BadMatch (invalid parameter attributes) 8 Extension: 150 (Uknown extension) Minor opcode: 11 (Unknown request) Resource id: 0x6000b8 If I run glxgears, this appears: [edwards@guero ~]$ glxgears libGL error: No matching fbConfigs or visuals found libGL error: failed to load driver: swrast X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 150 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) Value in failed request: 0x0 Serial number of failed request: 28 Current serial number in output stream: 30 [edwards@guero ~]$ Thank you! Kaley Message: 6 Date: Fri, 23 Sep 2016 18:53:45 -0400 From: Ruopeng Wang <rpw...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] freeview display problem To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <732e27d8-179e-4b66-8762-7bf26c1df...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Is there any error message on the terminal? What happens if you run ?glxgears? command? Does it run? Best, Ruopeng > On Sep 23, 2016, at 4:35 PM, KALEY E ELLIS <keedwar...@wisc.edu> wrote: > > Hello FreeSurfer Developers, > > I am attempting to open freeview to view the brainmask on a subject in our > study. Everything looks normal, except there is no image displayed (see > attachment). Could you please let me know how I can fix this? > > Thank you, > Kaley > > Associate Research Specialist > Center for Healthy Minds > Waisman Center for Brain Imaging and Behavior > University of Wisconsin-Madison > <Screen Shot 2016-09-23 at 3.34.25 > PM.png>_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160923/f890bd3a/attachment-0001.html ------------------------------ Message: 7 Date: Sat, 24 Sep 2016 11:36:46 -0400 From: Satrajit Ghosh <sa...@mit.edu> Subject: [Freesurfer] avoiding FSL when using T2pial To: Freesurfer Mailing List <freesurfer@nmr.mgh.harvard.edu> Message-ID: <ca+a4womxc6mvvyglvswthotesocr282mzba-u7jy803kool...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" hi doug, without hacking recon-all is there a way to avoid using FSL when using the T2pial flag? cheers, satra #@# Refine Pial Surfs w/ T2/FLAIR Sat Sep 24 08:42:34 UTC 2016 bbregister --s sub-01 --mov /subjects/sub-01/mri/orig/T2raw.mgz --lta /subjects/sub-01/mri/transforms/T2raw.lta --init-fsl --T2 Log file is /subjects/sub-01/mri/transforms/T2raw.dat.log Sat Sep 24 08:42:35 UTC 2016 setenv SUBJECTS_DIR /subjects cd /subjects/sub-01/scripts /opt2/freesurfer/bin/bbregister --s sub-01 --mov /subjects/sub-01/mri/orig/T2raw.mgz --lta /subjects/sub-01/mri/transforms/T2raw.lta --init-fsl --T2 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ Linux b62492e050ac 4.4.20-moby #1 SMP Thu Sep 8 21:27:34 UTC 2016 x86_64 GNU/Linux FREESURFER_HOME /opt2/freesurfer mri_convert /subjects/sub-01/mri/orig/T2raw.mgz /subjects/sub-01/mri/transforms/tmp.bbregister.4836/template.nii mri_convert /subjects/sub-01/mri/orig/T2raw.mgz /subjects/sub-01/mri/transforms/tmp.bbregister.4836/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /subjects/sub-01/mri/orig/T2raw.mgz... TR=2500.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.0675638, -0.9838, -0.166052) j_ras = (0.119725, -0.173224, 0.977578) k_ras = (0.990505, -0.0461684, -0.129489) writing to /subjects/sub-01/mri/transforms/tmp.bbregister.4836/template.nii... fslregister --s sub-01 --mov /subjects/sub-01/mri/transforms/tmp.bbregister.4836/template.nii --reg /subjects/sub-01/mri/transforms/tmp.bbregister.4836/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /subjects/sub-01/mri/transforms/tmp.bbregister.4836/fslregister --dof 6 --fsvol brainmask.mgz ERROR: you must have the FSLDIR environment variable defined and pointing to the FSL installation -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160924/ad492b07/attachment-0001.html ------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 151, Issue 30 ******************************************* 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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