During autorecon1, I find error message below during autorecon1, eventhough recon-all-status.log said 'recon-all finished without error ' Is it not considerable error message or important thing?
Thank you
bsjeong --------------------- Can't find the talairach xform 'spgr_nifti/N3/mri/transforms/talairach.xfm' Transform is not loaded into mri reading from orig.mgz... Talairach transform /spgr_nifti/N3/mri/transforms/talairach.xfm does not exist ... Cannot load tal xfm file /spgr_nifti/N3/mri/transforms/talairach.xfm TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to ./tmp.mri_nu_correct.mni.26912/nu0.mnc...
...........
#@# Talairach Thu Dec 14 14:00:02 EST 2006 /spgr_nifti/N3/mri
talairach --i nu.mgz --xfm transforms/talairach.auto.xfm
/spgr_nifti/N3/mri /freesurfer/bin//talairach --i nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.4 2006/04/18 23:05:05 nicks Exp $ Linux b2_tm128.bwh.harvard.edu 2.6.17-1.2157_FC5 #1 SMP Tue Jul 11 22:53:56 EDT 2006 x86_64 x86_64 x86_64 GNU/Linux Thu Dec 14 14:00:03 EST 2006 tmpdir is transforms/tmp.talairach.27507 /spgr_nifti/N3/mri mri_convert nu.mgz transforms/tmp.talairach.27507/src.mnc mri_convert nu.mgz transforms/tmp.talairach.27507/src.mnc Can't find the talairach xform '/spgr_nifti/N3/mri/transforms/talairach.xfm' Transform is not loaded into mri
Bum Seok,
The "Can't find the talairach xform..." message can be ignored. Recon- all will find that file by searching relative to the 'mri' directory. The message you see is a historical artifact from when the path to .xfm was hard-coded into the file.
Nick
On Thu, 2006-12-14 at 14:10 -0500, Bum Seok Jeong wrote:
During autorecon1, I find error message below during autorecon1, eventhough recon-all-status.log said 'recon-all finished without error ' Is it not considerable error message or important thing?
Thank you
bsjeong
Can't find the talairach xform 'spgr_nifti/N3/mri/transforms/talairach.xfm' Transform is not loaded into mri reading from orig.mgz... Talairach transform /spgr_nifti/N3/mri/transforms/talairach.xfm does not exist ... Cannot load tal xfm file /spgr_nifti/N3/mri/transforms/talairach.xfm TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to ./tmp.mri_nu_correct.mni.26912/nu0.mnc...
...........
#@# Talairach Thu Dec 14 14:00:02 EST 2006 /spgr_nifti/N3/mri
talairach --i nu.mgz --xfm transforms/talairach.auto.xfm
/spgr_nifti/N3/mri /freesurfer/bin//talairach --i nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.4 2006/04/18 23:05:05 nicks Exp $ Linux b2_tm128.bwh.harvard.edu 2.6.17-1.2157_FC5 #1 SMP Tue Jul 11 22:53:56 EDT 2006 x86_64 x86_64 x86_64 GNU/Linux Thu Dec 14 14:00:03 EST 2006 tmpdir is transforms/tmp.talairach.27507 /spgr_nifti/N3/mri mri_convert nu.mgz transforms/tmp.talairach.27507/src.mnc mri_convert nu.mgz transforms/tmp.talairach.27507/src.mnc Can't find the talairach xform '/spgr_nifti/N3/mri/transforms/talairach.xfm' Transform is not loaded into mri
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Nick Schmansky After finish autorecon1 step, I checked skull stripping results with command below. tkmedit N3 brainmask.mgz -aux T1.mgz
Then, I always face to an error message such as 'this may hart performance'. Am I also able to ignored it?
freeglut (tkmedit): Unable to create direct context rendering for window 'Medit: ' This may hurt performance. Reading /projects/fmri/fs/freesurfer/lib/tcl/tkm_common.tcl Reading /projects/fmri/fs/freesurfer/lib/tcl/tkm_wrappers.tcl
bsjeong
Nick Schmansky wrote:
Bum Seok,
The "Can't find the talairach xform..." message can be ignored. Recon- all will find that file by searching relative to the 'mri' directory. The message you see is a historical artifact from when the path to .xfm was hard-coded into the file.
Nick
On Thu, 2006-12-14 at 14:10 -0500, Bum Seok Jeong wrote:
During autorecon1, I find error message below during autorecon1, eventhough recon-all-status.log said 'recon-all finished without error ' Is it not considerable error message or important thing?
Thank you
bsjeong
Can't find the talairach xform 'spgr_nifti/N3/mri/transforms/talairach.xfm' Transform is not loaded into mri reading from orig.mgz... Talairach transform /spgr_nifti/N3/mri/transforms/talairach.xfm does not exist ... Cannot load tal xfm file /spgr_nifti/N3/mri/transforms/talairach.xfm TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to ./tmp.mri_nu_correct.mni.26912/nu0.mnc...
...........
#@# Talairach Thu Dec 14 14:00:02 EST 2006 /spgr_nifti/N3/mri
talairach --i nu.mgz --xfm transforms/talairach.auto.xfm
/spgr_nifti/N3/mri /freesurfer/bin//talairach --i nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.4 2006/04/18 23:05:05 nicks Exp $ Linux b2_tm128.bwh.harvard.edu 2.6.17-1.2157_FC5 #1 SMP Tue Jul 11 22:53:56 EDT 2006 x86_64 x86_64 x86_64 GNU/Linux Thu Dec 14 14:00:03 EST 2006 tmpdir is transforms/tmp.talairach.27507 /spgr_nifti/N3/mri mri_convert nu.mgz transforms/tmp.talairach.27507/src.mnc mri_convert nu.mgz transforms/tmp.talairach.27507/src.mnc Can't find the talairach xform '/spgr_nifti/N3/mri/transforms/talairach.xfm' Transform is not loaded into mri
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Bum Seok,
The message 'Unable to create direct context rendering...This may hurt performance" may be ignored. It refers to the inability to use maximal graphics capabilities, but this is not a major problem, as tkmedit will merely redraw the screen more slowly. This is likely due to your computer's graphics driver not supporting the OpenGL Extentions (GLX). As long the screen redraws are not painfully slow, you should be able to use the tools as normal.
Nick
Dear Nick Schmansky After finish autorecon1 step, I checked skull stripping results with command below. tkmedit N3 brainmask.mgz -aux T1.mgz
Then, I always face to an error message such as 'this may hart performance'. Am I also able to ignored it?
freeglut (tkmedit): Unable to create direct context rendering for window 'Medit: ' This may hurt performance. Reading /projects/fmri/fs/freesurfer/lib/tcl/tkm_common.tcl Reading /projects/fmri/fs/freesurfer/lib/tcl/tkm_wrappers.tcl
bsjeong
Nick Schmansky wrote:
Bum Seok,
The "Can't find the talairach xform..." message can be ignored. Recon- all will find that file by searching relative to the 'mri' directory. The message you see is a historical artifact from when the path to .xfm was hard-coded into the file.
Nick
On Thu, 2006-12-14 at 14:10 -0500, Bum Seok Jeong wrote:
During autorecon1, I find error message below during autorecon1, eventhough recon-all-status.log said 'recon-all finished without error ' Is it not considerable error message or important thing?
Thank you
bsjeong
Can't find the talairach xform 'spgr_nifti/N3/mri/transforms/talairach.xfm' Transform is not loaded into mri reading from orig.mgz... Talairach transform /spgr_nifti/N3/mri/transforms/talairach.xfm does not exist ... Cannot load tal xfm file /spgr_nifti/N3/mri/transforms/talairach.xfm TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to ./tmp.mri_nu_correct.mni.26912/nu0.mnc...
...........
#@# Talairach Thu Dec 14 14:00:02 EST 2006 /spgr_nifti/N3/mri
talairach --i nu.mgz --xfm transforms/talairach.auto.xfm
/spgr_nifti/N3/mri /freesurfer/bin//talairach --i nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.4 2006/04/18 23:05:05 nicks Exp $ Linux b2_tm128.bwh.harvard.edu 2.6.17-1.2157_FC5 #1 SMP Tue Jul 11 22:53:56 EDT 2006 x86_64 x86_64 x86_64 GNU/Linux Thu Dec 14 14:00:03 EST 2006 tmpdir is transforms/tmp.talairach.27507 /spgr_nifti/N3/mri mri_convert nu.mgz transforms/tmp.talairach.27507/src.mnc mri_convert nu.mgz transforms/tmp.talairach.27507/src.mnc Can't find the talairach xform '/spgr_nifti/N3/mri/transforms/talairach.xfm' Transform is not loaded into mri
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bum Seok Jeong -
Nick Schmansky