Hi guys,
On machine inv (more or less the same error on machine ai) nmr-dev-env (same error on nmr-std-env)
cd /space/cuzco/2/users/raij/avml_fmri_mctogether/
setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri/ setenv SUBJECT fsaverage
tksurfer fsaverage lh inflated -overlay avml07_session_BRISI08/bold/group_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat/sphsm10/h-lh.bhdr -timecourse avml07_session_BRISI08/bold/group_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat/sphsm10/h-lh.bhdr
Output:
surfer: current subjects dir: /space/cognito/5/users/raij/subjects_mri/ surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /autofs/space/cuzco_002/users/raij/avml_fmri_mctogether surfer: Reading header info from /space/cognito/5/users/raij/subjects_mri//fsaverage/mri/T1.mgz reading group avg surface area 822 cm^2 from file surfer: vertices=163842, faces=327680 INFO: bvolumeRead: min = 0, max = 0 *** glibc detected *** corrupted double-linked list: 0x00000000060b7db0 *** Abort
Oddly enough, on machine ai, if I leave out the -timecourse part of the command line, the FreeSurfer window opens with the correct overlay and I can scroll through conditions and time points. Further, if I then manually load the timecourse from File/Load Time Course... menu, this works giving the time course display just as it should
Even more oddly, on machine inv (which is spanking new and has lots of RAM etc) even the above basic command line with only loading the overlay gives the above glibc error.
I have 8 subjects * 66 labels = timecourses of 528 labels to extract, which makes this clearly a script job - the only practical solution would be to find a way to make the command line work.
Suggestions? For example, could it be that this has something to do with nvidia drivers?
Thanks,
Tommi
--- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.
Tommi,
Do you have a machine on which this script can run without the glibc error? I have been able to recreate the error you see in a debugger on inv, but can't figure out what is going wrong. (Doug, the glibc error occurs when fclose is called on line 565 of mriFunctionalDataAccess.c). Doug or I will need to look into this further.
Nick
On Wed, 2007-09-05 at 19:02 -0400, raij@nmr.mgh.harvard.edu wrote:
Hi guys,
On machine inv (more or less the same error on machine ai) nmr-dev-env (same error on nmr-std-env)
cd /space/cuzco/2/users/raij/avml_fmri_mctogether/
setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri/ setenv SUBJECT fsaverage
tksurfer fsaverage lh inflated -overlay avml07_session_BRISI08/bold/group_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat/sphsm10/h-lh.bhdr -timecourse avml07_session_BRISI08/bold/group_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat/sphsm10/h-lh.bhdr
Output:
surfer: current subjects dir: /space/cognito/5/users/raij/subjects_mri/ surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /autofs/space/cuzco_002/users/raij/avml_fmri_mctogether surfer: Reading header info from /space/cognito/5/users/raij/subjects_mri//fsaverage/mri/T1.mgz reading group avg surface area 822 cm^2 from file surfer: vertices=163842, faces=327680 INFO: bvolumeRead: min = 0, max = 0 *** glibc detected *** corrupted double-linked list: 0x00000000060b7db0 *** Abort
Oddly enough, on machine ai, if I leave out the -timecourse part of the command line, the FreeSurfer window opens with the correct overlay and I can scroll through conditions and time points. Further, if I then manually load the timecourse from File/Load Time Course... menu, this works giving the time course display just as it should
Even more oddly, on machine inv (which is spanking new and has lots of RAM etc) even the above basic command line with only loading the overlay gives the above glibc error.
I have 8 subjects * 66 labels = timecourses of 528 labels to extract, which makes this clearly a script job - the only practical solution would be to find a way to make the command line work.
Suggestions? For example, could it be that this has something to do with nvidia drivers?
Thanks,
Tommi
Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Nick,
Thanks for looking into this - we are stalled in our analysis until we find a way around this!
The answer to your question is no - I have tried the command in cuzco (via ssh), ai (directly), and inv (directly), and I receive the glibc error on all of them. If you think it would be a good idea to try it on more linux boxes, just let me know.
Bests,
Tommi
Tommi,
Do you have a machine on which this script can run without the glibc error? I have been able to recreate the error you see in a debugger on inv, but can't figure out what is going wrong. (Doug, the glibc error occurs when fclose is called on line 565 of mriFunctionalDataAccess.c). Doug or I will need to look into this further.
Nick
On Wed, 2007-09-05 at 19:02 -0400, raij@nmr.mgh.harvard.edu wrote:
Hi guys,
On machine inv (more or less the same error on machine ai) nmr-dev-env (same error on nmr-std-env)
cd /space/cuzco/2/users/raij/avml_fmri_mctogether/
setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri/ setenv SUBJECT fsaverage
tksurfer fsaverage lh inflated -overlay avml07_session_BRISI08/bold/group_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat/sphsm10/h-lh.bhdr -timecourse avml07_session_BRISI08/bold/group_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat/sphsm10/h-lh.bhdr
Output:
surfer: current subjects dir: /space/cognito/5/users/raij/subjects_mri/ surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /autofs/space/cuzco_002/users/raij/avml_fmri_mctogether surfer: Reading header info from /space/cognito/5/users/raij/subjects_mri//fsaverage/mri/T1.mgz reading group avg surface area 822 cm^2 from file surfer: vertices=163842, faces=327680 INFO: bvolumeRead: min = 0, max = 0 *** glibc detected *** corrupted double-linked list: 0x00000000060b7db0
Abort
Oddly enough, on machine ai, if I leave out the -timecourse part of the command line, the FreeSurfer window opens with the correct overlay and I can scroll through conditions and time points. Further, if I then manually load the timecourse from File/Load Time Course... menu, this works giving the time course display just as it should
Even more oddly, on machine inv (which is spanking new and has lots of RAM etc) even the above basic command line with only loading the overlay gives the above glibc error.
I have 8 subjects * 66 labels = timecourses of 528 labels to extract, which makes this clearly a script job - the only practical solution would be to find a way to make the command line work.
Suggestions? For example, could it be that this has something to do with nvidia drivers?
Thanks,
Tommi
Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.
freesurfer@nmr.mgh.harvard.edu
-
Nick Schmansky -
raij＠nmr.mgh.harvard.edu