Hi, I think there is a problem with my freesurfer installation (newest version 5.3). First, when trying this freeview command (see below) I found on the “Testing your freesurfer installation” page using my own data, freesurfer opened, but I am concerned about the “invalid drawable” lines. The message happened when I ran this command on the "bert" data.
[CoS-Psychology-Murphy-iMac-QAD:/Applications/freesurfer] cmurphy% freeview -v $SUBJECTS_DIR/ABU/mri/norm.mgz -v $SUBJECTS_DIR/ABU/mri/aseg.mgz:colormap=lut:opacity=0.2 -f $SUBJECTS_DIR/ABU/surf/lh.white:edgecolor=yellow -f $SUBJECTS_DIR/ABU/surf/rh.white:edgecolor=yellow -f $SUBJECTS_DIR/ABU/surf/lh.pial:annot=aparc:edgecolor=red -f $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red
2013-10-22 12:47:02.811 Freeview[4214:703] invalid drawable
2013-10-22 12:47:02.812 Freeview[4214:703] invalid drawable
2013-10-22 12:47:02.826 Freeview[4214:703] invalid drawable
2013-10-22 12:47:02.826 Freeview[4214:703] invalid drawable
2013-10-22 12:47:02.839 Freeview[4214:703] invalid drawable
2013-10-22 12:47:02.840 Freeview[4214:703] invalid drawable
2013-10-22 12:47:02.853 Freeview[4214:703] invalid drawable
2013-10-22 12:47:02.853 Freeview[4214:703] invalid drawable
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
MRISread(/Applications/freesurfer/elissa_thesis/bert/surf/rh.pial): could not open file
No such file or directory
MRISread failed
MRISread(/Applications/freesurfer/elissa_thesis/bert/surf/rh.pial): could not open file
rfer/average/colortable_desikan_killiany.txt)
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
CTABisEntryValid: index -1 was OOB
No such file or directory
CTABisEntryValid: index -1 was OOB
No such file or directory
CTABisEntryValid: index -1 was OOB
iginally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
CTABisEntryValid: index -1 was OOB
No such file or directory
CTABisEntryValid: index -1 was OOB
No such file or directory
CTABisEntryValid: index -1 was OOB
No such file or directory
CTABisEntryValid: index -1 was OOB
No such file or directory
CTABisEntryValid: index -1 was OOB
iginally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
Second, my next issue is that I am unable to use tkmedit to view my data. See command below and error message.
[CoS-Psychology-Murphy-iMac-QAD:/Applications/freesurfer] cmurphy% tkmedit ABU orig.mgz
dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib
Referenced from: /Applications/freesurfer/tktools/tkmedit.bin
Reason: image not found
Trace/BPT trap
I've tried other tkmedit commands and have gotten same error messages. I tried commands on "bert" data but got same errors.
Third, I'd like to know if it is normal that a recon all could only take between 8-9 hours.
I have attached the recon-all.log for the subject I am trying to view. Here is some additional information about my mac incase you see any glaring system inadequacies.
Processor 2.5 GHz Intel Core i5 Memory 4 GB 1333 MHz DDR3 Graphics AMD Radeon HD 6750M 512 MB Software Mac OS X Lion 10.7.5 (11G63)
Thank you, Elissa