Hi Elissa, The invalid drawable terminal output you can ignore when running Freeview.
Presumably bert is not located in /Applications/freesurfer/elissa_thesis/, so that's why the bert commands are failing. Not the same subjects directory that ABU is in.
To fix the tkmedit library error it looks like you just need to install xquartz on your mac.
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg26311.html
The recon-all.log for the 8.5hr recon looks fine. Was it processed locally and does your mac have a solid-state drive by chance?
-Louis
On Tue, 22 Oct 2013, Elissa McIntosh wrote:
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