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
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