[Freesurfer] freeview invalid drawable
Hi, When trying freeview command (see below) from 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 too. What does invalid drawable mean? [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/ABU/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) 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) Thank you, Elissa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] freeview invalid drawable
You can just ignore this warning message on Mac. Best, Ruopeng On Oct 23, 2013, at 8:52 PM, Elissa McIntosh mcintosh.eli...@gmail.com wrote: Hi, When trying freeview command (see below) from 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 too. What does invalid drawable mean? [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/ABU/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) 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) Thank you, Elissa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] [FreeSurfer] Freeview: Invalid drawable
Dear Koen, Freeview returns 8 lines of the error message invalid drawable whenever executed. The messages are as follows 2013-06-24 14:24:57.930 Freeview[1937:303] invalid drawable 2013-06-24 14:24:57.931 Freeview[1937:303] invalid drawable 2013-06-24 14:24:57.944 Freeview[1937:303] invalid drawable 2013-06-24 14:24:57.945 Freeview[1937:303] invalid drawable 2013-06-24 14:24:57.957 Freeview[1937:303] invalid drawable 2013-06-24 14:24:57.958 Freeview[1937:303] invalid drawable 2013-06-24 14:24:57.971 Freeview[1937:303] invalid drawable 2013-06-24 14:24:57.972 Freeview[1937:303] invalid drawable In the $FREESURFER_HOME directory, I tried sed -i 's/CA2_3/CA2\/3/g' FreeSurferColorLUT.txt sed -i 's/CA4_DG/CA4\/DG/g' FreeSurferColorLUT.txt as you suggested in http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22276.html(content copied at the end of this email) I checked in FreeSurferColorLUT.txt and made sure all CA2_3 was changed into CA2\3, all CA4_DG into CA4\DG, but the problem still persists. My computer is Mac OS X version 10.8.2. I downloaded freesurfer-Darwin-lion-stable-pub-v5.3.0.dmgftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg Would you please give me some guidance on how to fix the problem? Thank you very much! Sincerely, Ye Tian Hi Ed, It seems that the 5.1.0 release for the Mac was composed two days after the one for Linux, and during exactly those two days one of us made a change to the file $FREESURFER_HOME/FreeSurferColorLUT.txt. To correct this issue, please make a back-up copy of your FreeSurferColorLUT.txt file, and execute the following commands: cd $FREESURFER_HOME sed -i s/CA2_3/CA2\/3/g FreeSurferColorLUT.txt sed -i s/CA4_DG/CA4\/DG/g FreeSurferColorLUT.txt Thanks, Koen On Wed, Apr 4, 2012 at 9:32 AM, Ed Gronenschild ed.gronensch...@np.unimaas.nl wrote: I have downloaded the file freesurfer-Darwin-leopard-i686-stable-pub-v51.0..dmg, date 26/05/2011. Ed On 4 Apr 2012, at 13:09, Koen Van Leemput wrote: OK, I see why this is not working. We've been changing some name conventions in our internal FreeSurfer repository after the public release of version 5.1, and somehow you managed to get an incompletely updated version. It appears from ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0 that some versions for the Mac were updated *after* the release date (24 May 2011), so I'll check with the engineers what exactly happened. Do you remember which file you downloaded? Thanks, Koen On Wed, Apr 4, 2012 at 6:59 AM, Ed Gronenschild ed.gronensch...@np.unimaas.nl wrote: Hi Koen, No worries. The result of grep is: 500 right_CA2_3 17 85 136 0 550 left_CA2_3 17 85 137 0 Ed On 4 Apr 2012, at 12:41, Koen Van Leemput wrote: Hi Ed, Can you please do grep _CA2 $FREESURFER_HOME/FreeSurferColorLUT.txt and let me know what the result is? Thanks, and sorry this seems so difficult to sort out. Koen On Wed, Apr 4, 2012 at 6:14 AM, Ed Gronenschild ed.gronensch...@np.unimaas.nl wrote: Hi Koen, As already mentioned, I'm using v5.1.0, Mac Intel Leopard version. The voxel values of posterior_left_CA2-3.mgz and posterior_right_CA2-3.mgz are between 0 and 255, if that is what you mean by results. By the way: I always get the 8 lines with invalid drawable messages from freeview. Ed On 3 Apr 2012, at 21:29, Koen Van Leemput wrote: Hi Ed, What version of the FreeSurfer build are you using? Also, could you please let me know what the result is of ls posterior_left_CA2*? Thanks, Koen On Tue, Mar 27, 2012 at 8:29 AM, Ed Gronenschild ed.gronensch...@np.unimaas.nl wrote: Hi, I followed the instructions to visualize the hippocampal subfield segmentation by entering the command (in the subject's mri directory) freeview nu.mgz \ -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \ -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \ -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt and got the following messages: 2012-03-27 11:54:37.043 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.083 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.154 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.156 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.168 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.170 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.182 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.184 freeview.bin[34414:907] invalid drawable QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) CTABrgbAtIndexi: index -1 was OOB CTABrgbAtIndexi: index -1 was OOB Can not find index
