[Freesurfer] Visualizing individual ROI labels
Hello freesurfer experts, I am hoping that someone can tell me how I can create 3D representations of individual cortical ROIs (labels based on the Desikan/Killiany Atlas) to be used in figures. I'm trying to make figures that show the ROIs that I investigated (like this figure in Desikan et al. paper http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012853). I know that I can manually make a label in qdec, but I was hoping that there was an automated method to highlighting individual labels/ROIs. 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.
[Freesurfer] order of edits and autorecon commands
This is a basic question about the process for manual edits and the autorecon commands. I am going to follow the recommended reconstruction page (on fs wiki) to make manual edits on my data. The page says that you can make all the manual edits at once. But my question is, how do you go about running the autorecon commands specific to each type of edit? Do you run each command separately after you're done saving all your manual edits? It seems that some of the steps are redundant (like running autorecon 3 more than once). Also, if I make changes to skullstip, will I have to do the recon again before doing additional edits? Here is an example where my questions would need to be addressed. Say I had to add control points to wm, and erase some voxels from the pial. Do I make edits and run the commands to fix these problems separately (i.e. make wm edits and subsequently run appropriate recon steps specified in wiki, then make pial edits and run specified recon steps), or do I make any types of edits at once (control points, add/delete voxels, etc.) and then run each command separately, or do I make any types of edits at once and somehow combine these different commands into one step? I'm sorry if this is confusing - I am just trying to grasp how to approach manual edits in the "order" listed in the recommended reconstruction page. 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.
[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.
[Freesurfer] tkmedit error message
Hello, I am a new freesurfer user. I tried to view subject data with tkmedit for the first time after the recon-all process finished without errors. Here is what I typed and the message I got: [ariana:~/Desktop/ELISSA_ THESIS/ATO] cmurphy% tkmedit ATO brainmask.mgz -aux T1.mgz -surfs -aseg Wed Oct 16 14:35:57 ariana.local tkmedit.bin[66069] : kCGErrorFailure: Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are logged. xp_init: error: not initialized error: invalid CoreGraphics connection Abort Can someone explain this error message? Despite that the recon-all log said that the subject was completed without error, there were several places in the log that read invalid. Is this normal? Also, I realized that I have an older version of freesurfer and should upgrade. Should I delete the former version and re-install with new version? Thank you for your help, E ___ 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.
