So, we know that Human.003.L.LANDMARKS.borderproj did have a medial wall ventral border, but Human.003.L.LANDMARKS.updated.borderproj, for some reason, did not. (The difference in the filenames is the string "updated." preceding borderproj.)
Here is a relevant excerpt from the README.txt: > If any borders do need correction, use Caret's Layers: Border: Border > Update. When the borders are good, use File: Save Data File: > borderproj and > overwrite the borderproj named like *.updated.borderproj. (The > auto-landmarks routine copies Human.SAIS_001.L.LANDMARKS.borderproj to > Human.SAIS_001.L.LANDMARKS.updated.borderproj, so until the borders > are updated, these files are identical. The postborder.sh script uses > the *.updated.borderproj files for registration.) This suggests that somehow the medial wall ventral border got deleted during the manual border update process. You can cd 003/surf and launch Caret, opening the left hem spec file and loading scenes. Redo the tweaks, taking care not to delete the medial wall ventral border. Save as Human.003.L.LANDMARKS.updated.borderproj. Re-run postborder.sh on just that subject (i.e., edit subject list to include just 003). I can't think of a more straightforward way of doing it. If you spent a ton of time tweaking the borders in Human.003.L.LANDMARKS.updated.borderproj, and don't want to have to repeat those edits, then there are ways of salvaging them. But I'm guessing that is not likely. On 08/10/2010 06:29 AM, Kuk Wai Liu wrote: > Hi Donna, > > It appears that you are correct about the LANDMARK.MedWall.VENTRAL that is > missing from the Human.003.L.LANDMARKS.updated.borderproj. What would i need > to do to generate one? > > There does appear to be a medial wall ventral border capture in the html > directory. > > I've attached the images i've obtained for one subject (including both left > and right hemispheres) after running the preborder script. > > Regards > > Kwliu > ________________________________________ > From: [email protected] > [[email protected]] on behalf of Donna Dierker > [[email protected]] > Sent: 09 August 2010 16:48 > To: Caret, SureFit, and SuMS software users > Subject: Re: [caret-users] Postborder.sh problem > > Kwliu, > > It appears that Human.003.L.LANDMARKS.updated.borderproj is missing > LANDMARK.MedWall.VENTRAL, which causes all the downstream trouble. > > It is possible that the auto-landmark algorithm had trouble identifying this > landmark (although in our experience this is rare). Or it is possible that > it got deleted during tweaking. > > Or redrawn using the border name ATLAS_LANDMARK.MedWall.VENTRAL instead of > just LANDMARK.MedWall.VENTRAL. (All borders named like "ATLAS_*" get deleted > by the postborder.sh script. They are useful for showing where the target > borders lie, though.) > > Did the captures generated by preborder.sh (in the HTMLDIR) show a medial > wall ventral border? > > Donna > > > On 08/09/2010 06:18 AM, Kuk Wai Liu wrote: > >> Hi, >> >> Thanks for your help on the preborder.sh problem. Having run the >> preborder.sh command successfully without errors, i've now got errors >> in the postborder.sh command, could you help me out please? My output >> is attached with this email. >> >> Regards >> >> Kwliu >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> caret-users mailing list >> [email protected] >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------ > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
