Hmmm. Then I have a hunch what might have happened. Please upload your postborder.sh script here:
http://pulvinar.wustl.edu/cgi-bin/upload.cgi Do *not* email it. On 08/10/2010 10:22 AM, Kuk Wai Liu wrote: > Hi Donna, > > Sorry i was mistaken about there not being a LANDMARK.MedWall.VENTRAL that > was missing from the Human.003.L.LANDMARKS.updated.borderproj. I've just > taken another look inside the Human.003.L.LANDMARKS.updated.borderproj file > and there is a LANDMARK.MedWall.VENTRAL border. > > I've attached the file with this email. > > I apologise for my earlier email and for the time you spent analysing it. > > Regards > > Kwliu > ________________________________________ > From: Kuk Wai Liu > Sent: 10 August 2010 16:15 > To: Caret, SureFit, and SuMS software users > Subject: RE: [caret-users] Postborder.sh problem > > ________________________________________ > From: [email protected] > [[email protected]] on behalf of Donna Dierker > [[email protected]] > Sent: 10 August 2010 15:20 > To: Caret, SureFit, and SuMS software users > Subject: Re: [caret-users] Postborder.sh problem > > 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 > > ------------------------------------------------------------------------ > > _______________________________________________ > 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
