Hi Donna, I've run the preborder and postborder scripts and got the output. I was wondering if you could point me in the right direction as to how to view the Brodmann areas on the output.
Regards Kwliu ________________________________________ From: Kuk Wai Liu Sent: 18 August 2010 15:43 To: Donna Dierker Subject: RE: [caret-users] Postborder.sh problem Hi Donna, Thank you so much for all your help on this long running problem. Regards Kwliu ________________________________________ From: Donna Dierker [[email protected]] Sent: 18 August 2010 15:34 To: Kuk Wai Liu Subject: Re: [caret-users] Postborder.sh problem Hi Kwliu, Looks good. You're going to get errors like this on all left hems: WARNING: coordinate file deformed_Human.003.L.SPHERICAL.73730.MWS.SPHERE_CYCLE4.ALIGNED.73730.coord has 73711 crossovers after deformation. Don't worry about it. Ones like this are cause for concern when the number of crossovers exceeds 10: WARNING: coordinate file deformed_deformed_Human.003.L.Midthickness_711-2B.mws.73730.coord has 2 crossovers after deformation. Yep -- now edit your scripts to include the full list of subject directories. Donna On 08/18/2010 03:50 AM, Kuk Wai Liu wrote: > Hi Donna, > > Having run the Postborder script i haven't seen any more errors, although > there are 2 warnings in the outfput. If you could take a look, i would be > most gratefuul. > > To include the rest of the subjects, do i just include the subject names into > the DIRLIST of both the preborder and postborder scripts and run these > scripts again? > > Regards > > Kwliu > ________________________________________ > From: Donna Dierker [[email protected]] > Sent: 16 August 2010 15:55 > To: Kuk Wai Liu > Subject: Re: [caret-users] Postborder.sh problem > > + sed s/Medial/Med/g Human.003.L.LANDMARKS.borderproj > + mv Human.003.L.LANDMARKS.borderproj.rev Human.003.L.LANDMARKS.borderproj > + cp Human.003.L.LANDMARKS.borderproj Human.003.L.LANDMARKS.updated.borderproj > + /home/kukwai.liu/Desktop/caret/bin_linux/caret_command > -surface-border-unprojection deformed_Human.003.L.Midthickness_711-2B.coord > Human.003.L.CLOSED.73730.topo Human.003.L.LANDMARKS.borderproj > Human.003.L.LANDMARKS.border > > Looks good to me. Have a look at the resulting borders; tweak, if needed; > and save the tweaks as > Human.003.L.LANDMARKS.updated.borderproj. > > Then try running the postborder.sh script. > > > On 08/16/2010 06:43 AM, Kuk Wai Liu wrote: > >> Hi Donna, >> >> I've attached the preborder.out.txt file to this email after running the >> latest script you sent me. >> >> Regards >> >> Kwliu >> ________________________________________ >> From: Donna Dierker [[email protected]] >> Sent: 12 August 2010 21:39 >> To: Kuk Wai Liu >> Subject: Re: [caret-users] Postborder.sh problem >> >> Hi Kwliu, >> >> The preborder.out.txt shows no problems executing the sed and mv >> statements that apply this fix; however, on closer inspection, it looks >> like this is just a good, old-fashioned bug. Okay, maybe not good. >> >> This is the line that is the culprit, I think: >> >> 239a240 >> > cp $OUTBORDERPROJ >> Human.$CASE.$HEM_FLAG.LANDMARKS.$BORDER_UPDATE_STRING.borderproj >> >> Moving it down below the sed statement should fix this, but requires a >> variable name change: >> >> 315,316c316 >> < cp $BORDERPROJ_IN >> Human.$CASE.$HEM_FLAG.LANDMARKS.$BORDER_UPDATE_STRING.borderproj >> >> These edits have been made to this link: >> >> http://brainmap.wustl.edu/pub/donna/UK/MANCHESTER/preborder.sh >> login pub >> password download >> >> Do you mind trying it again? (I'm less worried about the output file >> this time around, but it wouldn't hurt.) >> >> Donna >> >> On 08/12/2010 07:14 AM, Kuk Wai Liu wrote: >> >> >>> Hi Donna, >>> >>> I enclose the preborder.out.txt file with this email. >>> >>> Regards >>> >>> Kwliu >>> ________________________________________ >>> From: Donna Dierker [[email protected]] >>> Sent: 11 August 2010 16:59 >>> To: Kuk Wai Liu >>> Subject: Re: [caret-users] Postborder.sh problem >>> >>> Hi Kwliu, >>> >>> I have modified your preborder.sh script slightly: >>> >>> http://brainmap.wustl.edu/pub/donna/UK/MANCHESTER/preborder.sh >>> login pub >>> password download >>> >>> I have removed all subjects except 003 from the list. And I have >>> changed the name of the HTML document: >>> >>> < HTMLDOC=$HTMLDIR/003_troubleshoot.html >>> --- >>> > HTMLDOC=$HTMLDIR/views.html >>> >>> Try running this script in the same directory where you ran it >>> previously; however, instead of typing just "preborder.sh", do this: >>> >>> preborder.sh >& preborder.out.txt >>> >>> And send me preborder.out.txt (via upload or email) when it is done running. >>> >>> Note that this will blow away any previously tweaked 003 left or right >>> borderproj files. So back those up if they took any time to tweak. >>> >>> I want to see the standard output and error near the lines that are >>> supposed to make the border names match (i.e., Medial -> Med). >>> >>> Thanks much, >>> >>> Donna >>> >>> On 08/11/2010 08:52 AM, Donna Dierker wrote: >>> >>> >>> >>>> Hmmm. I looked at your preborder.sh script, and as you said, it >>>> includes those key lines. >>>> >>>> And here is what happens when I apply them to your borderproj: >>>> >>>> it.wustl.edu 6% sed 's/Medial/Med/g' >>>> Human.003.L.LANDMARKS.updated.borderproj > >>>> Human.003.L.LANDMARKS.updated.borderproj.rev >>>> it.wustl.edu 7% diff Human.003.L.LANDMARKS.updated.borderproj.rev >>>> Human.003.L.LANDMARKS.updated.borderproj >>>> 195c195 >>>> < 3 117 FLATTEN.HOLE.MedWall 25.000000 1.000000 0.000000 0.000000 >>>> --- >>>> > 3 117 FLATTEN.HOLE.MedialWall 25.000000 1.000000 0.000000 0.000000 >>>> 793c793 >>>> < 10 62 LANDMARK.MedWall.DORSAL 25.000000 1.000000 0.000000 0.000000 >>>> --- >>>> > 10 62 LANDMARK.MedialWall.DORSAL 25.000000 1.000000 0.000000 0.000000 >>>> 857c857 >>>> < 11 39 LANDMARK.MedWall.VENTRAL 25.000000 1.000000 0.000000 0.000000 >>>> --- >>>> > 11 39 LANDMARK.MedialWall.VENTRAL 25.000000 1.000000 0.000000 0.000000 >>>> >>>> It should have worked. >>>> >>>> I would like to understand why it did not, which I think will entail >>>> your re-running preborder.sh on JUST case 003 and capturing the output >>>> for me. >>>> >>>> But I think it is time to take this thread off-list, because I think >>>> this problem is probably rare. Once we figure it out, and I can post >>>> the upshot to the list. >>>> >>>> I will email you offlist about how to capture the output. >>>> >>>> On 08/11/2010 04:56 AM, Kuk Wai Liu wrote: >>>> >>>> >>>> >>>> >>>>> Hi Donna, >>>>> >>>>> I've uploaded my preborder script onto the link you provided me. >>>>> >>>>> I do have the lines in my preborder script: >>>>> >>>>> # Sync source border names with target >>>>> sed 's/Medial/Med/g' $BORDERPROJ_IN > $BORDERPROJ_IN.rev >>>>> mv $BORDERPROJ_IN.rev $BORDERPROJ_IN >>>>> >>>>> Regards >>>>> >>>>> Kwliu >>>>> ________________________________________ >>>>> From: [email protected] >>>>> [[email protected]] on behalf of Donna Dierker >>>>> [[email protected]] >>>>> Sent: 10 August 2010 20:25 >>>>> To: Caret, SureFit, and SuMS software users >>>>> Subject: Re: [caret-users] Postborder.sh problem >>>>> >>>>> Kwliu, >>>>> >>>>> I figured out what is causing the problem. Your borderproj has these >>>>> landmarks: >>>>> >>>>> 10 62 LANDMARK.MedialWall.DORSAL 25.000000 1.000000 0.000000 0.000000 >>>>> 11 39 LANDMARK.MedialWall.VENTRAL 25.000000 1.000000 0.000000 0.000000 >>>>> >>>>> But the target borders are named LANDMARK.MedWall.DORSAL and >>>>> LANDMARK.MedWall.VENTRAL. There is a step in the preborder.sh script, >>>>> in the loop that does the border variability, that fixes this >>>>> inconsistency: >>>>> >>>>> # Sync source border names with target >>>>> sed 's/Medial/Med/g' $BORDERPROJ_IN > $BORDERPROJ_IN.rev >>>>> mv $BORDERPROJ_IN.rev $BORDERPROJ_IN >>>>> >>>>> Does your preborder.sh script have those lines in it? I'm wondering if >>>>> you are using an older version of preborder.sh, or if you somehow had >>>>> the border variability loop disabled. >>>>> >>>>> Dpmma >>>>> >>>>> On 08/10/2010 11:00 AM, Donna Dierker wrote: >>>>> >>>>> >>>>> >>>>> >>>>> >>>>>> 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
