Hi Kwliu, There are multiple ways of doing this. To avoid unnecessary confusion, I'll tell you the easiest one.
If you don't already have it on your disk somewhere, download this tutorial dataset: CARET_TUTORIAL_SEPT06.zip http://sumsdb.wustl.edu/sums/download.do?archive_id=6595030 Unzip it. cd $ATLAS_DIR caret5 deformed_Human.$CASE.$HEM_FLAG.73730.register.73730.spec File: Open Data File: Paint file and navigate to CARET_TUTORIAL_SEPT06/Human.PALS_B12.BOTH.COMPOSITE_Areas_Functional_WS.73730.paint File: Open Data File: Area Color File and navigate to CARET_TUTORIAL_SEPT06/Human.Cerebral.COMPOSITE_OrbFrontDistinct_WS_MWblack.areacolor D/C: Overlay/Underlay: Primary Overlay: Paint Select Brodmann column There are also borders for the Brodmann areas in the tutorial dataset, so those might be handier if you want to concurrently view fMRI activations. You might find it easier to use the spec files and scenes in the tutorial dataset, and then open your subjects' data (e.g., deformed midthickness surface, surface shape file, deformed thickness, or fMRI) on the already prepared scene. This is where it gets highly study-specific, and you generally need to have some knowledge of Caret's visualization and analysis capabilities. There is a PDF in the dataset linked above, and if you haven't taken this tutorial, now might be a good time to consider it. This is the fun part! Donna On 08/23/2010 09:41 AM, Kuk Wai Liu wrote: > 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
