Hi Marie, It appears that the problem was the program that I was using to create the . Qdecrc file. I was using Text Wrangler. I switched to TextMate and the problem has been resolved.
Thanks so much for your help! Krista On Tue, Mar 4, 2014 at 8:27 PM, Marie Schaer <marie.sch...@unige.ch> wrote: > > Hi Krista, > > Did you verify that your changes to .Qdecrc were properly saved? As long > as the command more ~/.Qdecrc doesn't give you a line with MEASURE1 = > pial_lgi, then you'll not have it in qdec menu. And version should not be > an issue. How do you edit the .Qdecrc file? Did you check to see whether > opening qdec had any effect on the line that you added (by running the > command more ~/.Qdecrc before and after opening qdec)? > > I need you to explain me a bit more how you did, otherwise it's > difficult for me to help you. > > Marie > > > On Mar 4, 2014, at 5:20 PM, krista kelly <krista.kell...@gmail.com> > wrote: > > Hi Marie, > > Thanks for the the response. I've done that a few times and still, the > lgi option does not come up in qdec as a measure. Could it be that I'm > using an outdated version of Qdec? My freesurfer v is 5.3 so unless I need > to update qdec on its own, I don't think that this is the problem. Any > other ideas? > > Best, > Krista > > > On Fri, Feb 28, 2014 at 4:16 PM, Marie Schaer <marie.sch...@unige.ch>wrote: > >> >> Hi Krista, >> >> You need to add the following line in your .Qdecrc: >> MEASURE1 = pial_lgi >> and save the change. >> >> I don't think it matters where you add it, I have it before all the >> Qdec lines. >> >> Then start qdec again, it should work. If not, check again the .Qdecrc >> file, and look whether starting qdec erases the added line. >> >> Let me know, >> >> Marie >> >> On Feb 28, 2014, at 1:09 PM, krista kelly <krista.kell...@gmail.com> >> wrote: >> >> Hi Marie, >> >> The ?h.pial_lgi.fwhm?.fsaverage.mgh files in the surf folder are there. Here >> is the output when I run more ~/.Qdecrc: >> >> # This file is automatically generated by the application >> # If you change any lines or add new lines, note that all >> # coments and empty lines will be deleted. Every line has >> # to be in format: >> # key = value >> # >> Qdec1\Dialogs\ExitApplication = 0 >> Qdec1\Dialogs\SendErrorLog = 0 >> Qdec1\Geometry\MainPanelSize = 375 >> Qdec1\Geometry\MainPanelVisibility = 1 >> Qdec1\Geometry\SaveUserInterfaceGeometry = 1 >> Qdec1\Geometry\SecondaryPanelSize = 250 >> Qdec1\Geometry\SecondaryPanelVisibility = 0 >> Qdec1\Geometry\ViewPanelPosition = Right >> Qdec1\Geometry\WindowGeometry = 900x700+787+1 >> Qdec1\MRU\File00 = >> /Applications/freesurfer/subjects/qdec/qdec.tableNoBV45orBV46.dat >> Qdec1\MRU\File00Cmd = LoadDataTable >> Qdec1\RunTime\MostRecentVersionLaunched = 1.4 >> Qdec1\RunTime\PrintTargetDPI = 100.000000 >> Qdec1\RunTime\ShowBalloonHelp = 1 >> Qdec1\RunTime\ShowSplashScreen = 1 >> Qdec1\RunTime\ToolbarFlatButtons = 1 >> Qdec1\RunTime\ToolbarFlatFrame = 1 >> >> >> Thanks! >> Krista >> >> >> On Wed, Feb 26, 2014 at 7:12 PM, Marie Schaer <marie.sch...@unige.ch>wrote: >> >>> >>> Hi Krista, >>> >>> Can you please run: >>> more ~/.Qdecrc >>> and copy paste the output for me? >>> >>> The "rm: No match" issue in the qcache is not a problem, it's >>> independent from the issue of listing lGI in the qdec menu. Even with the >>> no match output in the qcache command, all the files should have been >>> created properly (you can check that you have some files named >>> ?h.pial_lgi.fwhm?.fsaverage.mgh in the surf folder of one of your subject >>> if you want to be sure. >>> >>> Let me know, >>> >>> Marie >>> >>> On Feb 25, 2014, at 6:55 PM, krista kelly <krista.kell...@gmail.com> >>> wrote: >>> >>> Hi Marie, >>> >>> I have tried adding the .Qdecrc file into the home folder as well but >>> that does not work. The lgi measure is not appearing in the dropdown menu >>> in the design tab in Qdec. Further, when I ran recon-all -qcache -measure >>> pial_lgi, there were error messages saying 'rm: No match', although the >>> -qcache exited without errors. Could this be the problem? If not, does >>> anyone have any ideas? >>> >>> Thanks! >>> Krista >>> >>> >>> On Mon, Feb 24, 2014 at 4:29 PM, Marie Schaer <marie.sch...@unige.ch>wrote: >>> >>>> >>>> Hi Krista, >>>> >>>> Can you be more specific about what is not coming up? If lGI not listed >>>> in the menu of qdec, look at the following post: >>>> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg33427.html >>>> >>>> Otherwise can you describe more precisely the issue? >>>> >>>> Best, >>>> >>>> Marie >>>> >>>> On Feb 24, 2014, at 1:21 PM, krista kelly <krista.kell...@gmail.com> >>>> wrote: >>>> >>>> > Hello, >>>> > >>>> > I followed instructions on how to incorporate the lgi_pial measure >>>> into QDec, however, it's not coming up when I go to choose this as a >>>> measure. I ran recon-all -s my_subject_id -qcache -measure pial_lgi and >>>> created a Qdecrc file in my $SUBJECTS_DIR directory. Does anyone have any >>>> insight as to why this may be occurring? >>>> > >>>> > Thanks, >>>> > Krista >>>> > _______________________________________________ >>>> > 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. >>>> >>>> >>> >>> >> >> > >
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