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<mailto: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 Could it be that I'm using an outdated version of Qdec?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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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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