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.kelly16@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.Schaer@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.kelly16@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.Schaer@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.kelly16@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.