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 a
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Hi experts,
I am using qdec software for the statistic of LGI. I have created the .Qdecrc
file. However, when I set Monte Carlo Null-Z Simulation (fwhm=10), there is an
error: "Error running mri_surfcluster, Error: fwhm out-of-range(<1 or >30)".
Then
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, a
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 th
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
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
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 er
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outdated version of Qdec?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
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 w
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 wrote:
>
> Hi Krista,
>
>
Hi Zheng, qdec is not longer being supported. Use the "command line"
stream, see here
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
On 3/12/19 7:47 AM, 郑凤莲 wrote:
>
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>
> Hi experts,
> I am using qdec software for the statistic of LGI. I
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Hi experts,
To give more detail re my previous post I have created the .Qdecrc
file in my Subjects directory and QDEC folder, which contains one line
: MEASURE1
= pial_lgi . However, LGI is still not appearing in the drop down menu on
QDEC.
When I
: [Freesurfer] LGI in QDEC menu please respond soon
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Hi experts,
To give more detail re my previous post I have created the .Qdecrc file in
my Subjects directory and QDEC folder, which contains one line : MEASURE1 =
pial_lgi . However, LGI is still not
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
>
> *From: *Avi Gharehgazlou
> *Sent: *Tuesday, April 23, 2019 12:06 PM
> *To: *Freesurfer support list
> *Subject: *[Freesurfer] LGI in QDEC menu please respond soon
>
&g
: Freesurfer support list
Subject: Re: [Freesurfer] LGI in QDEC menu please respond soon
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Yes I did
On Tue, Apr 23, 2019 at 12:59 PM Pan Yunzhi wrote:
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Did you run this command “recon-all -s my_subject_id -qcache
pial_lgi into .Qdecrc file.
>
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
>
> *From: *Avi Gharehgazlou
> *Sent: *Tuesday, April 23, 2019 1:34 PM
> *To: *Freesurfer support list
> *Subject: *Re: [Freesurfer
23, 2019 2:27 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] LGI in QDEC menu please respond soon
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Where should I type "ctrl +H"? In my linux terminal (in QDEC) folder? when I do
that it gives this error: bash: ctrl + H: command not f
t: Re: [Freesurfer] LGI in QDEC menu please respond soon
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Where should I type "ctrl +H"? In my linux terminal (in QDEC) folder? when I do
that it gives this error: bash: ctrl + H: command not found
When I open my .Qdecrc file (with geddit) I s
harehgazlou
> *Sent: *Tuesday, April 23, 2019 2:27 PM
> *To: *Freesurfer support list
> *Subject: *Re: [Freesurfer] LGI in QDEC menu please respond soon
>
>
>
> *External Email - Use Caution*
>
> Where should I type "ctrl +H"? In my linux terminal (in QDE
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