Hi,
I copied the default average subject from $FREESURFER_HOME/subjects dir
to my analysis dir.
Then, I make a FSGD file and some contrast matrices and put them into my
analysis dir.
After that, I start to run group analysis.
But, when I type the following commands:
mris_preproc --fsgd noise_0.5-1-5.fsgd --target fsaverage -- hemi lh --meas
thickness --out lh.noise_0.5-1-5.thickness.00.mgh
The terminal shows:
ERROR: flag -- not recognized
Now, I have two problems want to ask.
1) What's wrong about the commands that I type? And, how to solve the
problem?
2) I found this commands from the FreeSurfer web. And, I'm confused about
that two ways to do analysis.
One is cached (qcached) data, and the other is uncached data. What's
way is suitable to my subjects? (My subjects is one factor and three
levels, had run QDEC before, but QDEC is not good job to analysis, and, I
want to change the analysis method from QDEC to DODS)
So, which way do I choose to analysis my subjects?? Idon't understand
the differences from them.
Thank you in advance!
Feng-Xian
On Fri, 26 Jun 2009 15:25:12 -0400, Nick Schmansky wrote
> in general, it is not necessary to run make_average_subject prior to
> performing an analysis. using the default average subject that
> freesurfer provides, named 'fsaverage', is sufficient for most cases,
> because it doesnt affect the analysis, its only used as a target upon
> which to project results. the 'fsaverage' subject is in the
> $FREESURFER_HOME/subjects dir, and you should copy it to your own
> SUBJECTS_DIR prior to performing any group analysis.
>
> Nick
>
> On Fri, 2009-06-26 at 10:48 +0800, Feng-Xian wrote:
> > Hi,
> >
> > I know I wont to do QDEC now, so I want to change the method of group
> > analysis from QDEC to the web you tell me. But, I did QDEC before.
> >
> > Before I do DODS, should I do make_average_subject to view the result of
my
> > subjects? Or, I have another method to view the results??
> >
> > Thank you in advance!
> >
> > Feng-Xian
> >
> >
> >
> >
> > On Thu, 25 Jun 2009 12:01:21 -0400, Nick Schmansky wrote
> > > Feng-xian,
> > >
> > > I should also mention that i dont think creating your own average
> > > subject will solve the problem you describe, where you need to work
with
> > > three levels in your group. for that, you wont be able to use qdec,
> > > but will need to run things manually. these pages give examples:
> > >
> > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
> > >
> > > and note one of them is 1 Factor, 3 Levels.
> > >
> > > Nick
> > >
> > > On Thu, 2009-06-25 at 11:55 -0400, Nick Schmansky wrote:
> > > > Feng-Xian,
> > > >
> > > > It appears that you do not have permission on your system to change
the
> > > > limits. So you will have to edit the scripts make_average_volume,
> > > > make_average_surface and make_average_subject to comment out
the 'limit'
> > > > line, so that it looks like this:
> > > >
> > > > #limit descriptors unlimited
> > > >
> > > >
> > > > Nick
> > > >
> > > > On Thu, 2009-06-25 at 15:51 +0800, Feng-Xian wrote:
> > > > > Hi,
> > > > >
> > > > > I have a problem with make_average_subject.
> > > > >
> > > > > After running all commands (including ln -s
> > > > > $FREESURFER_HOME/subjects/fsaverage
> > > > > and recon-all -s <subjid> -qcache for all my subjects) about
running
> > QDEC, I
> > > > > found that QDEC could not analysis my group.
> > > > >
> > > > > Because the group have 1 factor and three levels, QDEC can't run.
> > > > >
> > > > > So, I want to change the method of analysis from QDEC to DODS.
> > > > >
> > > > >
> > > > > I had a fsaverage file when I running QDEC, but the fsaverage did
not
> > use my
> > > > > subjects to make.
> > > > >
> > > > > So, can I use the fsaverage file to run DODS?
> > > > >
> > > > > If not, I should make a new fsaverage with my subjects.
> > > > >
> > > > > But, I encounter the problem about make_average_subject.
> > > > >
> > > > >
> > > > > When I type:
> > > > >
> > > > > make_average_subject --subects <subjid1> <subjid2> ...
> > > > >
> > > > > the terminal show that:
> > > > >
> > > > > limit: descriptors: Can't remove limit
> > > > >
> > > > >
> > > > > What's wrong about the command I type? And, how to solve the
problem?
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > Thank you in advance!
> > > > >
> > > > > Feng-Xian
> > > > >
> > > > >
> > > > > -------------------------------------------------
> > > > > Chang Gung University Mail Server Web Mail system
> > > > > By Chang-Gung University Information Center
> > > > > (http://www.cgu.edu.tw/ic/)
> > > > >
> > > > > _______________________________________________
> > > > > Freesurfer mailing list
> > > > > Freesurfer@nmr.mgh.harvard.edu
> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > > >
> > > > >
> >
> >
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> > Chang Gung University Mail Server Web Mail system
> > By Chang-Gung University Information Center
> > (http://www.cgu.edu.tw/ic/)
> >
> >
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