I did type the same line es mentioned in your Email and I did not put the 1.3 in quotes.
However, it is still not working:-( Any other ideas???
 
Thanks.
 
DH
 

> Subject: Re: [Freesurfer] Extracting thickness, area and folding values from Qdec
> From: dgwakeman@gmail.com
> Date: Thu, 13 Mar 2014 18:28:32 -0400
> CC: greve@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu
> To: dusanhirjak@hotmail.com
>
> I think Doug meant the 1.3. Therefore the line should be something like:
>
> mri_glmfit-sim --glmdir mc-z.neg.th13.pdf.dat --cache 1.3 --sim-sign neg
>
> What exactly did you type? (try separating it with lines instead of quotes)
>
> HTH,
> D
> On Mar 13, 2014, at 6:22 PM, Dusan Hirjak wrote:
>
> > Dear Doug,
> >
> > no, I did not put it in quotes. I just typed the mentioned command, but it is still not working.
> > I can not find the file comprising the thickness, area or folding values at peak maxima after Monte Carlo simulation.
> > Sorry for asking so many questions, but it is still not working.
> > What should I do next?
> >
> > Best regards,
> >
> > DH
> >
> > > Date: Thu, 13 Mar 2014 15:15:23 -0400
> > > From: greve@nmr.mgh.harvard.edu
> > > To: dusanhirjak@hotmail.com; freesurfer@nmr.mgh.harvard.edu
> > > Subject: Re: [Freesurfer] Extracting thickness, area and folding values from Qdec
> > >
> > > are you puttting it in quotes? If so, don't
> > > doug
> > >
> > > On 03/13/2014 01:46 PM, Dusan Hirjak wrote:
> > > > Dear Doug,
> > > >
> > > > I typed 1.3 but it is still not working.
> > > >
> > > > Any other ideas???
> > > >
> > > > Thanks for your help.
> > > >
> > > > DH
> > > >
> > > > > Date: Thu, 13 Mar 2014 12:20:57 -0400
> > > > > From: greve@nmr.mgh.harvard.edu
> > > > > To: freesurfer@nmr.mgh.harvard.edu
> > > > > Subject: Re: [Freesurfer] Extracting thickness, area and folding
> > > > values from Qdec
> > > > >
> > > > > Use 1.3 not 1,3
> > > > >
> > > > > doug
> > > > > On 03/13/2014 10:12 AM, Dusan Hirjak wrote:
> > > > > > Dear Freesurfer Experts,
> > > > > >
> > > > > > I did a correlational analysis in qdec and found several significant
> > > > > > clusters after Monte-Carlo simulation (0.05).
> > > > > > Now, I would like to extract the mean cortical thickness, area and
> > > > > > folding values (peak maximum) of each study subject above the
> > > > > > significant cluster.
> > > > > >
> > > > > > I tried to run "mri_glmfit-sim --glmdir mc-z.neg.th13.pdf.dat --cache
> > > > > > "1,3" --sim-sign neg"
> > > > > >
> > > > > > However, I got the ERROR: thresh = 1.3 not completely converted
> > > > > >
> > > > > > What am I doing wrong? Any other ideas?
> > > > > >
> > > > > > Is the pdf.dat file the right one to use???
> > > > > >
> > > > > > Thanks!
> > > > > >
> > > > > > DH
> > > > > >
> > > > > >
> > > > > >
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> > > > >
> > > > > --
> > > > > Douglas N. Greve, Ph.D.
> > > > > MGH-NMR Center
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> > > --
> > > Douglas N. Greve, Ph.D.
> > > MGH-NMR Center
> > > greve@nmr.mgh.harvard.edu
> > > Phone Number: 617-724-2358
> > > Fax: 617-726-7422
> > >
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> > >
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