Maybe your fsaverage directory is not in the default place
I've updated the wiki page
# Script created December 2007 by Pedro Paulo Jr.
# Use with Freesurfer 4.x
# Updated: 24/03/2010
set FSAVERAGE_DIR = "../../fsaverage" #set fsaverage dir
cd #your directory where qdec data are stored.
set numsubject = 17 #your value
for i in `seq 1 $numsubject`
do
mri_convert --frame $i y.mgh $FSAVERAGE_DIR/surf/lh.$i.mgh
mris_convert -c $i.mgh $FSAVERAGE_DIR/surf/lh.inflated lh.$i.asc
done
-----------------------------------------------------------
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
--- Novo Netfilter 3.4 www.Netfilter.com.br
--- Novo Netfilter Small Business
Em 24 de março de 2010 06:30, Prapti Gautam <prapti.gau...@anu.edu.au>escreveu:
> I run mri_glmfit the usual way, as detailed in the GroupAnalysis tutorial..
> I couldn't get the script to run either with qdec or mri_glmfit output
> directory, so figured it must be a permission issue with fsaverage?
>
>
>
> -----Original Message-----
> From: Pedro Paulo de Magalhães Oliveira Junior [mailto:
> p...@netfilter.com.br]
> Sent: Wed 3/24/2010 7:27 PM
> To: Prapti Gautam
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] extract thickness values for vertex
>
> Maybe I need to change that script.
>
> How do you usually run you glmfit analysis?
>
> 2010/3/24, Prapti Gautam <prapti.gau...@anu.edu.au>:
> > Dear FreeSurfers,
> >
> >
> > Is there a way to extract thickness values for individual subjects for a
> > vertex that are obtained after analyses with mri_glmfit? I have seen a
> > script that does this with qdec - but most of the analyses I run are on
> > mri_glmfit, so was wondering if the script on the user contribution
> > section needs to be modified for mri_glmfit. I ran the script where the
> > output files are located and get the following error:
> >
> >
> >
> >
> >
> > ERROR: failure writing ./media...../fsaverage/surf/lh.1.mgh
> >
> >
> >
> > Reading group avg surface area 864 cm^2 from file
> >
> >
> >
> > mghRead( /media/...../fsaverage/suf/lh.1.mgh, -1) : could not open file
> >
> >
> >
> >
> >
> >
> >
> > Is this simply a permission issue with the fsaverage folder?
> >
> >
> >
> >
> >
> > Thanks for your help,
> >
> >
> >
> >
> >
> > Prapti
> >
> >
> >
> >
> >
> >
> >
> >
>
>
> --
> -----------------------------------------------------------
> Pedro Paulo de M. Oliveira Junior
> Diretor de Operações
> Netfilter & SpeedComm Telecom
> --- Novo Netfilter 3.4 www.Netfilter.com.br
> --- Novo Netfilter Small Business
>
>
>
>
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