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.Gautam@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:ppj@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.Gautam@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