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.auescreveu:
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