You are not doing it right.

That script is to be run inside a script.

Create a file try.sh paste that lines in try.sh Execute chmod +x try.sh Run ./try.sh

good luck

PPJ

Sent from my Nokia phone @E71 -----Msg original----- De: Marina.Lopez@crccorp.es Enviada: 27/04/2009 06:00:30 Assunto: Re: Re: Re: RES: [Freesurfer] Individual thickness data extraction from plot

Hi Nick and Pedro Paulo,

Thanks a lot for your help and explanations. I have tried to do what you told me but still find only one asc file.

I am copying to you what I did, just in case you could detect my mistake:

(mailto:marina@linux4:~/FS$) marina@linux4:~/FS$ export SUBJECTS_DIR=/data/User/marina/FS Where my subjects data folders are (mailto:marina@linux4:~/FS$) marina@linux4:~/FS$ echo $SUBJECTS_DIR /data/User/marina/FS (mailto:marina@linux4:~/FS$) marina@linux4:~/FS$ #!/bin/bash        Writing this will imply using bash? (mailto:marina@linux4:~/FS$) marina@linux4:~/FS$ cd qdec/LHTOTS_graficProva    Where my specific qdec analysis was performed (from which plot data were extracted)  (mailto:marina@linux4:~/FS/qdec/LHTOTS_graficProva$) marina@linux4:~/FS/qdec/LHTOTS_graficProva$ set numsubject =  53    my number of subjects in this analysis (mailto:marina@linux4:~/FS/qdec/LHTOTS_graficProva$) marina@linux4:~/FS/qdec/LHTOTS_graficProva$ for i in `seq 1 $numsubject`

do           mri_convert --frame $i y.mgh ../../fsaverage/surf/lh.$i.mgh           mris_convert -c $i.mgh ../../fsaverage/surf/lh.inflated lh.$i.asc     done

mri_convert --frame 1 y.mgh ../../fsaverage/surf/lh.1.mgh $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ reading from y.mgh... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) keeping frame 1 writing to ../../fsaverage/surf/lh.1.mgh... reading group avg surface area 822 cm^2 from file (mailto:marina@linux4:~/FS/qdec/LHTOTS_graficProva$) marina@linux4:~/FS/qdec/LHTOTS_graficProva$

When I look for my asc files in LHTOTS_graficProva  I only find lh.1.asc and the data inside this folder does not correspond to any of my subjects, as far as I have checked it.

Thanks again for all your help! i really need it.

Marina

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