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.lo...@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:mar...@linux4:~/FS$) mar...@linux4:~/FS$ export SUBJECTS_DIR=/data/User/marina/FS Where my subjects data folders are (mailto:mar...@linux4:~/FS$) mar...@linux4:~/FS$ echo $SUBJECTS_DIR /data/User/marina/FS (mailto:mar...@linux4:~/FS$) mar...@linux4:~/FS$ #!/bin/bash Writing this will imply using bash? (mailto:mar...@linux4:~/FS$) mar...@linux4:~/FS$ cd qdec/LHTOTS_graficProva Where my specific qdec analysis was performed (from which plot data were extracted) (mailto:mar...@linux4:~/FS/qdec/LHTOTS_graficProva$) mar...@linux4:~/FS/qdec/LHTOTS_graficProva$ set numsubject = 53 my number of subjects in this analysis (mailto:mar...@linux4:~/FS/qdec/LHTOTS_graficProva$) mar...@linux4:~/FS/qdec/LHTOTS_graficProva$ 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:mar...@linux4:~/FS/qdec/LHTOTS_graficProva$) mar...@linux4:~/FS/qdec/LHTOTS_graficProva$ 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 Av�s | Aquest correu i qualsevol fitxer adjunt existent, contenen informaci� confidencial que van dirigits �nica i exclusivament al seu destinatari. Queda totalment prohibit realitzar-ne c�pies, aix� com difondre el seu contingut a altres persones que no siguin les destin�taries. Aviso | Este correo y cualquier fichero adjunto existente, contienen informaci�n confidencial que va dirigida �nica y exclusivamente a su destinatario. Est� completamente prohibido hacer copias, as� como difundir su contenido a otras personas que no sean los destinatarios. This message and any files attached are confidential. It is intended solely for the use of the addressee(s). If you are not the intended recipient of this e-mail, please note that any review, dissemination, disclosure, alteration, printing, copying or transmission of this e-mail and/or any file transmitted with it, is prohibited and may be unlawful. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
