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Dear Dr Mark,

This is what I have typed in the script:

#!/bin/sh

bet vol vol_brain

/Users/neuro/Desktop/fsl/Data\ Files\ FDT/fsl_course_data/scripting/im1.nii.gz

chmod +x bet_vol

./bet_vol

-uu-:---F1 bet_vol All L1 (Shell-script[sh])------------------------

Indentation setup for shell type sh

And this is what is in the shell terminal:

Last login: Thu Aug 7 13:31:47 on ttys000

[neuros-iMac-2:~] neuro% ls

#bet# Dropbox Public bet_vol~ logs

Applications Library Wine Files build.log ls

Desktop Movies bedpostx fsl.csh ls.out

Documents Music bet fsl.sh matlab

Downloads Pictures bet_vol jobs }

[neuros-iMac-2:~] neuro% ls-la

ls-la: Command not found.

[neuros-iMac-2:~] neuro% ls -la

total 1120

-rw-r--r-- 1 neuro staff 0 Sep 3 2013 #bet#

drwxrw-r--+ 56 neuro staff 1904 Aug 7 10:40 .

drwxr-xr-x 5 root admin 170 Mar 5 2013 ..

-rw-r--r-- 1 neuro staff 485133 Nov 27 2013 ..nii.gz

-rw------- 1 neuro staff 3 Mar 5 2013 .CFUserTextEncoding

-rw-r--r--@ 1 neuro staff 6148 Jul 24 18:46 .DS_Store

drwx------ 2 neuro staff 68 Aug 7 13:43 .Trash

-rw------- 1 neuro staff 273 Aug 4 15:50 .Xauthority

drwxr-xr-x 4 neuro staff 136 Mar 5 2013 .adobe

drwxr-xr-x 3 neuro staff 102 Jul 16 2013 .assistant

-rw------- 1 root staff 169 May 29 2013 .bash_history

-rw-------@ 1 neuro staff 123 Jul 8 12:11 .bash_profile

-rw-r--r--@ 1 neuro staff 123 Jul 8 12:28 .bash_profile copy.txt

drwxr-xr-x 3 neuro staff 102 Jul 4 2013 .cache

drwxr-xr-x 3 neuro staff 102 May 29 11:07 .config

-rw-r--r-- 1 neuro staff 132 Nov 27 2013 .cshrc

drwx------ 3 neuro staff 102 Mar 20 2013 .cups

drwxr-xr-x 3 neuro staff 102 Oct 3 2013 .dcm2nii

drwxr-xr-x 3 neuro staff 102 Oct 3 2013 .dcm2niigui

drwx------ 10 neuro staff 340 Aug 7 11:39 .dropbox

drwxr-xr-x 4 neuro staff 136 Jul 7 13:47 .emacs.d

drwxr-xr-x 2 neuro staff 68 May 28 2013 .fslconf

-rw------- 1 neuro staff 0 Jul 10 13:47 .lesshst

drwxr-xr-x 3 neuro staff 102 May 29 11:07 .local

-rw-r--r-- 1 neuro staff 188 Nov 27 2013 .mat

drwxr-xr-x 5 neuro staff 170 Oct 3 2013 .mricron

-rw------- 1 neuro staff 12288 Mar 21 13:42 .myscript.swp

drwxr-xr-x 3 neuro staff 102 Oct 3 2013 .npm

-rw------- 1 neuro staff 1024 Aug 4 10:28 .rnd

-rw------- 1 neuro staff 128 Mar 21 13:09 .serverauth.415

-rw------- 1 neuro staff 2416 Jul 25 18:37 .sh_history

-rw------- 1 neuro staff 4024 Mar 21 13:45 .viminfo

drwxr-xr-x 2 neuro staff 68 Mar 5 2013 Applications

drwx------+ 15 neuro staff 510 Aug 7 13:43 Desktop

drwx------+ 23 neuro staff 782 Jul 24 19:21 Documents

drwx------+ 206 neuro staff 7004 Aug 7 12:39 Downloads

drwx------@ 13 neuro staff 442 Aug 7 11:39 Dropbox

drwx------@ 50 neuro staff 1700 Jun 3 11:15 Library

drwx------+ 3 neuro staff 102 Mar 5 2013 Movies

drwx------+ 5 neuro staff 170 Apr 23 2013 Music

drwx------+ 14 neuro staff 476 Dec 17 2013 Pictures

drwxr-xr-x+ 4 neuro staff 136 Mar 5 2013 Public

drwxr-xr-x 9 neuro staff 306 May 29 11:07 Wine Files

drwxr-xr-x 4 neuro staff 136 Mar 11 10:46 bedpostx

-rw-r--r-- 1 neuro staff 0 Sep 3 2013 bet

-rw-r--r-- 1 neuro staff 130 Aug 4 15:33 bet_vol

-rw-r--r-- 1 neuro staff 28 Aug 4 15:32 bet_vol~

-rw-r--r-- 1 neuro staff 84 Jul 16 2013 build.log

-rw-r--r-- 1 neuro staff 33 May 28 2013 fsl.csh

-rw-r--r-- 1 neuro staff 48 May 28 2013 fsl.sh

drwxr-xr-x 2 neuro staff 68 Jul 31 2013 jobs

drwxr-xr-x 2 neuro staff 68 Jul 31 2013 logs

drwxr-xr-x 2 neuro staff 68 Jul 22 2013 ls

-rw-r--r-- 1 neuro staff 166 Jul 10 17:43 ls.out

drwxr-xr-x 4 neuro staff 136 Sep 26 2013 matlab

drwxr-xr-x 2 neuro staff 68 Apr 23 2013 }

[neuros-iMac-2:~] neuro% cd Desktop

[neuros-iMac-2:~/Desktop] neuro% ls

Alfred_2.3_264.zip UMMC Division of Neurosurgery

Isobel's_Master's_Project \.mkv

Niftii_Files fsl

Normal.dotm osx-2

OsiriX_Data startfsl.sh

SPM startfsl.txt

[neuros-iMac-2:~/Desktop] neuro% cd fsl

[neuros-iMac-2:~/Desktop/fsl] neuro% ls

Data Files FDT build extras

FSL instructions.docx build.log include

LICENCE config lib

README data refdoc

autoPtx_0_1_1 doc src

bin etc tcl

[neuros-iMac-2:~/Desktop/fsl] neuro% cd "Data Files FDT"

[neuros-iMac-2:~/Desktop/fsl/Data Files FDT] neuro% ls

fsl_course_data fsl_course_data 5 fsl_course_data4.tar.gz

fsl_course_data 2 fsl_course_data1.tar.gz fsl_course_data5.tar.gz

fsl_course_data 3 fsl_course_data2.tar.gz

fsl_course_data 4 fsl_course_data3.tar.gz

[neuros-iMac-2:~/Desktop/fsl/Data Files FDT] neuro% cd fsl_course_data

[neuros-iMac-2:fsl/Data Files FDT/fsl_course_data] neuro% ls

intro reg scripting seg_struc

[neuros-iMac-2:fsl/Data Files FDT/fsl_course_data] neuro% cd scripting

[neuros-iMac-2:Data Files FDT/fsl_course_data/scripting] neuro% ls

bet-vol im3.nii.gz vol0002.nii.gz

bet_vol im4.nii.gz vol0003.nii.gz

bet_vol~ im5.nii.gz vol0004.nii.gz

design.fsf settings.txt vol0005.nii.gz

example_func.nii.gz stim1.txt vol0006.nii.gz

highres.nii.gz visualmask.nii.gz vol0007.nii.gz

hr_zstat1.nii.gz vol vol0008.nii.gz

im1.nii.gz vol0000.nii.gz vol0009.nii.gz

im2.nii.gz vol0001.nii.gz zstat2.nii.gz

[neuros-iMac-2:Data Files FDT/fsl_course_data/scripting] neuro% emacs bet_vol

[neuros-iMac-2:Data Files FDT/fsl_course_data/scripting] neuro% ./bet_vol

./bet_vol: Permission denied.

[neuros-iMac-2:Data Files FDT/fsl_course_data/scripting] neuro% emacs bet_vol

[neuros-iMac-2:Data Files FDT/fsl_course_data/scripting] neuro%

Can you tell me what I am doing wrong? Tqvm!

Best regards,

Isobel French

Academic Coordinator and Research Officer

Division of Neurosurgery

Department of Surgery

Faculty of Medicine

University of Malaya

016-7937605

03-79493138

On Tue, Aug 5, 2014 at 4:03 PM, Mark Jenkinson <[log in to unmask]> wrote:

Hi,

In general we would strongly recommend against the use of sudo for new users, especially when learning how to use unix/linux. This is because there is a much greater danger of removing/corrupting important files when things are run as sudo. So please do not use sudo in general (there might be occasions when you install new software when it is necessary, but it should be clearly indicated in that case, and you should not need it for your own scripts and analyses).

In order to get to the bottom of this problem we need to see the result of running "ls -la" in the directory that your script is in, and when also need to know exactly what command you are typing into the terminal. It would also be helpful to see the contents of the script file.

All the best,

Mark

On 4 Aug 2014, at 08:36, Isobel French <[log in to unmask]>

wrote:

H Erdem,

I have tried what you said but still the same response: 'Permission denied'. What could be the problem here?

Best regards,

Isobel French
Academic Coordinator and Research Officer
Division of Neurosurgery

Department of Surgery

Faculty of Medicine

University of Malaya

016-7937605

03-79493138

On Mon, Aug 4, 2014 at 2:35 PM, Erdem Ergen <[log in to unmask]> wrote:

Do you execute script with "sudo" ? Maybe you should type it as "sudo chmod +x bet_vol" "sudo ./bet_vol" then system can request root password, after you type it, system should execute script.

2014-08-04 7:29 GMT+03:00 Isobel French <[log in to unmask]>:

Dear Dr Stephen and Erdem,

I have done both of what you have suggested. However, i still get the same response which is 'Permission denied". I really do not know what it is that I am doing wrong. Please advise. Thanks.

Best regards,

Isobel French
Academic Coordinator and Research Officer
Division of Neurosurgery

Department of Surgery

Faculty of Medicine

University of Malaya

016-7937605

03-79493138

On Fri, Jul 25, 2014 at 7:12 PM, Erdem Ergen <[log in to unmask]> wrote:

Actually this subject is not related with MRI subject exactly. You can find lots of information about operating system commands in linux/unix forums such as "http://stackoverflow.com/questions/18960689/ubuntu-says-bash-program-permission-denied".

Just give permission to the "./bet_vol" script/program as typing "chmod +x bet_vol".

--
Erdem Ergen
Bilg. Müh.