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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. >> > > >