thank you so much that has sorted it

On 24 April 2012 12:41, Mark Jenkinson <[log in to unmask]> wrote:

Dear Michael,

In this email you seem to be missing the ">>" between the "echo $g" and the "template_list".
This would definitely cause the error you are seeing.
You need to have a line of the form:
 "echo $g >> template_list"
and then it should work.
Your previous email had such a line, but maybe there is something odd about it and
you should look at this.

All the best,
       Mark

On 24 Apr 2012, at 12:37, Michael Maxwell wrote:

> The command line in my previous email (found below) is from your website, my actual command line and the error message that appears is as follows:
>
>
> macbook-air-3:~ volumetry$ cd desktop
> macbook-air-3:desktop volumetry$ cd vbm-t1dm
> iain-wilkinsons-macbook-air-3:vbm-t1dm volumetry$ for g in HV115047.nii.gz HV115053.nii.gz HV115059.nii.gz HV115158.nii.gz HV115397.nii.gz HV115658.nii.gz HV115665.nii.gz HV116122.nii.gz HV116137.nii.gz HV116999.nii.gz HV118436.nii.gz HV119832.nii.gz HV119875.nii.gz \ NN115427.nii.gz NN115667.nii.gz NN117211.nii.gz NN117930.nii.gz NN117946.nii.gz NN118162.nii.gz NN118326.nii.gz NN118568.nii.gz NN118627.nii.gz NN119206.nii.gz NN120800.nii.gz NN120862.nii.gz NN121186.nii.gz \ P114320.nii.gz P114467.nii.gz P114547.nii.gz P114609.nii.gz P115013.nii.gz P115259.nii.gz P117214.nii.gz P117585.nii.gz P119627.nii.gz P119733.nii.gz P119873.nii.gz P121192.nii.gz P121317.nii.gz \ UP115148.nii.gz UP115394.nii.gz UP115413.nii.gz UP115523.nii.gz UP117318.nii.gz UP117410.nii.gz UP118102.nii.gz UP118117.nii.gz UP118128.nii.gz UP118318.nii.gz UP118872.nii.gz UP118887.nii.gz UP119867.nii.gz; do
>> echo $g
>>
>> template_list
>> done
> HV115047.nii.gz
> -bash: template_list: command not found
> HV115053.nii.gz
> -bash: template_list: command not found
> HV115059.nii.gz
> -bash: template_list: command not found
> HV115158.nii.gz
> -bash: template_list: command not found
> HV115397.nii.gz
> -bash: template_list: command not found
> HV115658.nii.gz
> -bash: template_list: command not found
> HV115665.nii.gz
> -bash: template_list: command not found
> HV116122.nii.gz
> -bash: template_list: command not found
> HV116137.nii.gz
> -bash: template_list: command not found
> HV116999.nii.gz
> -bash: template_list: command not found
> HV118436.nii.gz
> -bash: template_list: command not found
> HV119832.nii.gz
> -bash: template_list: command not found
> HV119875.nii.gz
> -bash: template_list: command not found
> NN115427.nii.gz
> -bash: template_list: command not found
> NN115667.nii.gz
> -bash: template_list: command not found
> NN117211.nii.gz
> -bash: template_list: command not found
> NN117930.nii.gz
> -bash: template_list: command not found
> NN117946.nii.gz
> -bash: template_list: command not found
> NN118162.nii.gz
> -bash: template_list: command not found
> NN118326.nii.gz
> -bash: template_list: command not found
> NN118568.nii.gz
> -bash: template_list: command not found
> NN118627.nii.gz
> -bash: template_list: command not found
> NN119206.nii.gz
> -bash: template_list: command not found
> NN120800.nii.gz
> -bash: template_list: command not found
> NN120862.nii.gz
> -bash: template_list: command not found
> NN121186.nii.gz
> -bash: template_list: command not found
> P114320.nii.gz
> -bash: template_list: command not found
> P114467.nii.gz
> -bash: template_list: command not found
> P114547.nii.gz
> -bash: template_list: command not found
> P114609.nii.gz
> -bash: template_list: command not found
> P115013.nii.gz
> -bash: template_list: command not found
> P115259.nii.gz
> -bash: template_list: command not found
> P117214.nii.gz
> -bash: template_list: command not found
> P117585.nii.gz
> -bash: template_list: command not found
> P119627.nii.gz
> -bash: template_list: command not found
> P119733.nii.gz
> -bash: template_list: command not found
> P119873.nii.gz
> -bash: template_list: command not found
> P121192.nii.gz
> -bash: template_list: command not found
> P121317.nii.gz
> -bash: template_list: command not found
> UP115148.nii.gz
> -bash: template_list: command not found
> UP115394.nii.gz
> -bash: template_list: command not found
> UP115413.nii.gz
> -bash: template_list: command not found
> UP115523.nii.gz
> -bash: template_list: command not found
> UP117318.nii.gz
> -bash: template_list: command not found
> UP117410.nii.gz
> -bash: template_list: command not found
> UP118102.nii.gz
> -bash: template_list: command not found
> UP118117.nii.gz
> -bash: template_list: command not found
> UP118128.nii.gz
> -bash: template_list: command not found
> UP118318.nii.gz
> -bash: template_list: command not found
> UP118872.nii.gz
> -bash: template_list: command not found
> UP118887.nii.gz
> -bash: template_list: command not found
> UP119867.nii.gz
> -bash: template_list: command not found
> macbook-air-3:vbm-t1dm volumetry$
>
>
>
> I have tried it without the backslahes as suggested but it makes no difference. Please help
>
> Thank you for your time
>
> Michael Maxwell
>
>
> On 23 April 2012 14:13, Paul Robinson <[log in to unmask]> wrote:
>
> Hi, Michael.
>
> Is the backslash part of your list, or are you just showing us that the line continues? That's the only thing that doesn't look quite right to me. For a short list like this, you could also just open a text editor and out the name of each image on a separate line.
>
> Hth,
> Paul
>
>
>
> On Monday, April 23, 2012, Michael Maxwell <[log in to unmask]> wrote:
>> I'm following the instructions for VBM from your website but when entering the following command line:
>>
>> for g in CON_2304.nii.gz CON_2878.nii.gz CON_3456.nii.gz CON_4133.nii.gz CON_4690.nii.gz \
>> PAT_2042.nii.gz PAT_2632.nii.gz PAT_3193.nii.gz PAT_4134.nii.gz PAT_6659.nii.gz; do
>> echo $g >> template_list
>> done
>>
>> it tells me:
>>
>> -bash: template_list: command not found
>>
>> What should I do?
>>
>> Thank you
>>
>> Michael Maxwell
>>
>