Hi Anna,
Looks like the shell didn’t substitute anything for ${j}, which is a bit strange if this is the only thing that you changed. Could you copy a few more lines from your script so that I can see what is going on?
Best,
Eelke
> On 8 Feb 2016, at 17:23, Anna Pajkert <[log in to unmask]> wrote:
>
> Hi Eelke ,
>
> thank you for your help. I registered my data non-linearly and after changing my command from:
>
> applywarp -r ${j}/reg/standard.nii.gz -i ${j}/filtered_func_data.nii.gz -o ${j}/filtered_func_data_standard --premat=${j}/reg/example_func2standard.mat
>
> to
>
> applywarp -r ${j}/reg/standard.nii.gz -i ${j}/filtered_func_data.nii.gz -o ${j}/filtered_func_data_standard -w ${j}/reg/example_func2standard.nii.gz
>
> I'm getting following error:
> An error occured while reading file: ${j}/reg/example_func2standard.nii.gz
>
> Do you have any idea why it is not working? I'm using Linux Lucid 10.04 and FSL 5.0.8.
>
> Best,
> Anna
|