Hi,
It looks like it can’t find the files, so there is probably an error in your path. I would suggest to check this path to see where the error is: /home/control_group/9003tbi/1/rest.feat/filtered_func_data_standard.nii.gz and then change your script accordingly.
Cheers,
Janine
> On 10 May 2018, at 23:22, John <[log in to unmask]> wrote:
>
> I am experiencing some troubles with preparing my data for group ICA on an independent sample of 30 subjects for use with dual regression later on. I have already run preprocessing with FEAT.
>
> I ran the following script:
> #!/bin/sh
> for j in `ls -d /home/control_group/*tbi/1/rest.feat` ; do
> applywarp -r ${j}/reg/standard.nii.gz \
> -i ${j}/filtered_func_data.nii.gz \
> -o ${j}/filtered_func_data_standard \
> --premat=${j}/reg/example_func2highres.mat \
> -w ${j}/reg/highres2standard_warp.nii.gz
> done
> ls -1 /home/control_group/*tbi/1/rest.feat/filtered_func_data_standard.nii.gz >> \
> /home/MEL_DR/inputlist_all_controls.txt
>
>
>
> However, I got the following error message:
>
> -bash-4.1$ ./appwar
> Error: failed to open file /home/control_group/9003tbi/1/rest.feat/filtered_func_data_standard.nii.gz
> Image Exception : #22 :: ERROR: Could not open image /home/control_group/9003tbi/1/rest.feat/filtered_func_data_standard
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> ./appwar: line 2: 27971 Aborted (core dumped) applywarp -r ${j}/reg/standard.nii.gz -i ${j}/filtered_func_data.nii.gz -o ${j}/filtered_func_data_standard --premat=${j}/reg/example_func2highres.mat -w ${j}/reg/highres2standard_warp.nii.gz
> Error: failed to open file /home/control_group/9006tbi/1/rest.feat/filtered_func_data_standard.nii.gz
> Image Exception : #22 :: ERROR: Could not open image /home/9006tbi/1/rest.feat/filtered_func_data_standard
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> ./appwar: line 2: 28089 Aborted (core dumped) applywarp -r ${j}/reg/standard.nii.gz -i ${j}/filtered_func_data.nii.gz -o ${j}/filtered_func_data_standard --premat=${j}/reg/example_func2highres.mat -w ${j}/reg/highres2standard_warp.nii.gz
>
>
> ...and so forth.
>
> Any thoughts on what I am doing wrong would be highly appreciated.
>
>
> Best,
>
> John
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