Hello community

Regarding the scripts. I have the order/names of folders, as you recommend.
subjs0001subjs0001/anat/anat.nii.gzsubjs0001/func1/rest_1.nii.gzsubjs0001/func2/rest_2.nii.gzI recently update the version of the Ubuntu to 12.04, I have to source all the programs again (AFNI, FSL, FREESURFER), because I lost all the configuration files (.bashrc - .cshrc), actually I have a problem with fslview, which I'm trying to solve with neurodebian team.

I don't know if this is related to the scripts, because I can run the commands individually and open the GUI's (some in bash and others in tcsh).I set all the required lines in order to run batch_process.sh with option 1 (preprocessing). But when it runs, it shows several errors regarding it can't open several files (which I guess, the script itself must be create or call somewhere) and then in the segmentation step, Ubuntu shows an error regarding fsl/flirt stops. 

Before I had the version 10.10 and the scripts run perfect.

Hope somebody can help me or give me an advice.

Best regards, 

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Carolina Valencia