fMRIPREP - Not able to run the code

1

Hello everyone,

I am new here and I have a beginner’s problem :slight_smile:

I have installed docker and the required packages and everything went well until the moment that I had to run the code (the fmriprep_singleSubj.sh from the tutorial). I have tried many things but nothings seems to work, it either does nothing (when for example I try bash fmripr.sh) or a couple of times it gave me a permission denied error when I used ./ to run it. I have tried to run it form the windows command prompt, from the ubuntu, from the power shell, I tried as an administrator, I checked that it has the permissions required and nothing has worked so far so I 'd appreciate any leads

Thank you very much in advance,
SM

2

What tutorial are you referring to? Have you tried using the example code on the fMRIPrep website?

docker run -ti --rm \
    -v /PATH/TO/DATA:/data:ro \
    -v /PATH/TO/DATA/derivatives:/out \
    -v /PATH/TO/license.txt:/opt/freesurfer/license.txt \
    nipreps/fmriprep:latest \
    /data /out \
    participant \
    --PUT OTHER OPTIONS HERE AS NEEDED
3

Thank you very much for your answer!

I am referring to this tutorial BIDS App Tutorial #2: fMRIPrep — Andy's Brain Book 1.0 documentation
When I save the code as a .sh file, there is no way to run it.

4

To fix permission errors, you can usually allow something to run as a program by right clicking the file and going to properties menu (but exact method depends on your OS). In general, you should try to use a Linux shell if possible (ubuntu or install cygwin if you want to use Windows). Did the code I posted worked (after changing it to match your needs)?

5

I did all the things you mentioned but nothing seems to work. As far as I understand the problem is not the code but the fact that I cannot run the .sh file at all. It’s not that it runs and it gives me an error or something, it doesn’t run at all.

6

Is it still only saying permission denied? Also, you can run the code I posted right from your terminal without putting it in an .sh file first.

7

Either it says permission denied or it just does nothing (!). I will try your code now directly and let you know thanks a lot!