search

pnlbwh / pnl_randomise

FSL randomise related scripts
9 stars 4 forks source link

Error message - no such file path? #2

Closed SabreA7 closed 3 years ago

SabreA7 commented 3 years ago

Hi,

I am pretty new to coding and neuroimaging.

I am trying to run pnl_randomise with the randomise summary script, but i am encountering the following error.

FileNotFoundError: No such file or no access: '/data/pnl/soft/pnlpipe3/tbss/data/enigmaDTI/ENIGMA_DTI_FA_skeleton_mask.nii.gz'

This file path doesn't actually exist in my computer, do i need to download another program for the script to work? I had similar issues prior to this point but i had managed to resolve it by changing the actual script to reroute to another file path.

Thank you so much for your help!

kcho commented 3 years ago

Hi @SabreA7,

Thanks for pointing this out. This script requires ENIGMA DTI templates, which you can download and unzip using the following command.

wget http://enigma.ini.usc.edu/wp-content/uploads/2013/02/enigmaDTI.zip
unzip enigmaDTI.zip

Then, please try changing the line to that of your enigmaDTI path. Let me know if this works for you.

SabreA7 commented 3 years ago

Brilliant, thank you that worked!