I recently installed QSIprep. I ran sMRIPrep and fMRIPrep on a subject and now want to run DWI preprocessing on their data. I have a FreeSurfer license; I used it to run fMRIPrep.
Traceback (most recent call last):
File “/usr/local/miniconda/bin/qsiprep”, line 8, in
sys.exit(main())
File “/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/cli/run.py”, line 595, in main
set_freesurfer_license(opts)
File “/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/cli/run.py”, line 552, in set_freesurfer_license
raise RuntimeError("""
RuntimeError: ERROR: a valid license file is required for FreeSurfer to run. fMRIPrep looked for an existing license file at several paths, in this order: 1) command line argument --fs-license-file; 2) $FS_LICENSE environment variable; and 3) the $FREESURFER_HOME/license.txt path. Get it (for free) by registering at FreeSurfer Registration form
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I used the same license file for my fMRIPrep run. Thanks for your help!
you are “mounting” a path into the docker container. For docker run commands, everything after the name of the image will refer to the folder structure inside the container, which will generally be different than your own folder structure. That -v lines says something like “take the folder from your machine located at /Users/salinasf/Desktop/PTSD-database/bids/derivatives and put it in the container at a location called /out”. That’s why the updated command had --fs-license-file /out/license.txt
Out of curiosity, would you be able to share how you ran fMRIPrep?