Hi, I saw your tweet. Assuming that you’re still using this command (I reordered slightly, as we tend to put the input, output and participant
before any other options):
fmriprep-docker /Users/elvadags/Desktop/mybids \
/Users/elvadags/Desktop/mybids \
participant \
--fs-license-file $HOME/.licenses/freesurfer/license.txt \
-w /Users/elvadags/Desktop/mybids
I have a couple comments:
- I would not use the same input and output directory. If you would like your derivatives to be in a sub-folder of your BIDS directory, the spec-recommended place is
<bids-root>/derivatives
.
- I would not use the input directory as a working directory. I would not choose a sub-directory; the working directory can be deleted once processing is complete, and is emphatically not BIDS-formatted.
So you could try the following (after upgrading to the latest fmriprep-docker
with pip install --user --upgrade fmriprep-docker
):
fmriprep-docker /Users/elvadags/Desktop/mybids \
/Users/elvadags/Desktop/mybids/derivatives \
participant \
--fs-license-file $HOME/.licenses/freesurfer/license.txt \
-w /Users/elvadags/Desktop/mybids-wd
Note that fmriprep now bundles the BIDS validator, so if your dataset isn’t valid, you’re going to need to fix it up to some degree. Often enough, invalid datasets somehow exhibit as odd errors, so we bundle it to rule out these cases.
If that fails, you can add a --shell
option to your fmriprep-docker
command to drop into a bash shell inside the container. Then you should look in $FREESURFER_HOME
for your license file and make sure that it’s valid. You can also test it with a basic mri_convert
call.
Let me know how that all goes. Hopefully somewhere in there we’ll find your problem.