Fmriprep: Error using ubuntu 20.04.2

Dear all,

I will appreciate your help.
I’m using Ubuntu 20.04.2, thus I believe I do not need a container.
I get this error:

File "/home/taliw/.local/bin/fmriprep", line 11, in <module>
load_entry_point('fmriprep==20.2.1', 'console_scripts', 'fmriprep')()
  File "/home/taliw/.local/lib/python3.8/site-packages/fmriprep-20.2.1-py3.8.egg/fmriprep/cli/", line 21, in main
ModuleNotFoundError: No module named 'sentry_sdk'

My script:


export TEMPLATEFLOW_HOME=$HOME/openneuro_tutorial/templateflow
export FS_LICENSE=$HOME/openneuro_tutorial/license.txt

fmriprep $bids_root_dir $preprocess_output_dir participant
–participant-label $subj
–fs-license-file $HOME/openneuro_tutorial/license.txt
–output-spaces MNI152NLin2009cAsym:res-1
–nthreads $nthreads
-w $HOME

My second question in on
–output-spaces MNI152NLin2009cAsym:res-1
“the res-* modifier does not define the resolution used for the spatial normalization.”
So, if it is not for registration step, for what is it for?

Thank you,

For the first issue, use pip install sentry-sdk or pip install fmriprep[sentry].

I’ve opened an issue here: sentry-sdk is imported unconditionally by the CLI, but not part of install_requires · Issue #2411 · nipreps/fmriprep · GitHub

res selects the resolution that you resample to post-registration. The notice is there to let you know that selecting the resolution has no impact on the registration process, and specifically that requesting a lower resolution output will not degrade the quality of the registration by using a lower resolution template.