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.

I am using ubuntu 22.04
the output was lock
I used the chm 777 and for permission
now when I want to open any html files in the output I face this eeror;

Access to the file was denied

The file at /home/roya/outputmp14/sub-mp0014.html is not readable.

It may have been removed, moved, or file permissions may be preventing access.

The images in figures file are opened, but in different shape that I have through the ubuntu 20.04;

May the reason for this problem be that the installed packages are not compatible with Ubuntu 22, for example Freesurfer or Afni or anything else?

I appreciate your time and help.


Hi Chirs!
It would be grateful if there is any suggestion for me.