Fmriprep: Error using ubuntu 20.04.2

#1

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/run.py", line 21, in main
ModuleNotFoundError: No module named 'sentry_sdk'

My script:

bids_root_dir=$HOME/openneuro_tutorial/ds000102
preprocess_output_dir=$HOME/openneuro_tutorial/ds000102/fmriprep
subj=01

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
–skip_bids_validation
–md-only-boilerplate
–fs-license-file $HOME/openneuro_tutorial/license.txt
–fs-no-reconall
–output-spaces MNI152NLin2009cAsym:res-1
–nthreads $nthreads
–stop-on-first-crash
-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,
Tali

#2

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.

#3

Hello,
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;

sub-mp0014_ses-01_task-rest_desc-rois_bold
sub-mp0014_ses-01_task-rest_desc-rois_bold1280×960 172 KB

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.

Best,
roqa

#4

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

Best,
roqa