Fmriprep argument analysis_level: invalid choice error

I have downloaded and installed fmriprep using a Manually Prepared Environment (we cannot use docker/singularity at this time) and have tested every step along the way to make sure that all requirements have been met.

In trying to test fmriprep out on a single subject, I am running the following code:

source /home/despoB/adameich/.bashrc;
source activate fmriprep;
cd /home/despoB/adameich/Experiments/HLearning/scripts/preproc/fmriprep;
fmriprep \
    --participant_label 103 \
    --nthreads 4 \
    --ignore slicetiming \
    --template MNI152NLin2009cAsym \
    --output-space template T1w \
    --no-freesurfer \
    --ants-nthreads 2 \
    /home/despoB/adameich/Experiments/HLearning/data/bids/complete_data/ \
    /home/despoB/adameich/Experiments/HLearning/data/fmriprep/ \
    participant \
    -w /home/despoB/adameich/Experiments/HLearning/preproc/work/;
echo "fmriprep run completed successfully at $END_TIME";

bids_dir --> /home/despoB/adameich/Experiments/HLearning/data/bids/complete_data/
output_dir --> /home/despoB/adameich/Experiments/HLearning/data/fmriprep/
The bids dir is the location of a BIDs validated path where participants niftis are stored, including sub-103.

However whenever I submit the command I receive the following error:
fmriprep: error: argument analysis_level: invalid choice: '/home/despoB/adameich/Experiments/HLearning/data/fmriprep/' (choose from u'participant')

I have tried many different permutations of the order of flags and paths, and none of them resolve the issue at all.

If anyone could offer some suggestions I would greatly appreciate it.

This looks pretty reasonable, but --ants-nthreads is now --omp-nthreads. I wonder if the old option is causing the option parser to behave oddly.

Ahh, great call. That resolved it. Unfortunately now I am encountering a separate problem which I can’t seem to figure out.

  File "/home/despoB/adameich/anaconda2/envs/fmriprep/lib/python2.7/site-packages/niworkflows/viz/", line 18, in <module>
    from lxml import etree
ImportError: cannot open shared object file: No such file or directory

A different thread recommended conda install 'icu=56.*', but that resulted in a conflict issue between icu 56.*, navigator-updater and matplotlib. Installing icu 58.* as someone else recommended resulted in a similar problem, but instead of matplotlib, there is a conflict between icu 56.*, navigator-updater and seaborn.

Yeah, I’m not positive how to deal with that. Possibly you can try upgrading lxml.

I would also strongly recommend running FMRIPREP in a Python 3 environment. Although we accept patches from interested parties to fix bugs that exhibit in Python 2, we don’t test or actively support Python 2.

That is great to know. I’ll create a new environment now with python 3. Thank you very much for your help and suggestions!