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/;
END_TIME=$(date);
echo "fmriprep run completed successfully at $END_TIME";
where:
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.