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 activate fmriprep;
--participant_label 103 \
--nthreads 4 \
--ignore slicetiming \
--template MNI152NLin2009cAsym \
--output-space template T1w \
--ants-nthreads 2 \
echo "fmriprep run completed successfully at $END_TIME";
bids dir is the location of a BIDs validated path where participants niftis are stored, including
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.