This app is part of a validation framework for fMRI analysis tools. It builds upon the BIDS file structure and can be used to verify the integrity in terms of reproduction of ground truth of e.g. prf-models.
This app is an alternative implementation to validation framework, i.e. the prfanalyze part is taking over here. Hence, the prfsynth dockerimage should be used to synthesize data in order to know the ground truth. After using this app, the prfreport dockerimage can be used to create meaningful and insightful visual reports about the goodness of fit achieved by this and/or other analysis tools.
This app will apply a user-specified analysis to a given BIDS dataset.
This App has the following command line arguments:
usage: run.py [-h]
[--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
bids_dir config_file
prfanalyze-prfpy entry point script.
positional arguments:
bids_dir The directory with the input dataset formatted
according to the BIDS standard.
config_file The path to a yaml file containing all necessary information to perform the prf-fitting
optional arguments:
-h, --help show this help message and exit
--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
The label(s) of the participant(s) that should be
analyzed. The label corresponds to
sub-<participant_label> from the BIDS spec (so it does
not include "sub-"). If this parameter is not provided
all subjects will be analyzed. Multiple participants
can be specified with a space separated list.
To run it in (for one participant):
docker run -i --rm \
-v $basedir/BIDS:/bids_dataset \
-v analyze-prfpy/default_config.yml:/config.yml \
niklasmueller/prfanalyze-prfpy \
/bids_dataset \
/config.yml --participant_label 01