Various objective measures for MRI data quality have been proposed over the years. However, until now no software has allowed researchers to obtain all these measures in the same place with relative ease. The Quality Assessment Protocol package allows you to obtain spatial and anatomical data quality measures for your own data.
This App has the following command line arguments:
usage: run.py [-h]
[--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
[--pipeline_file PIPELINE_FILE] [--n_cpus N_CPUS]
[--save_working_dir] [--group_level_report]
bids_dir output_dir
PCP-QAP Pipeline Runner
positional arguments:
bids_dir The directory with the input dataset formatted
according to the BIDS standard.
output_dir The directory where the output CSV files should be
stored.
optional arguments:
-h, --help show this help message and exit
--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
The label of the participant 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 should be
analyzed. Multiple participants can be specified with
a space separated list.
--pipeline_file PIPELINE_FILE
Name for the pipeline configuration file to use
--n_cpus N_CPUS Number of execution resources available for the
pipeline
--save_working_dir Save the contents of the working directory.
--group_level_report Generates a group level report pdf.
To run it in participant level mode (for one participant):
docker run -i --rm \
-v /Users/filo/data/ds005:/bids_dataset \
-v /Users/filo/outputs:/outputs \
bids-apps/qap:v1.0.0 \
/bids_dataset /outputs --participant_label 01
To run all subjects and generate the group level analysis report:
docker run -i --rm \
-v /Users/filo/data/ds005:/bids_dataset \
-v /Users/filo/outputs:/outputs \
bids-apps/qap:v1.0.0 \
--group_level_report \
/bids_dataset /outputs