default_pipeline.yml

# name for this run
pipeline_name: QAP_bids_app_default

# how many processors you wish to use in the run
num_processors: 1

# how many participants to run per workflow
num_sessions_at_once: 1

# the amount of memory (in GB) to allocate to each participant
available_memory: 2

# which cluster system being used, if any
cluster_system: None

# where to place output files
output_directory: /output 

# where to place Nipype workflow working files
working_directory: /scratch

# path to skull template
# only required if you have anatomical scans
template_head_for_anat: /qap_resources/qap_templates/MNI152_T1_2mm.nii.gz

# exclude zero-value voxels from the background of the anatomical scan
# this is meant for images that have been manually altered (ex. ears removed
# for privacy considerations), where the artificial inclusion of zeros into
# the image would skew the QAP metric results
# (optional) will default to False if not included in this config file
exclude_zeros: False

# for functional timeseries, do not include timepoints before this
# (optional) will default to 0 if not included in this config file
start_idx: 0

# for functional timeseries, only include timepoints up to this
# "End" means it will include all of the timepoints up until the scan's end
# (optional) will default to "End" if not included in this config file
stop_idx: End

# produce PDF reports visualizing the results of the QAP metrics
# (optional) will default to False if not included in this config file
write_report: False

# produce workflow dependency graphs
# (optional) will default to False if not included in this config file
write_graph: False

# whether or not to keep all output files, or only the QAP numbers CSVs
# (optional) will default to False if not included in this config file
write_all_outputs: False

# AWS Cloud Settings
####################

# all optional

# whether or not to upload output files to S3 bucket
upload_to_s3: False

# bucket prefix (where to pull data from in S3, if applicable)
bucket_prefix: bucket/prefix/path

# bucket output prefix (where to push output files to S3, if applicable)
bucket_out_prefix: bucket/prefix/output/destination

# where to download input files to, locally, from S3
local_prefix: /path/to/local/dir

# name of your S3 bucket
bucket_name: bucket_name

# local path to your AWS credentials
creds_path: /path/to/AWS/creds.csv