Usage

This page provides an example of how this application can be called, and further what the different arguments mean. The design of the application is meant to follow general BIDS-App guidelines. For more details on general usage principles of BIDS-Apps, see the linked publication. For more details on the overall workflow of the containerized application see the Expected Inputs, Processing Pipeline Details, and Configuration of MRS Processing sections.

As described in the installation section, this tool is meant to be interacted with in containerized form. The example below shows the general layout for how you may want to interact with the container to conduct processing if you have the container downloaded as a singularity image:

container_path=/path/to/container.sif
bids_dir=/path/to/bids
output_dir=/path/to/output
bibsnet_dir=/path/to/bibsnet
settings_file=/path/to/settings.json
singularity run -B $bids_dir:/bids \
 -B $output_dir:/output \
 -B $bibsnet_dir:/bibsnet \
 -B $settings_file:/settings_file/file.json \
 $container_path /bids /output participant /settings_file/file.json

To see more specific information about how this tool expects the inputs to be formatted (i.e. file naming conventions), see the Expected Inputs page.

Command-Line Arguments

usage: osprey [-h] [--participant_label PARTICIPANT_LABEL]
              [--session_id SESSION_ID] [--segmentation_dir SEGMENTATION_DIR]
              [--localizer_registration]
              [--localizer_search_term LOCALIZER_SEARCH_TERM]
              [--preferred_anat_modality {T1w,T2w,none}]
              [--terms_not_allowed_in_anat TERMS_NOT_ALLOWED_IN_ANAT [TERMS_NOT_ALLOWED_IN_ANAT ...]]
              [--require_same_mrs_localizer_suid]
              bids_dir output_dir analysis_level json_settings

Positional Arguments

bids_dir

The path to the BIDS directory for your study (this is the same for all subjects)

output_dir

The path to the folder where outputs will be stored (this is the same for all subjects)

analysis_level

Should always be participant

json_settings

The path to the subject-agnostic JSON file that will be used to configure processing settings

Named Arguments

--participant_label, --participant-label

The name/label of the subject to be processed (i.e. sub-01 or 01)

--session_id, --session-id

OPTIONAL: the name of a specific session to be processed (i.e. ses-01)

--segmentation_dir, --segmentation-dir

The path to the folder where segmentations are stored (this is the same for all subjects)

--localizer_registration, --localizer-registration

OPTIONAL: Use localizer to register anatomical images to MRS scan. Also requires the use of –segmentation_dir argument

--localizer_search_term, --localizer-search-term

OPTIONAL: The search term to use to find localizer images (i.e. localizer)

Default: '*localizer*.nii*'

--preferred_anat_modality, --preferred-anat-modality

Possible choices: T1w, T2w, none

OPTIONAL: The preferred modality to use for anatomical images (must be one of: T1w, T2w, none). If set to none, no anatomical information will be used in processing. This can be of interest for QC purposes.

Default: 'T2w'

--terms_not_allowed_in_anat

One or more terms (seperated by spaces) that are not allowed in the file name of high-res anatomical reference images. Useful for getting rid of localizer images that can be confused for high-res anatomical scans. example - “–terms_not_allowed_in_anat mrs ax coronal”

--require_same_mrs_localizer_suid

If activated, OSPREY will only try to match MRS scans with localizers if the StudyInstanceUID field in the BIDS JSON matches across the localizer/mrs images. Note: if the StudyInstanceUID is undefined for the MRS acquisition, denoted by a value of None, then a localizer will be chosen without taking the StudyInstanceUID into account.