Settings¶

Settings in p3, are defined in JSON format and can be loaded in through the -s or –settings command line flags. This document describes the settings available to default workflows of p3.

bids_query¶

Sets the bids query for the bidsselector workflow. The input to this settings key should be a dictionary containing the anat and func keys. See pybids docs for more information.

# This sets the anatomy images to be of modality 'anat' and type 'T1w'
# and the functional images to be modality 'func' and type 'rest'
{
'anat':{
    'modality': 'anat',
    'type':'T1w',
    },
'func':{
    'modality':'func',
    'task':'rest'
    }
}

func_reference_run¶

Selects the epi run to take the reference image from. It is 0 indexed so the first run loaded in to the func key would be 0.

func_reference_frame¶

Selects the epi reference frame to use. It is 0 indexed and taken from the whatever run was set to the func_reference_run.

anat_reference¶

Selects the anat to align to if multiple anat images in dataset. It is 0 indexed. Anatomy imagess are ordered from lowest session, lowest run to highest session, highest run. Leave as 0 if only 1 anat.

atlas¶

Sets the atlas align target. You can specify a path to an atlas here, or use one of p3’s built in templates. Currently the only availiable template in p3 is MNI152.nii.gz

avganats¶

True or False. Averages all anats in the dataset if multiple T1s. Set this to False if you only have 1 anatomy image or you will probably get an error!

field_map_correction¶

True or False. Sets whether the pipeline should run field map correction. You should have field maps in your dataset for this to work. p3 currently only supports gradient echo field maps.

slice_time_correction¶

True or False. Sets whether the functional images should be slice time corrected.

despiking¶

True of False. Sets whether epi images should be despiked.

run_recon_all¶

True or False. Sets whether pipeline should run recon-all (if you decide not to you should place your own p3_freesurfer data under output p3_freesurfer_output, where each folder is {NAME} in sub-{NAME} in the bids dataset)

num_threads¶

Sets the number of threads for all ANTs programs.

brain_radius¶

Sets the brain radius for FD calculations (in mm).

min_bpm¶

Sets the breathing rate for lower bound of the respiratory filter.

max_bpm¶

Sets the breathing rate for upper bound of the respiratory filter.

FD_threshold¶

FD threshold for creating tmask outputs.

FD_filtered_threshold¶

Filtered FD threshold for creating filtered tmask outputs.

workflows¶

Defines the workflows to import.

"workflows": [
    "p3_bidsselector",
    "p3_freesurfer",
    "p3_skullstrip",
    "p3_stcdespikemoco",
    "p3_fieldmapcorrection",
    "p3_alignanattoatlas",
    "p3_alignfunctoanat",
    "p3_alignfunctoatlas",
    "p3_create_fs_masks"
]

See Creating New Workflows for more details.

connections¶

Defines the connections between workflows.

"connections": [
    {
        'source': 'p3_bidsselector', # the source workflow
        'destination': 'p3_freesurfer', # the destination workflow
        'links': [
            [ # this sets the anat of p3_bidsselector to T1 of p3_freesurfer
                'output.anat',
                'input.T1'
            ],
            [ # this sets the subject of p3_bidsselector to subject of p3_freesurfer
                'output.subject',
                'input.subject'
            ]
        ]
    },
    {
        'source': 'p3_bidsselector', # the source workflow
        'destination': 'p3_skullstrip', # the destination workflow
        'links': [
            [ # this sets the anat of p3_bidsselector to T1 of p3_skullstrip
                'output.anat',
                'input.T1'
            ]
        ]
    },
    ...
]