xcp_d-2afa9081+0ef9c88a (CBRAIN Tool Config ID: 11419)
Container: docker://pennlinc/xcp_d:0.12.0
Documentation: https://xcp-d.readthedocs.io/en/latest/index.html
Boutiques Descriptor: https://portal.cbrain.mcgill.ca/tool_configs/11419/boutiques_descriptor.json
name: XCP-D
description: A Robust Postprocessing Pipeline of fMRI data
Configuration Details
This version of XCP-D processing utilizes Nibabies outputs that were generated with the Infant FreeSurfer cortical surface reconstruction workflow.
External Requirements
These are file-based requirements, external to the pipeline, that must be satisfied for processing to occur. The “Argument IDs” field corresponds to input “id”s within the tool Boutiques Descriptor. “Value”s correspond to either specific configuration files (if there is a numeric value), or otherwise broader file types within CBRAIN (if the entry is text-based).
Argument ID |
Flag |
Value |
Description |
|---|---|---|---|
subject_dir |
n/a |
BidsSubject |
Subject folder for BIDS (folders name should be sub-XXXXX). This folder is not used under the current implementation but is present for ease of processing workflows. |
preproc_fmri_dir |
n/a |
NibabiesOutput ([‘25.2.0-2afa9081’]) |
The root folder of a preprocessed fMRI output from Nibabies, fMRIPREP, or DCAN/HCP outputs that are formed as BIDS derivatives. |
preproc_output_json |
n/a |
The json descriptor of the original fmri preprocessing derivatives. |
|
fs_license_file |
n/a |
4323067 |
Path to FreeSurfer license key file. Get it (for free) by registering at https://surfer.nmr.mgh.harvard.edu/registration.html |
Ancestor Pipelines
This pipeline utilizes outputs from the following pipelines that are also ran in CBRAIN:
nibabies_25.2.0-2afa9081
bibsnet
Other Processing Settings
These additional settings cover everything outside of files that are used as inputs during processing. The settings cover numeric values, flags, outputs directories, and other settings that are used to configure processing.
Argument ID |
Flag |
Value |
Description |
|---|---|---|---|
output_dir |
n/a |
output |
The folder to store outputs of XCPD processing. |
derivatives_prefix |
n/a |
Folders to put before the pipeline specific folder. By default this will look like DataProvider/derivatives/PipelineName, where pipeline name is specific to the current pipeline. The provided string must end in / |
|
input_type |
–input-type |
nibabies |
fMRIPprep/nibabies are default structures, DCAN and HCP are optional |
despike |
–despike |
y |
Despike the nifti/cifti before postprocessing |
warp_surfaces |
–warp-surfaces-native2std |
y |
If used, a workflow will be run to warp native-space (fsnative) reconstructed cortical surfaces (surf.gii files) produced by Freesurfer into standard (fsLR) space. These surface files are primarily used for visual quality assessment. By default, this workflow is disabled. IMPORTANT: This parameter can only be run if the –cifti flag is also enabled. |
fd_thresh |
–fd-thresh |
0.3 |
Framewise displacement threshold for censoring |
head_radius |
–head_radius |
auto |
Head radius for computing FD, default is 50mm, 35mm is recommended for baby |
combineruns |
–combine-runs |
y |
Combines all runs into one file. |
verbose |
-vvv |
true |
Increases log verbosity |
smoothing |
–smoothing |
6 |
Smoothing the postprocessed output (fwhm) |
lower_bpf |
–lower-bpf |
0.01 |
Lower cut-off frequency (Hz) for the butterworth bandpass filter |
upper_bpf |
–upper-bpf |
0.08 |
Upper cut-off frequency (Hz) for the butterworth bandpass filter |
bpf_order |
–bpf-order |
2 |
Number of filter coefficients for butterworth bandpass filter |
nuisance_regressors |
–nuisance-regressors |
36P |
Nuisance parameters to be selected |
min_time |
–min-time |
210 |
Minimum amount of time (in seconds) that a run must have following censoring for it to be processed. |
mode |
–mode |
hbcd |
The mode of operation for XCP-D. The mode sets several parameters, with values specific to different pipelines. For more information, see the documentation at https://xcp-d.readthedocs.io/en/latest/workflows.html#modes |
dummy_scans |
–dummy-scans |
4 |
Number of volumes to remove from the beginning of each run. If set to auto, xcp_d will extract non-steady-state volume indices from the preprocessing derivatives’ confounds file. |
motion_filter_type |
–motion-filter-type |
none |
Type of band-stop filter to use for removing respiratory artifact from motion regressors |
create_matrices |
–create-matrices |
all |
If used, this parameter will produce correlation matrices limited to each requested amount of time. If there is more than the required amount of low-motion data, then volumes will be randomly selected to produce denoised outputs with the exact amounts of time requested. If there is less than the required amount of ‘good’ data, then the corresponding correlation matrix will not be produced. Use ‘all’ for all available data. |
linc_qc |
–linc-qc |
y |
Add LINC QC to the output |
output_layout |
–output-layout |
multiverse |
Output layout for the BOLD data. If ‘auto’, the output layout will be inferred from the processing mode. |
report_output_level |
–report-output-level |
session |
Where should the html reports be written? ‘root’ will write them to the –output-dir. ‘subject’ will write them into each subject’s directory. ‘session’ will write them into each session’s directory. The default is ‘auto’, which will default to ‘root’ for ‘none’ mode, ‘session’ for ‘abcd’ and ‘hbcd’ modes, and ‘root’ for ‘linc’ and ‘nichart’ modes. |
Pipeline Outputs
Following processing, a number of files and folders are identified as outputs that should be saved for future reference. In the following table the ‘Path Relative to Working Directory’ column specifies the location of files that should be saved (with ‘*’ denoting wildcards). The output location for these files in the final ‘DataProvider’ is specified in the ‘Path in Output Data Provider’ column. In the case of HBCD the [DERIVATIVES_PREFIX] entry is empty.
ID |
Path Relative to Working Directory |
Path in Output DataProvider |
Description |
|---|---|---|---|
xcpd_output_dir |
[OUTPUT_DIR]/xcp_d-2afa9081+0ef9c88a/[SUBJECT_DIR] |
[DERIVATIVES_PREFIX]xcp_d-2afa9081+0ef9c88a |
Subject level output for XCP-D |
Command Line Template
The following code-snippet highlights how the tool is referenced on the command-line. The code being displayed is executed within the tool’s container. Some of the directives may describe file manipulations to prepare for processing, and other directives will describe the primary processing command. At the time of processing, the text in brackets will be replaced by text that has been provided to configure processing.
true [SESSION_ID]; true [SUBJECT_DIR]; true [DERIVATIVES_PREFIX]; mkdir -p work; export FS_LICENSE=$PWD/[FS_LICENSE_FILE]; xcp_d [SUBJECT_PREPROC_FMRI_DIR] [OUTPUT_DIR] participant --omp-nthreads 2 [MODE] [COMBINERUNS] [VERBOSE] [INPUT_TYPE] [TASK] [SMOOTHING] [DESPIKE] [LINC_QC] [MIN_TIME] [NUISANCE] --fs-license-file [FS_LICENSE_FILE] [DUMMY_SCANS] [BPF] [LOWER_BPF] [UPPER_BPF] [BPF_ORDER] [MOTION_FILTER_TYPE] [BAND_STOP_MIN] [BAND_STOP_MAX] [MOTION_FILTER_ORDER] [HEAD_RADIUS] [FD_THRESH] [WARP_SURFACES] [BIDS_FILTER] [CREATE_MATRICES] [OUTPUT_LAYOUT] -w work --notrack [REPORT_OUTPUT_LEVEL]