nibabies_25.2.0-2afa9081 (CBRAIN Tool Config ID: 11356)

Container: docker://nipreps/nibabies:25.2.0
Documentation: https://nibabies.readthedocs.io/
Boutiques Descriptor: https://portal.cbrain.mcgill.ca/tool_configs/11356/boutiques_descriptor.json
name: nibabies
description: NiBabies is an open-source software pipeline designed to process anatomical and functional magnetic resonance imaging data.

Configuration Details

This configuration of Nibabies processing uses Infant FreeSurfer for cortical surface reconstruction.

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).
cabinet_output	–derivatives	BibsnetOutput	FileCollection containing CABINET precomputed output.
cabinet_output_json	n/a	`4942229`	The json descriptor of the CABINET precomputed output.
fs_license_file	–fs-license-file	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:

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_name	n/a	output	The name of the output for the outcomes of preprocessing and visual reports. When processing is ran via CBRAIN only subject-specific files/folders will be saved, so the naming of the output folder will not influence the final naming/destination of files/folders.
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 /
surface_recon_method	–surface-recon-method	infantfs	Method to use for surface reconstruction.
project_goodvoxels	–project-goodvoxels	true	Remove high variance voxels from surface projection.
cifti_output	–cifti-output	91k	Output preprocessed BOLD as a CIFTI dense timeseries. Optionally, the number of grayordinate can be specified (default is 91k, which equates to 2mm resolution). Possible choices 91k, 170k.
output_spaces	–output-spaces	MNI152NLin6Asym:res-2 fsnative anat func	Standard and non-standard spaces to resample anatomical and functional images to. Standard spaces may be specified by the form <SPACE>[:cohort-<label>][:res-<resolution>][…], where <SPACE> is a keyword designating a spatial reference, and may be followed by optional, colon-separated parameters. Non-standard spaces imply specific orientations and sampling grids. Important to note, the res-* modifier does not define the resolution used for the spatial normalization. To generate no BOLD outputs, use this option without specifying any spatial references For further details, please check out https://fmriprep.readthedocs.io/en/latest/spaces.html
dummy_scans	–dummy-scans	4	Number of non steady state volumes.
multi_step_reg	–multi-step-reg	true	For certain adult templates (MNI152NLin6Asym), perform two step registrations (native -> MNIInfant -> template) and concatenate into a single xfm.
stop_on_first_crash	–stop-on-first-crash	true	Force stopping on first crash, even if a work directory was specified.
output_layout	–output-layout	multiverse	Organization of outputs.

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
nibabies_output_dir	[OUTPUT_DIR]/nibabies-25.2.0-2afa9081/[SUBJECT_DIR]	[DERIVATIVES_PREFIX]nibabies-25.2.0-2afa9081	This is the directory where the nibabies outputs are to be stored.
freesurfer_output_dir	[OUTPUT_DIR]/nibabies-25.2.0-2afa9081/sourcedata/freesurfer-2afa9081/[SUBJECT_DIR]*	[DERIVATIVES_PREFIX]freesurfer-2afa9081	This is the directory where the freesurfer-like outputs are to be stored.
nibabies_html_report	[OUTPUT_DIR]/nibabies-25.2.0-2afa9081/[SUBJECT_DIR]*.html	[DERIVATIVES_PREFIX]nibabies-25.2.0-2afa9081	This is the html report generated by nibabies.

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 [DERIVATIVES_PREFIX]; nibabies [SUBJECT_DIR] [OUTPUT_DIR] participant --skip_bids_validation [SESSION_ID] --nthreads 4 --omp-nthreads 4 --mem_mb 30000 [VERBOSE] [OUTPUT_SPACES] [DUMMY_SCANS] [FS_LICENSE_FILE] [CIFTI_OUTPUT] --work-dir work [STOP_ON_FIRST_CRASH] [CABINET_OUTPUT] [PROJECT_GOODVOXELS] [SURFACE_RECON_METHOD] [MULTI_STEP_REG] [OUTPUT_LAYOUT]

File Selection For Processing

The first step of selecting a candidate for processing is determining whether the right files are present. In HBCD processing, pipelines are always run on one session worth of data at a time. With that in mind, we (mostly) query the contents of a subject’s session folder to determine if processing should occur and also which files should be included in processing. For every pipeline there will be at least one requirement group that determines what files are needed for processing to occur. Within a requirement group, there may be criteria that address multiple file (or modality) types, which are known as ‘File Groups’. For processing to occur, the minumum number of files surviving all Included/Excluded terms for a given ‘File Group’ must be satisfied.

To allow for more flexible selection of files for processing, there are often multiple ‘Requirement Groups’. The contents of each ‘File Group’ across ‘Requirement Groups’ must be the same, but which ‘File Groups’ are defined can be different. If multiple ‘Requirement Groups’ are present for the current pipeline, there will be multiple tables in this section. Only one ‘Requirement Group’ needs to be satisfied for processing to occur. If one requirement group is satisfied, then files from all ‘File Groups’ will be included in processing.

Beyond the files that are chosen from this procedure, other associated files defined via the table here will also be included in processing.

Requirement Group: nibabies_25.2.0-2afa9081_1

File Group	How Many To Keep	Term	Included (True)/Excluded (False)
T1	1	T1w.nii.gz	True
		rec-undistorted	False
		acq-svslocalizer	False
		acq-mrsLoc	False
		_QALAS.nii.gz	False
T2	1	T2w.nii.gz	True
		rec-undistorted	False
		acq-svslocalizer	False
		acq-mrsLoc	False
		_QALAS.nii.gz	False
FMRI	All	bold.nii.gz	True
		rec-undistorted	False
		rec-biascorrected	False
AP_FMAP	All	epi.nii.gz	True
		dir-AP	True
PA_FMAP	All	epi.nii.gz	True
		dir-PA	True
scans.tsv	All	scans.tsv	True
sessions.tsv	All	sessions.tsv	True

Quality Control Selection Information

The previous section of this page highlighted how to look at a file’s name to determine whether it may belong to a specific ‘File Group’ (such as T2w images) that are needed for processing. Beyond this, it is often necessary to look at some QC criteria to determine whether a file should be included in processing. This section defines the QC criteria that is used to evaluate specific images. These QC criteria always operate on one file group at a time. If a file group uses QC criteria to select images, at least one table will be displayed below. Depending on the context, these criteria will be used to exclude certain images from processing, to find the best available image(s) within a specific category, or to exclude a session from processing. If sorting is the goal, the first row will be considered the most important criteria. In certain cases, not all images will have ratings for a specific QC field. In this case, a backup table (which will be displayed after the first table if available), will be used for that file group.

File Group: T1

Processing will look for best 1 file(s) to keep using the following criteria(s).

scans.tsv Field	Operator	Value
QC	equals	1
QU_motion	less_than	2.01
aqc_motion	less_than	10000
brain_SNR	greater_than	-1000

scans.tsv Field	Operator	Value
QC	equals	1
aqc_motion	less_than	10000
brain_SNR	greater_than	-1000

File Group: T2

Processing will look for best 1 file(s) to keep using the following criteria(s).

scans.tsv Field	Operator	Value
QC	equals	1
QU_motion	less_than	2.01
aqc_motion	less_than	10000
brain_SNR	greater_than	-1000

scans.tsv Field	Operator	Value
QC	equals	1
aqc_motion	less_than	10000
brain_SNR	greater_than	-1000

File Group: FMRI

Processing will include all files passing the following criteria.

scans.tsv Field	Operator	Value
QC	equals	1

File Group: AP_FMAP

Processing will include all files passing the following criteria.

scans.tsv Field	Operator	Value
QC	equals	1

File Group: PA_FMAP

Processing will include all files passing the following criteria.

scans.tsv Field	Operator	Value
QC	equals	1