qsiprep (CBRAIN Tool Config ID: 7808)

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).

eddy_config

n/a

5132213

Path to a json file with settings for the call to eddy. If no json is specified, a default one will be used. The current default json can be found here: https://github.com/PennBBL/qsiprep/blob/master/qsiprep/data/eddy_params.json

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

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

qwerty

The name of the output for the outcomes of preprocessing and visual reports

output_resolution

–output-resolution

1.7

The isotropic voxel size in mm the data will be resampled to after preprocessing. If set to a lower value than the original voxel size, your data will be upsampled using BSpline interpolation.

subject_anat_reference

–subject-anatomical-reference

sessionwise

How to define subject-specific anatomical space. sessionwise will produce one anatomical space per session. The others combine anatomical data across sessions to define one anatomical space per subject.

AnatModality

–anat-modality

T2w

Possible choices: T1w, T2w, none. Modality to use as the anatomical reference. Images of this contrast will be skull stripped and segmented for use in the visual reports and reconstruction. If –infant, T2w is forced.

infant

–infant

True

Configure pipelines to process infant brains

unringing_method

–unringing-method

rpg

Method for Gibbs-ringing removal. - none: no action - mrdegibbs: use mrdegibbs from mrtrix3. rpg: Gibbs from TORTOISE, suggested for partial Fourier acquisitions (default: none).

DENOISE_METHOD

–denoise-method

dwidenoise

Image-based denoising method. Either “dwidenoise” (MRtrix), “patch2self” (DIPY) or none. (default: dwidenoise)

B1_BIAS_CORRECT

–b1-biascorrect-stage

none

Which stage to apply B1 bias correction. The default ‘final’ will apply it after all the data has been resampled to its final space. ‘none’ will skip B1 bias correction and ‘legacy’ will behave consistent with qsiprep < 0.17.

PEPOLAR_METHOD

–pepolar-method

TOPUP+DRBUDDI

Possible choices: TOPUP, DRBUDDI, TOPUP+DRBUDDI. Select which SDC method to use for PEPOLAR fieldmaps (default: TOPUP)

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 /

verbose

-v

True

Increases log verbosity for each occurence (-vvv).

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

output_dir

[QSIPREP_OUTPUT_DIR]/[SUBJECT_DIR]

[DERIVATIVES_PREFIX]qsiprep

This is the directory where the QSIPREP Preproc outputs are to be stored.

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]; qsiprep [SUBJECT_DIR] [QSIPREP_OUTPUT_DIR] participant --skip-bids-validation --work-dir "$PWD"/work [SESSION_ID] [FS_LICENSE_FILE] [BIDS_FILTER_FILE] --omp-nthreads 8 --n-cpus 8 --stop-on-first-crash --eddy-config "$PWD"/[EDDY_CONFIG] [SUBJECT_ANAT_REFERENCE] [SKIP_ANAT_BASED_SPATIAL_NORM] [ANAT_MODALITY] [SEPARATE_ALL_DWIS] [PEPOLAR_METHOD] [USE_PLUGIN] [ANAT_ONLY] [DWI_ONLY] [B1_BIAS_CORRECT] [INFANT] [BOILERPLATE] [VERBOSE] [IGNORE] [LONGITUDINAL] [B0_THRESHOLD] [DWI_DENOISE_WINDOW] [UNRINGING_METHOD] [NO_B0_HARMONIZATION] [DENOISE_AFTER_COMBINING] [DENOISE_METHOD] [DISTORTION_GROUP_MERGE] [TEMPLATE] [OUTPUT_RESOLUTION] [B0_TO_T1W_TRANSFORM] [INTRAMODAL_TEMPLATE_ITERS] [INTRAMODAL_TEMPLATE_TRANSFORM] [B0_MOTION_CORR_TO] [HMC_TRANSFORM] [HMC_MODEL] [SHORELINE_ITERS] [FMAP_BSPLINE] [FMAP_NO_DEMEAN] [USE_SYN_SDC] [FORCE_SYN] [REPORTS_ONLY] [WRITE_GRAPH] [SLOPPY]

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: qsiprep_1

File Group

How Many To Keep

Term

Included (True)/Excluded (False)

DWI_AP

1

dwi.nii.gz

True

dir-AP

True

DWI_PA

1

dwi.nii.gz

True

dir-PA

True

T2

1

T2w.nii.gz

True

rec-undistorted

False

acq-svslocalizer

False

acq-mrsLoc

False

_QALAS.nii.gz

False

scans.tsv

All

scans.tsv

True

sessions.tsv

All

sessions.tsv

True

Requirement Group: qsiprep_2

File Group

How Many To Keep

Term

Included (True)/Excluded (False)

DWI_AP

1

dwi.nii.gz

True

dir-AP

True

DWI_PA

1

dwi.nii.gz

True

dir-PA

True

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

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: DWI_AP

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

scans.tsv Field

Operator

Value

QC

equals

1

QU_cutoff

less_than

10000

QU_sus

less_than

10000

QU_line

less_than

10000

ngood_frames

greater_than

0

line_mean_score

less_than

10000

tSNR_b0

greater_than

0

scans.tsv Field

Operator

Value

QC

equals

1

ngood_frames

greater_than

0

line_mean_score

less_than

10000

tSNR_b0

greater_than

0

File Group: DWI_PA

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

scans.tsv Field

Operator

Value

QC

equals

1

QU_cutoff

less_than

10000

QU_sus

less_than

10000

QU_line

less_than

10000

ngood_frames

greater_than

0

line_mean_score

less_than

10000

tSNR_b0

greater_than

0

scans.tsv Field

Operator

Value

QC

equals

1

ngood_frames

greater_than

0

line_mean_score

less_than

10000

tSNR_b0

greater_than

0

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

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: 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

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