Modules

1. Module Import

Functions

function ExploreASL_Import(imPar, bCopySingleDicoms, bUseDCMTK, bCheckPermissions, bRunDCM2NII, bClone2Source, x)

Description

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function imPar = ExploreASL_ImportConfig(StudyRoot)

Description

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function [x] = ExploreASL_Initialize(DataParPath, ProcessData, iWorker, nWorkers)

Description

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2. Module Structural

Function

function [result, x] = xASL_module_Structural(x)

Description

This first ExploreASL module processes the structural images, i.e. high-resolution T1w and FLAIR (if present), on an individual (i.e. subject-to-subject) basis. If a FLAIR is present, this is processed first to obtain a WMH mask to fill the hypointense lesions on the T1w, before segmenting the T1w. For the T1w segmentation this module uses CAT12 by default but if this fails it falls back to SPM after trying to optimize the image contrast.

Workflow

LinearReg_T1w2MNI: Ensure the alignment of subjects' anterior commissure (AC) with the AC in MNI & apply this to all images
LinearReg_FLAIR2T1w: Align the FLAIR (if present) with T1w
FLAIR_BiasfieldCorrection: Perform a biasfield correction (if not performed by LST in following steps)
LST_Segment_FLAIR_WMH: Segment WMH lesions on FLAIR (if present)
LST_T1w_LesionFilling_WMH: Use WMH segmentation to fill lesions on T1w
Segment_T1w: Tissue segmentation on T1w
CleanUpWMH_SEGM: Extra WMH cleanup of some over- and under-segmentation
Resample2StandardSpace: Clone all images to standard space
GetVolumetrics: Obtain whole-brain volumes of GM, WM, CSF, WMH
VisualQC: Obtain QC parameters & save QC Figures
DoWADQCDC: QC for WAD-QC DICOM server (optional)

Recommended usage

% Initialize dataset
DataParPath = "ExamplePath";
ProcessData = true;
iWorker = 1;
nWorkers = 1;
x = ExploreASL_Initialize(DataParPath, ProcessData, iWorker, nWorkers);
% Run the structural module
[~, x] = xASL_Iteration(x,'xASL_module_Structural');

Interface definition

Input: x structure

Required input fields of the x structure:

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Output

Added output fields of the x structure:

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Generated files:

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3. Module ASL

Function

function [result, x] = xASL_module_ASL(x)

Description

This ExploreASL module processes the ASL images, i.e. ASL4D, M0, etc (if present), on an individual (i.e. session-to-session, where session indicates BIDS "run") basis. Both 2D and 3D options are automatially chosen, as well as processing of time-series (if available), such as motion correction and outlier exclusion.

Workflow

TopUpASL: FSL TopUp geometric distortion correction (if M0 images with reversed phase-encoding are present)
RealignASL: If time-series are present, motion correction and outlier exclusion (ENABLE)
RegisterASL: Registration of ASL to T1w anatomical images (if lacking, to MNI images)
ResliceASL: Resample ASL images to standard space
PreparePV: Create partial volume images in ASL space with ASL resolution
ProcessM0: M0 image processing
Quantification: CBF quantification
CreateAnalysisMask: Create mask using FoV, vascular outliers & susceptibility atlas
VisualQC_ASL: Generate QC parameters & images
WADQC: QC for WAD-QC DICOM server (OPTIONAL)

Recommended usage

[~, x] = xASL_Iteration(x,'xASL_module_ASL');

Interface definition

Input: x structure

Required input fields of the x structure:

...

Output

Added output fields of the x structure:

...

Generated files:

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4. Module Population

Function

function [result, x] = xASL_module_Population(x)

Description

This ExploreASL module processes all available images on the group level. It assumes that all images were adequately processed in the previous modules.

Workflow

CreatePopulationTemplates: Create population average images, to compare scanners, cohorts etc without physiological variance
CreateAnalysisMask: Generate a group-level mask by combining individuals masks, for ROI-based analysis & VBA
CreateBiasfield: When there are multiple scanners, create scanner-specific biasfields (uses Site.mat for this)
GetDICOMStatistics: Create TSV file with overview of DICOM parameters
GetVolumeStatistics: Create TSV file with overview of volumetric parameters
GetMotionStatistics: Create TSV file with overview of motion parameters
GetROIstatistics: Create TSV file with overview of regional values (e.g. qCBF, mean control, pGM etc)
SortBySpatialCoV: Sort ASL_Check QC images by their spatial CoV in quality bins
DeleteAndZip: Delete temporary files and gzip all NIfTIs

Recommended usage

[~, x] = xASL_Iteration(x,'xASL_module_Population');

Interface definition

Input: x structure

Required input fields of the x structure:

...

Output

Added output fields of the x structure:

...

Generated files:

...