existing packages

Existing Packages

Michael A. [email protected]

www.ibme.ox.ac.uk/QuBIc

Institute of Biomedical Engineering & Oxford Centre for Functional MRI of the BrainUniversity of Oxford.

Existing Packages : M.A. Chappell

Overview

• Scanner manufacturers

➡ Siemens➡ GE➡ Philips

• Olea

• ASLtlbx

• CBFBIRN

• FSL / BASIL


Siemens

• Single-delay: pASL w. QUIPSSII

➡ Absolute perfusion (in theory)➡ acquisition of a calibration (M0) image.

• Multi-delay: pASL (3D-GRASE)

➡ relative CBF (no M0 estimation)➡ (future version might include M0 calibration)➡ Arrival time estimated (by Fourier transform method)➡ corrected relative CBF calcuated


GE

• Single-delay: pcASL

➡ Output is a difference image (after tag-control subtraction)

➡ Absolute perfusion➡ A calibration (M0) image is acquired.


Philips

• single-delay: pASL w. QUIPSSII (EPISTAR)

➡ No post processing


Olea

• Post-processing solution:

➡ loads tag-control pairs➡ 2D rigid motion correction➡ denoising➡ quantification for pASL w. QUIPSSII and pcASL➡ Uses a (M0) calibration image if available.

http://www.olea-medical.com


ASLtlbx

• Post-processing solution compatible with Matlab and SPM

• Useful wrapper function (also Matlab):

➡ http://www.mccauslandcenter.sc.edu/CRNL/tools/asl

➡ Absolute perfusion➡ single-delay: pASL or pcASL➡ Estimates M0 from WM or CSF using calibration (M0) image➡ denoising➡ motion correction➡ registration, segmentation and group analysis

https://cfn.upenn.edu/~zewang/ASLtbx.php


CBFBIRN

• Quantification of single-delay ASL (using CBFBIRN sequence)

➡ Subtraction (averaging).

➡ Kinetic model inversion.

➡ M0 calculation via CSF reference.

• Group analysis➡ Registration to standard space.

➡ Voxelwsie or ROI analyses.

https://cbfbirn.ucsd.edu


FSL & BASIL

• FSL: The FMRIB Software Library (v5.0)

➡ OS X, Linux and Windows* compatible.

• BASIL: a toolset for resting ASL quantification:

➡ All varietiesSingle and multi-delay, pASL and pcASL ...

➡ Absolute perfusion quantification.➡ Calibration / M0 estimation.➡ Registration➡ Partial volume correction.

➡ Command line tools and Graphical User Interface (beta in v5.0.4)

www.fmrib.ox.ac.uk/fsl

Perfusion Imaging : ASL Analysis : M.A. Chappell

Example 1

• What I have...➡ASL data➡ (calibration images)

• What I want...➡ Perfusion in ml/100g/min

• What should I do?➡Tag-control subtraction. ➡Kinetic model inversion.➡M0 calculation.

- =

✓← pcASL with

labeling duration: 1.4 spost-label delay: 1.0 s

AssumeT1 (blood): 1.6 sT1 (tissue): 1.3 sBAT : 1.3 s


Example 1

pcASL with tagging duration: 1.4 spost-label delay: 1.0 s

AssumeT1 (blood): 1.6 sT1 (tissue): 1.3 sBAT : 1.3 s


Example 1

Perfusion (arbitrary units)

out1/native_space/perfusion.nii.gz


Example 2

• What I have...➡ASL data➡ (calibration images)


• What should I do?➡Tag-control subtraction. ➡Kinetic model inversion.➡M0 calculation.

✓

←✓

Calibration image

Steady stateTR = 6 s

Calibration reference

Background suppression on


Example 2

pcASL with tagging duration: 1.4 spost-label delay: 1.0 s

Calibration image with TR = 6 sCalibration reference (body coil)


Example 2

Perfusion (ml/100g/min)

out2/native_space/perfusion_calib.nii.gz

Calibration: CSF mask

out2/calibration/refmask.nii.gz(overlaid on raw data)


EXAMPLE 3

• What I have...➡ASL data - multi-TI/PLD➡ (calibration images)


• What should I do?➡Tag-control subtraction.➡Kinetic model inversion.➡M0 calculation.

pcASL with labeling duration: 1.4 spost-label delays: 0.25, 0.5, 0.75,1.0, 1.25, 1.5 s

1.65 1.9 2.15 2.4 2.65 2.9TI:


Example 3

pcASL with tagging duration: 1.4 spost-label delays: 0.25, 0.5, 0.75,1.0, 1.25, 1.5 s


Single-TI vs Multi-TI

• Data:➡ pcASL➡ tagging duration: 1.4 s

➡Single-TIpost-label delay: 1.0 sAssume BAT of 1.3 s

➡Multi-TIPLDs:1.65,1.9,2.15,2.4,2.65,2.9

Perfusion (ml/100g/min) Arrival (seconds)Multi-TI


• FMRIB, Oxford➡ Peter Jezzard➡ Tom Okell➡ Michael Kelly➡ James Meakin➡ Matthew Webster

• Brad MacIntosh (Univ. Toronto)

• Manus Donahue (Vanderbilt)

• Xavier Golay (UCL, London)

• Esben Petersen (Utrecht)

• Marco Castellaro (Padova)

• Ilaria Boscolo Galazzo (Verona)

FSL: The FMRIB Software Library (v5.0)

➡ BASIL: www.fmrib.ox.ac.uk/fsl/basil

User guide & tutorials

Acknowledgements

existing packages

Documents