Existing Packages. Overview. Siemens. Michael A. Chappell
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1 Existing Packages Michael A. Chappell Institute of Biomedical Engineering & Oxford Centre for Functional MRI of the Brain University of Oxford. Scanner manufacturers Siemens GE Philips Olea ASLtlbx CBFBIRN FSL / BASIL Overview Single-delay: pasl w. QUIPSSII Absolute perfusion (in theory) acquisition of a calibration (M0) image. Siemens 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 Single-delay: pcasl Output is a difference image (after tagcontrol subtraction) Absolute perfusion A calibration (M0) image is acquired. GE
2 single-delay: pasl w. QUIPSSII (EPISTAR) No post processing Philips 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. ASLtlbx Post-processing solution compatible with Matlab and SPM Useful wrapper function (also Matlab): 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 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.
3 FSL & BASIL FSL: The FMRIB Software Library (v5.0) OS X, Linux and Windows* compatible. BASIL: a toolset for resting ASL quantification: All varieties Single 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) What I have... ASL data (calibration images) Perfusion in ml/100g/min - = Tag-control subtraction. Kinetic model inversion. M0 calculation. labeling duration: 1.4 s Assume T1 (blood): 1.6 s T1 (tissue): 1.3 s BAT : 1.3 s Assume T1 (blood): 1.6 s T1 (tissue): 1.3 s BAT : 1.3 s Perfusion (arbitrary units) out1/native_space/perfusion.nii.gz
4 What I have... ASL data (calibration images) Perfusion in ml/100g/min Tag-control subtraction. Kinetic model inversion. M0 calculation. Background suppression on Calibration image Steady state TR = 6 s Calibration reference Calibration image with TR = 6 s Calibration reference (body coil) Perfusion (ml/100g/min) Calibration: CSF mask out2/native_space/perfusion_calib.nii.gz out2/calibration/refmask.nii.gz (overlaid on raw data) EXAMPLE 3 What I have... ASL data - multi-ti/pld (calibration images) Perfusion in ml/100g/min Tag-control subtraction. Kinetic model inversion. M0 calculation. labeling duration: 1.4 s post-label delays: 0.25, 0.5, 0.75,1.0, 1.25, 1.5 s TI:
5 Example 3 post-label delays: 0.25, 0.5, 0.75,1.0, 1.25, 1.5 s Data: pcasl Single-TI vs Multi-TI Perfusion (ml/100g/min) Arrival (seconds) Multi-TI Single-TI Assume BAT of 1.3 s Multi-TI PLDs:1.65,1.9,2.15,2.4,2.65,2.9 FSL: The FMRIB Software Library (v5.0) BASIL: User guide & tutorials FMRIB, Oxford Peter Jezzard Tom Okell Michael Kelly James Meakin Matthew Webster Acknowledgements Brad MacIntosh (Univ. Toronto) Manus Donahue (Vanderbilt) Xavier Golay (UCL, London) Esben Petersen (Utrecht) Marco Castellaro (Padova) Ilaria Boscolo Galazzo (Verona)
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