Arterial Spin Labelling: Non-invasive measurement of perfusion

Transcription

1 Arterial Spin Labelling: Non-invasive measurement of perfusion Michael A. Chappell Institute of Biomedical Engineering & Oxford Centre for Functional MRI of the Brain University of Oxford.

2 Perfusion Perfusion is a measurement of delivery of blood to capillary bed Related to nutrient delivery to cells and waste removal. Altered by task activity. Changes in disease. Quantity of blood delivered per unit of tissue per unit of time ml blood / 100g tissue / min (Dimensions of [T] -1 ) Grey matter magic number: 60 ml/100g/min Cerebral Blood Flow (CBF) is a misleading name! To image perfusion we need a tracer.

3 FSL for Arterial Spin Labelling BASIL: a toolset for resting ASL quantification: CBF quantification. Calibration / M0 estimation Registration. Partial volume correction. Command line tools oxford_asl, basil, asl_reg, asl_calib Graphical User Interface asl_gui NEW VERSION! available as a pre-release - you will be using this version on the course.

4 What Have I Got Here!? What I have... What I want... What should I do? I just want to do something simple/easy! I must have absolute perfusion (ml/100g/min) Command line instructions here for future reference...

5 Outline Acquisition Keep it simple! Perfusion weighted images. Quantitative perfusion: Kinetics: A short course in tracer kinetics. Calibration: Measuring arterial blood magnetization. Preparing for group analysis. Advanced quantification: Distortion Correction Macro vascular contamination Partial Volume Correction

6 Arterial Spin Labelling A tracer experiment with an endogenous tracer - blood water. LABEL CONTROL Aquire image of brain Wait for blood to reach brain Label blood by magnetic inversion

7 Spot the difference? LABEL ASL Acquisition CONTROL Perfusion is ~60 ml/100g/min = 0.01 s -1 Signal is ~ 1-2%

8 Nuts & bolts: Labelling pasl: Pulsed ASL ASL Acquisition casl: Continuous ASL pcasl: psuedo-continous ASL Label a region in a single pulse Label blood by magnetic inversion Label blood flowing through a plane for some time pcasl uses pulses and is more widely available

9 ASL Nuts & bolts: Inflow time Acquisition casl/pcasl Wait for blood to reach brain Label blood by magnetic inversion casl label pasl label pasl Post-labeling delay (PLD) imaging time imaging Inversion time (TI) time

10 Nuts & bolts: Bolus/label duration ASL Acquisition Wait for blood to reach brain Label blood by magnetic inversion Label duration (τ) pasl label casl label TI1 pcasl Post-labeling delay (PLD) pasl QUIPSS II imaging time imaging pasl Label duration is undefined in pasl. QUIPSSII pulses cut off the end of the labeled bolus. Inversion time (TI) time

11 Nuts & Bolts: Readout ASL Acquisition Aquire image of brain Wait for blood to reach brain Label blood by magnetic inversion EPI (stack of 2D slices) Different PLD/TI for each slice GRASE/RARE (3D) Higher SNR Long echo-train: blurring Pre-saturation Saturate static signal at start of TR Background suppression Null static signal - reduce physiological noise

12 ASL Acquisition The ASL white paper - a good place to begin: Use pcasl where possible Label duration 1800 ms Post labeling delay ~1800 ms Otherwise pasl with QUIPSSII Inversion time ~1800 ms TI1 of 800 ms Slab thickness cm Ideally 3D readout. 2D EPI an acceptable alternative. Resolution: 3-4 mm in plane. 4-8 mm through plane. Use background suppression. Recommended Implementation of Arterial Spin Labeled Perfusion MRI for Clinical Applications: A consensus of the ISMRM Perfusion Study Group and the European Consortium for ASL in Dementia Magnetic Resonance in Medicine - 73 (1) p , 2015.

13 Outline Acquisition Keep it simple! Perfusion weighted images. Quantitative perfusion: Kinetics: A short course in tracer kinetics. Calibration: Measuring arterial blood magnetization. Preparing for group analysis. Advanced quantification: Distortion Correction Macro vascular contamination Partial Volume Correction

14 What I have... ASL data! Example (simple) Control Tag (labelled) Perfusion (difference) What I want... A perfusion image (in this subject). What should I do? Label-control subtraction Average Tissue + blood - = Tissue - blood 2 * blood asl_file --data={asldata.nii.gz} --ntis=1 --iaf=tc --diff --out={diffdata.nii.gz} asl_file --data={asldata.nii.gz} --ntis=1 --iaf=tc --diff --mean={diffdata_mean.nii.gz}

15 Outline Acquisition Keep it simple! Perfusion weighted images. Quantitative perfusion: Kinetics: A short course in tracer kinetics. Calibration: Measuring arterial blood magnetization. Preparing for group analysis. Advanced quantification: Distortion Correction Macro vascular contamination Partial Volume Correction

16 Example What I have... ASL data (calibration images) What I want... Perfusion in ml/100g/min - = What should I do? Label-control subtraction. Kinetic model inversion. M0 calculation.

17 Introduce tracer Kinetic Model Inversion Tissue (voxel) Arterial Input Function Residue Function ΔM(t) = F AIF(t) * r(t)

18 Kinetic Model Inversion Arterial Input Function Tracer conc n Tells us about the delivery of the tracer Time

19 Kinetic Model Inversion LABEL AIF T1 decay Tissue (voxel) Parameters: Arterial Transit time Bolus duration T1 decay (in blood) pasl

20 Kinetic Model Inversion LABEL AIF T1 decay Tissue (voxel) Parameters: Arterial Transit time Bolus duration T1 decay (in blood) casl/pcasl

21 Kinetic Model Inversion Residue Function 100% Tells us what happens to the tracer after is has arrived. Tracer Remaining time

22 Kinetic Model Inversion Rapid exchange: single well mixed compartment No spins leave the compartment Decay with T1 r(t) Well mixed T1 decay Parameters: Arterial Transit time Bolus duration T1 decay (in blood)

23 Kinetic Model Inversion LABEL T1 decay Well mixed AIF r(t) * M(t) = Parameters: Perfusion - F Arterial Transit time Bolus duration T1 decay (in blood) ΔM(t) = F AIF(t) * r(t)

24 Kinetic Model Inversion Arterial Input Function Residue Function Concentration time curve time time

25 Kinetic Model Inversion LABEL T1b decay The simple model Only one T1 value (blood) Well mixed T1t decay 1 :/ / I Spins never leave tissue The standard model: Separate T1 for blood and tissue (T1t < T1b). Spins leave voxel at rate determined by perfusion and partition coefficient. r(t) T1 (set) Time (sec) r(sec) Buxton et al., MRM 40(3), 1998.

26 What I have... ASL data (calibration images) What I want... Perfusion in ml/100g/min Example What you need to know about your data: Labeling pasl (pulsed) Inversion time(s) Bolus duration (if QUIPSS/Q2TIPS) or pcasl (continuous) Post-labeling delay(s) Labeling duration What should I do? Label-control subtraction. Kinetic model inversion. M0 calculation. Reado ut Model 3D/2D (slice timing) T1 (tissue and blood) Arterial Transit time oxford_asl -i {asl_data} -o {output_dir} --iaf={tc} {--casl} --tis={list_of_tis} bolus={bolus_duration} slicedt={time_per_slice} {model/analysis options}

27 assumption is not likely to be strictly 2. Labeled blood water is well mixed with tissue before outflow occurs Because the tissue water pool is much larger than the blood water pool,which and water assumption, are related to th exchange between blood and tissue is rapid, this is typically good assumption are typicallya relatively small. (Zhou J, Wilson D, et al. JCBFM, 21:440, 2001). Under these assumptions CBF in each vo Kinetic Model Inversion 3. The relaxation of the labeled spins are governed by blood T1. While this!"#!"""! (!"!!" assumption is not likely to be strictly true, the errors introduced by!"#$! this)!!!,!"##$!"#$%!" Analytical solutions - Simple model (ASL white paper ): CBF =![ml/10!! assumption, which are related to the difference in T1 between blood and tissue,!!!!!,!"##$!"!" (!!!!,!"##$ ) are typically pcaslrelatively small. pasl QUIPSS II and for QUIPSS II PASL using (37): Under these assumptions CBF in each voxel can be calculated for PCASL using (10): CBF =!"""! (!"!"#$%!"!!"!"#$!!!!!,!"##$!"!" (!!!!"#!!,!"##$ )!!!!!,!"##$ )![ml/100!g/min] CBF =!"""! (!"!"#$%"&!!"!"#$! )!!!!"!!"!"!"!!,!"##$![ml/10 where λ is the brain/blood partition coeffici and for QUIPSS II PASL using (37):!" averaged intensities in theimaging control a Post-labeling!!,!"##$ Label duration (τ) imaging pasl label signal QUIPSS II!"""! (!"!"#$%"&!!"!"#$! )! delay (PLD) CBF =![ml/100!g/min] longitudinal TI1 relaxation time of blood in sec!!!"!" casl label!!" signal intensity ofsialabel proton density where λ is the brain/blood partition coefficient in ml/g, SI are the time- weighte control and time time averaged signal intensities in the control and tag images respectively, and TI1 are as defined above. The factor blood is the Inversion timet1,(ti) longitudinal α=0.85 relaxation time of blood in seconds,ml/(100g)/min, α is the labelingwhich efficiency, SIPD is the in the p is customary α=0.98 signal intensity of a proton density weighted image, and τ is the label duration. PLD,inTICBF qu summary of parameters for use and TI1 are as defined above. TheFixed factor value: of 6000 converts the units from ml/g/s to II modification cannot be reliably T1bloodin=the 1650 msquipss (3T) literature. ml/(100g)/min, which is customary physiological See Table 3 for a Assumes AAT = 0 Single TI PASL without the summary of parameters for use in CBF that quantification. Arterialintensities Spin Labelling of : M.A. Chappell To scale the signal the subtra QUIPSS II modification cannot be reliably converted into CBF. signal intensity of fully relaxed blood spins To scale the signal intensities of the subtractedyield ASL-images to absolute CBF units, estimates of this value, we the recomme

28 What I have... ASL data (calibration images) What I want... Perfusion in ml/100g/min Example pcasl with labeling duration: 1.8 s post-label delay: 1.8 s 2D readout 45.2 ms per slice Assume white paper T1 : 1.6 s ATT : 0 s What should I do? Label-control subtraction. Kinetic model inversion. M0 calculation.

29 What I have... ASL data (calibration images) What I want... Perfusion in ml/100g/min Example pcasl with labeling duration: 1.8 s post-label delay: 1.8 s 2D readout 45.2 ms per slice Assume white paper T1 : 1.6 s ATT : 0 s What should I do? Label-control subtraction. Kinetic model inversion. M0 calculation. #Do label control subtraction asl_file --data={asldata.nii.gz} --ntis=1 --iaf=tc --diff --out={asldiffdata.nii.gz} \ --mean={asldiffdata_mean.nii.gz}

30 Example pcasl with labeling duration: 1.8 s post-label delay: 1.8 s 2D readout 45.2 ms per slice Assume white paper T1 : 1.6 s ATT : 0 s #Do label control subtraction > asl_file --data={asldata.nii.gz} --ntis=1 --iaf=tc --diff --out={asldiffdata.nii.gz} \ --mean={asldiffdata_mean.nii.gz}

31 Example pcasl with labeling duration: 1.8 s post-label delay: 1.8 s 2D readout 45.2 ms per slice Assume white paper T1 : 1.6 s ATT : 0 s # Do the analysis using oxford_asl > oxford_asl -i {ASLdata.nii.gz} -o {oxasl} --iaf=tc --casl --tis=3.6 --bolus=1.8 / --slicedt= wp --mc

32 Example pcasl with labeling duration: 1.8 s post-label delay: 1.8 s 2D readout 45.2 ms per slice Assume white paper T1 : 1.6 s ATT : 0 s Do motion correction # Do the analysis using oxford_asl > oxford_asl -i {ASLdata.nii.gz} -o {oxasl} --iaf=tc --casl --tis=3.6 --bolus=1.8 / --slicedt= wp --mc

33 Example Perfusion (arbitrary units) oxasl/native_space/perfusion.nii.gz

34 Example 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.

35 M0 Calculation LABEL M0a -M0a T1 decay Well mixed AIF r(t) M(t) 2.M0a * = ΔM(t) = 2 M0a CBF AIF(t) * r(t)

36 Cannot measure M0a directly. indirect via brain tissue magnetization. Calculate M0t. (M0 of tissue ) M0t to M0a. M0 Calculation Steady state magnetization With pre-saturation: ( ) S = M 0 1 e TR T 1 S = M ( 0 1 Ae t T ) 1t With background suppression: No static tissue - need separate calibration images i.e. a control image with BGS off. Account for relative proton densities: M 0a = M 0t λ oxford_asl... -c {calibration_image.nii.gz} --tr={tr} asl_calib --mode longtr... asl_calib --mode satrecov...

37 M0 Calculation Cannot measure M0a directly. indirect via brain tissue magnetization. Calculate M0t. (M0 of tissue ) M0t to M0a. Practicalities Reference tissue? Voxelwise? Voxelwise voxelwise M0a value Calculate M0t M0t M0a Reference tissue Reference tissue mask (CSF or WM) Single global M0a value (coil sensitivity correction) Perfusion (ml/100g/min) = (Perfusion / M0a) * 6000 oxford_asl... -c {calibration_image.nii.gz} --tr=[tr] asl_calib --mode longtr... asl_calib --mode satrecov... fslmaths {perfusion.nii.gz} -div [M0a] -mul 6000 {perfusion_calib.nii.gz}

38 assumption not likely to be strictly tr 2. Labeled blood water is well mixed with tissue before outflowis occurs Because the tissue water pool is much larger than the blood water pool, and water assumption, which are related to the d exchange between blood and tissue is rapid, this typically relatively a good assumption areistypically small. (Zhou J, Wilson D, et al. JCBFM, 21:440, 2001). Under these assumptions CBF in each voxel M0 Calculation 3. The relaxation of the labeled spins are governed by blood T1. While this!"#!!"""! (!" )!!,!"##$ assumption is not likely to be strictly true, the errors introduced this!"#$%!"!!"by!"#$! Analytical solutions - Simple model CBF =(ASL white paper ):![ml/100!! assumption, which are related to the difference in T1 between blood!and tissue,!!,!"##$!!!!,!"##$!"!" (!!! ) are typically relatively small. pcasl pasl QUIPSS II and for QUIPSS II PASL using Under these assumptions CBF in each voxel can be calculated for PCASL using (37): (10): CBF =!"""! (!"!"#$%!"!!"!"#$!!!!!,!"##$!"!" (!!!!"#!!,!"##$ )!!!!!,!"##$ ) CBF =![ml/100!g/min]!"""! (!"!"#$%"&!!"!"#$!!!!"!!"!"!"! )!!,!"##$![ml/100! where λ is the brain/blood partition coefficien α =intensities 0.98 α = 0.85!" averaged signal in the control and!!,!"##$!"""! (!"!"#$%"&!!"!"#$! )! longitudinal relaxation time of blood in secon CBF =![ml/100!g/min]!!!"!!"!" Perfusion (ml/100g/min) = (Perfusion / M0a) * 6000 of asiproton density weighted i where λ is the brain/blood partition coefficientsignal in ml/g,intensity SIcontrol and label are the timeti1 arerespectively, as definedtabove. The factor of 6 voxelwise approach: averaged signal intensities inathe control and and tag images 1, blood is the longitudinal relaxation time ofm blood efficiency, SIPD is thein the phy which is =customary with λ 0.9 ml/g Mseconds, = αsiispdthe/ λlabeling 0a = in 0t / λml/(100g)/min, signal intensity of a proton density weighted image, and τofisparameters the label duration. PLD, TI quan summary for use in CBF and are as defined The factorwith of 6000 the units fromcannot ml/g/s to SIPD is TI a 1proton density above. weighted image long converts TR II modification QUIPSS be reliably co ml/(100g)/min, which is customary in the physiological literature. See Table 3 for a For TR < 5s correct using: TR T1 and for QUIPSS II PASL using (37): S = M (1 e ) 0 quantification. Single TI PASL without the summary of parameters for use in CBF Arterial Spin Labelling : M.A.subtract Chappell To scale the signal intensities of the QUIPSS II modification cannot be reliably converted into CBF. signal intensity of fully relaxed blood spins is yield estimates this value, we recommend To scale the signal intensities of the subtracted ASL-images to of absolute CBF units, the

39 What I have... ASL data (calibration images) What I want... Perfusion in ml/100g/min Example pcasl with labeling duration: 1.8 s post-label delay: 1.8 s 2D readout 45.2 ms per slice Assume T1 (blood) : 1.6 s T1 (tissue) :1.3 s ATT : 1.3 s What should I do? Label-control subtraction. Kinetic model inversion. M0 calculation.

40 Calibration image No background-suppression TR: 4.8 s Example

41 Example Calibration image TR: 4.8 s Calibration mode Voxelwise # Do the analysis using oxford_asl > oxford_asl -i {ASLdata.nii.gz} -o {oxasl} --iaf=tc --casl --tis=3.6 --bolus=1.8 / --slicedt= wp --mc c {calibration_image.nii.gz} --tr=4.8

42 Perfusion (ml/100g/min) Example Correct for edge effects (and distortion) oxasl/native_space/perfusion_calib.nii.gz

43 Example Calibration image TR: 4.8 s Calibration mode Reference region CSF (ventricles) Calibration mask (derived automatically from structural image) # Do the analysis using oxford_asl > oxford_asl -i {ASLdata.nii.gz} -o {oxasl} --iaf=tc --casl --tis=3.6 --bolus=1.8 / --slicedt= wp --mc c {calibration_image.nii.gz} --tr=4.8 / --fslanat=t1.anat

44 Example Perfusion (ml/100g/min) Voxelwise Reference region Ventricular mask (automatically generated) oxasl/native_space/perfusion_calib.nii.gz

45 EXAMPLE What I have... ASL data - multi-ti/pld (calibration images) What I want... Perfusion in ml/100g/min What should I do? Label-control subtraction. Kinetic model inversion. M0 calculation. pcasl with labeling duration: 1.4 s post-label delays: 0.25, 0.5, 0.75,1.0, 1.25, 1.5 s TI: # Label control subtraction for each PLD individually > asl_file --data={asldata.nii.gz} --ntis=6 --iaf=tc --ibf=rpt --diff --split \ --mean={asldiffdata_mean_at_each_pld.nii.gz}

46 Kinetic Model Inversion LABEL T1 decay Well mixed AIF r(t) * M(t) = Parameters: Perfusion - F Bolus arrival time Bolus duration T1 decay (in blood) T1 decay (in tissue) ΔM(t) = F AIF(t) * r(t)

47 Kinetic Model Inversion Parameters: Perfusion - F Arterial Transit Time Bolus duration T1tissue Model white noise Data T1blood Single-TI/PLD Analytic solution Multi-TI/PLD Non-linear fitting (least squares) Bayesian inference (BASIL) Chappell et al., IEEE TSP 57(1), 2009.

48 Kinetic Model Inversion Perfusion Want to know this - variable Bolus/Arterial arrival time Want to correct for this - variable but limited to a sensible range Bolus/Label duration Set by sequence - fixed T1 tissue 1.3 s at 3T might not be that well fixed, pasl? - fixed T1 blood 1.66 at 3T Doesn't T1 vary a bit? - fixed Variability

49 Priors: Perfusion Bolus arrival time Bolus duration T1 Spatial 0.7 s 1.0 s 1.3 s Kinetic Model Inversion Spatial prior: Prior distribution for perfusion in voxel defined over its neighbours σ σ - spatial scale of prior (determined from the data)

50 EXAMPLE What I have... ASL data - multi-ti/pld (calibration images) What I want... Perfusion in ml/100g/min What should I do? Label-control subtraction. Kinetic model inversion. M0 calculation. pcasl with labeling duration: 1.4 s post-label delays: 0.25, 0.5, 0.75,1.0, 1.25, 1.5 s TI: # Label control subtraction for each PLD individually > asl_file --data={asldata.nii.gz} --ntis=6 --iaf=tc --ibf=rpt --diff --split \ --mean={asldiffdata_mean_at_each_pld.nii.gz}

51 Example pcasl with labeling duration: 1.4 s post-label delays: 0.25, 0.5, 0.75,1.0, 1.25, 1.5 s > oxford_asl -i {ASLdata.nii.gz} -o {oxasl} iaf=tc --ibf=rpt --casl \ --tis=1.65,1.9,2.15,2.4,2.65,2.9 --bolus=1.4 --slicedt= \ --fixbolus --artoff --mc \ -c {calibration_image.nii.gz} --tr=4.8

52 Data: pcasl Single-PLD label duration: 1.8 s post-label delay: 1.8 s Assume ATT of 1.3 s Example Ratio Perfusion (ml/100g/min) (multi/single) Single-TI Multi-TI Arrival (seconds) Multi-TI Multi-PLD label duration: 1.4 s PLDs: 0.25, 0.5, 0.75,1.0, 1.25, 1.5 s oxasl/native_space/perfusion_calib.nii.gz oxasl/native_space/arrival.nii.gz

53 Outline Acquisition Keep it simple! Perfusion weighted images. Quantitative perfusion: Kinetics: A short course in tracer kinetics. Calibration: Measuring arterial blood magnetization. Preparing for group analysis. Advanced quantification: Distortion Correction Macro vascular contamination Partial Volume Correction

54 Preparing for Group Analysis Group analysis and quantitative comparisons between individuals requires consistent representation Consistent geometry: Spatial normalization (registration) Transform perfusion map to a common space, e.g. MNI152 Consistent intensity: Quantitive maps - perfusion in ml/100g/min. Intensity normalization to a reference.

55 Registration to standard space ASL Structural linear - 6 DOF Structural Standard linear - 12 DOF non-linear Preparing for Group Analysis oxford_asl... --s {structural_image.nii.gz} See also: asl_reg, flirt, fnirt

56 Example Run fsl_anat on structural image BASIL will then do registration and transformation to: structural space standard space > fsl_anat {T1.nii.gz} > oxford_asl -i {ASLdata.nii.gz} -o {oxasl} --iaf=tc --casl --tis=3.6 --bolus=1.8 / --slicedt= wp --mc c {calibration_image.nii.gz} --tr=4.8 / --fslanat=t1.anat

57 Preparing for Group Analysis Quantitative maps requires estimate of M0a - calibration data. Pros: An absolute scale - can potentially relate to physiology Ought to be able to set consistent thresholds e.g. perfusion < 20 ml/100g/min is ischaemia Cons: Requires calibration information. Global perfusion appears to be quite variable between individuals. Intensity normalization: requires a reference. e.g. a brain structure: thalamus e.g. a global value: mean in GM or WM Pros: No need for calibration. NB still might want coil sensitivity correction. Removes inter subject variability in global perfusion. Cons: Relies on a consistent reference.

58 Preparing for Group Analysis Intensity normalization: Pick a ROI: Manually From atlas From a segmentation Calculate mean within ROI. Scale perfusion maps. oxford_asl... --norm oxford_asl... --report Transform ROI into perfusion space or vice versa? ROI in high-res -> perfusion space Interpolation on ROI mask: sharp boundaries in high-res become soft requiring thresholding - possible bias. Perfusion image -> high-res Interpolation occurs on perfusion values, ROI untouched. Exception is soft segmentations e.g. GM/WM on a structural image. Transform soft segmentations first and THEN threshold to create ROI.

59 GM PVE Preparing for Group Analysis Transform Threshold at 0.7 Threshold at 0.7 Transform Threshold at 0.7 High res GM mask

60 ROI GM / WM(?) partial volume issues Structures Voxelwise Designs Group mean Group differences/paired differences Feat (higher-level analysis) Randomise Group analysis Absolute perfusion: A direct physiological measurement e.g. Asllani et al., JCBFM, 28, A consistent baseline (c.f BOLD) e.g. Wang et. al, MRM, 49, Inter subject and inter session variability e.g Gevers et al., JCBFM, 31, Petersen et al., NeuroImage, 49(1), Arrival time (multi-ti/pld): Potential confound An extra quantitative measurement e.g. Bokkers et al., AJNR, 29(9), MacIntosh et al, AJNR, 33(10), 2012.

61 Outline Acquisition Keep it simple! Perfusion weighted images. Quantitative perfusion: Kinetics: A short course in tracer kinetics. Calibration: Measuring arterial blood magnetization. Preparing for group analysis. Advanced quantification: Distortion Correction Macro vascular contamination Partial Volume Correction

62 Advanced: Distortion Correction EPI readout will include distortion in regions of field inhomogeneity cf BOLD fmri Need to correct for: geometric distortion AND intensity AP encoding PA encoding Corrected Need: field map OR phase encode reversed image oxford_asl... --cblip={asl_calibration_phase_reversed} pedir=[direction] \ --echospacing=[value] oxford_asl... --fmap={fieldmap_image} --fmapmag={fieldmap_magnitude_image} \ --fmapmagbrain={brain_extracted_fmapmag} --pedir=[direction] --echospacing=[value]

63 Example pcasl with labeling duration: 1.8 s post-label delay: 1.8 s 2D readout 45.2 ms per slice Calibration images TR: 4.8 s (1) AP encoding (2) PA encoding echo spacing (dwell time): 0.06 ms # Do the analysis using oxford_asl > oxford_asl -i {ASLdata.nii.gz} -o {oxasl} --iaf=tc --casl --tis=3.6 --bolus=1.8 / --slicedt= wp --mc c {calibration_image.nii.gz} --tr=4.8 / --cblip={calibration_pa.nii.gz} --pedir=y --echospacing=0.06

64 Example Perfusion (ml/100g/min) oxasl/native_space/perfusion_calib.nii.gz

65 Advanced: Macro Vascular Contamination Early TIs may contain label still within larger arteries. perfusion overestimation Use long TI/PLD(s) Use flow suppressing gradients Include in model - multi-ti data provides estimate of arterial blood volume abv and TOF MIP oxford_asl: MV component included by default, use --artoff to turn off Ye et al., MRM 37(2), Chappell et al., MRM 63(5), 2010.

66 Advanced: Macro Vascular Contamination An extended model for ASL: CBF/aBV ΔM(t) = CBF ΔM tiss (t) + abv ΔM IV (t) Bolus arrival time Bolus duration Flat 0.7 s 1.0 s ARD 0.5 s 1.0 s ARD prior: ~N(0,v) v determines the relevance of the prior. v is determined from the data. Restrictive v 0 prior: parameter forced to prior mean v T1 1.3 s 1.6 s Liberal prior: parameter free to be estimated from data

67 EXAMPLE What I have... ASL data - multi-ti/pld (calibration images) What I want... Perfusion in ml/100g/min Arterial blood volume in ml/ml. What should I do? Tag-control subtraction. Kinetic model inversion. M0 calculation. pcasl with labeling duration: 1.4 s post-label delays: 0.25, 0.5, 0.75,1.0, 1.25, 1.5 s TI: > oxford_asl -i {ASLdata.nii.gz} -o {oxasl} iaf=tc --ibf=rpt --casl \ --tis=1.65,1.9,2.15,2.4,2.65,2.9 bolus=1.4 --slicedt= \ --fixbolus --artoff --mc -c {calibration_image.nii.gz} --tr=4.8

68 Example Perfusion ml/100g/min Arterial cerebral blood volume % (ml/ml * 100) middle slice lower slice ~ Circle of Willis oxasl/native_space/perfusion_calib.nii.gz oxasl/native_space/acbv_calib.nii.gz

69 Advanced: Partial Volume Correction Partial voluming of grey and white matter inevitable. Leads to GM perfusion underestimation WM perfusion < GM WM blood arrival > GM Correction PV estimates from segmentation of structural image. Note: partial volume estimates NOT a hard segmentation or probabilities. Make separate GM and WM perfusion estimates in every voxel. An under determined problem.

70 Advanced: Partial Volume Correction Does it matter that much? Resolution of ASL ~ 3 x 3 x 5 mm Cortical thickness ~ 2-4 mm Unlikely to have many pure GM or WM voxels in the cortex Structural resolution Partial Volume Estimate Threshold at 90% ASL resolution Partial Volume Estimate Threshold at 90%

71 Does it matter that much? Resolution of ASL ~ 3 x 3 x 5 mm Cortical thickness ~ 2-4 mm What is this? Advanced: Partial Volume Correction 60 * PVEGM + 10 * PVEWM Estimated perfusion from ASL

72 Advanced: Partial Volume Correction What do we mean when we report GM or WM perfusion? Perfusion ml/100g/ min GM WM Whole brain Threshold on % PVE GM mask threshold at 90% oxford_asl... --report

73 Advanced: Partial Volume Correction Partial volume correction exploiting kinetic data: T1 decay GM WM BAT CBF: GM > WM Bolus arrival: WM > GM

74 Advanced: Partial Volume Correction Multi-component model: ΔM(t) = PV GM ΔM GM (t) + PV WM ΔM WM (t) + PV CSF ΔM CSF (t) + abv ΔM MV (t) Grey matter White matter CSF Macro vasc. ΔM CSF = 0 Spatial priors on CBF for GM and WM

75 Advanced: Partial Volume Correction Chappell et al., MRM 65(4), 2011.

76 EXAMPLE What I have... ASL data - multi-ti/pld (calibration images) What I want... Grey matter perfusion in ml/100g/min What should I do? Tag-control subtraction. Kinetic model inversion. M0 calculation. Partial volume correction pcasl with labeling duration: 1.4 s post-label delays: 0.25, 0.5, 0.75,1.0, 1.25, 1.5 s TI: Segmented structural image, e.g. fsl_anat output > oxford_asl -i {ASLdata.nii.gz} -o {oxasl} iaf=tc --ibf=rpt --casl \ --tis=1.65,1.9,2.15,2.4,2.65,2.9 bolus=1.4 --slicedt= \ --fixbolus --mc --pvcorr --fslanat=t1.anat \ -c {calibration_image.nii.gz} --tr=4.8

77 Perfusion (uncorrected) ml/100g/min EXAMPLE Grey matter perfusion ml/100g/min White matter perfusion ml/100g/min oxasl/native_space/perfusion_calib.nii.gz oxasl/native_space/pvcorr/perfusion_calib_masked.nii.gz oxasl/native_space/pvcorr/perfusion_wm_calib_masked.nii.gz

78 Need to know more FSL: The FMRIB Software Library BASIL: User guide & tutorials for FSL v5.0+ Follow the link for the pre-release and updated user guide/tutorials Oxford Neuroimaging Primers: Introduction to Perfusion Quantification using Arterial Spin Labelling Cover material in this lecture and more. Examples using BASIL (extended from the FSL course)

79 QuBIc, Engineering Science, Oxford Martin Craig Moss Zhao Flora Kennedy McConnell Tom Kirk WIN/FMRIB, Oxford Peter Jezzard Tom Okell Joe Woods Michael Kelly James Meakin Matthew Webster Mark Jenkinson Acknowledgements Brad MacIntosh (Univ. Toronto) Manus Donahue (Vanderbilt) Xavier Golay (UCL, London) Esben Petersen (Utrecht) Marco Castellaro (Padova) Ilaria Boscolo Galazzo (Verona)

80 Task-Based ASL Why use ASL for a functional experiment? A direct measure of perfusion changes - physiological response. (Potentially) fully quantitative - possible to calculate absolute perfusion. Good for low frequency designs. What are the challenges? SNR Temporal sampling - TR and the need for tag and control scans. Time series data will contain both ASL (tag-control difference) and BOLD effects (depends upon the TE used).

81 Task-Based ASL What I have... ASL data during a functional task. T C T C T C T C T C What I want... Activations What should I do? Tag-control subtraction GLM

82 Task-Based ASL Two options in FEAT Do subtraction before GLM (FILM prewhitening OFF) ONLY considers the perfusion contribution, subtraction removes BOLD signal. asl_file --data={asldata.nii.gz} --ntis=1 --iaf=tc --diff --out={diffdata.nii.gz} perfusion_subtract {ASLdata.nii.gz} {diffdata.nii.gz}

83 Task-Based ASL Two options in FEAT Full model Includes perfusion and BOLD contributions EV1 - Tag vs. Control EV2 - BOLD EV3 - Interaction

84 Special: QUASAR QUASAR multi-ti pasl acquisition. Mixture of flow suppression on and off. Saturation recovery control images Analysis model-based - include MV component model-free - numerical deconvolution (c.f. DSC) quasil -i {QUASAR_image} -o {out_dir} quasil -i {QUASAR_image} -o {out_dir} --mfree Petersen et al., MRM 55(2),2006. Chappell et al., MRM e-print, 2013.