BLM is a recipient of EPSRC PhD studentship and received a travel grant to University of Eastern Finland from the School of Experimental Psychology, University of Bristol. MJK is funded by the Elizabeth Blackwell Institute and by the Wellcome Trust international strategic support fund [ISSF2: 105612/Z/14/Z]. KTJ and OHJG are funded by Academy of Finland, UEF-Brain strategic funding from University of Eastern Finland and by Biocenter Finland. The work was supported by The Dunhill Medical Trust [grant number R385/1114].

Animal procedures were conducted according to European Community Council Directives 86/609/EEC guidelines and approved by the Animal Care and Use Committee of the University of Eastern Finland, Kuopio, Finland.
1. Animal Model
<ol>
	<li>Anesthetize male Wistar rats weighing 300 - 400 g with isoflurane in N2/O2 flow (70%/30%) through a facemask for the duration of the operation and MRI experiments. Induce anesthesia in ventilated hood. Maintain isoflurane levels between 1.5 and 2.4%.
	<ol>
		<li>Monitor depth of anesthesia during MRI from breathing frequency via a pneumatic pillow under the torso. Lack of response to pinch reflex is taken as a sign of sufficient depth for surgical anesthesia. Use isoflurane scavenger attached to a magnet bore.</li>
	</ol>
	</li>
	<li>Perform permanent middle cerebral artery occlusion (MCAO) to induce focal ischemic stroke. Use the intraluminal thread model for MCAO and carry out the operation according to methods given by Longa et al.22.
	<ol>
		<li>Leave the occluding thread (silicon-PTFE tempered monofil filament, diameter 0.22 mm) in place for the duration of the MRI experiment.</li>
	</ol>
	</li>
	<li>Analyze arterial blood gases and pH using a blood analyzer.
	<ol>
		<li>During the MRI, monitor the breathing rate with a pneumatic pillow placed under the torso and the rectal temperature using a rectal temperature monitoring system. Maintain a core temperature close to 37 &#176;C using a water heating pad under the torso.</li>
		<li>Immediately after MCAO, secure the rat in a cradle at the center of the magnet bore using a rat head holder. Inject 2 mL of saline intraperitoneally before transferring the rats into the magnet bore.</li>
	</ol>
	</li>
</ol>
2. MRI
<ol>
	<li>Acquire MRI data using a 9.4T/31 cm (with the 12-cm gradient insert) horizontal magnet interfaced to a console equipped with an actively decoupled linear volume transmitter and quadrature receiver coil pair.</li>
	<li>Scan each rat for up to 5 h post MCAO. At hourly intervals (60, 120, 180, 240 min post MCAO), acquire 12 congruently sampled (0.5 mm slice-gap, slice thickness = 1 mm, field of view = 2.56 cm x 2.56 cm) coronal slices of the trace of diffusion tensor (2.2.1.), Carr-Purcell-Meiboom-Gill T2 (2.2.2.) and Fast Low Angle Shot T1 (2.2.3.).
	<ol>
		<li>Obtain the trace of the diffusion tensor images (Dav= 1/3 trace [D]) with three bipolar gradients along each axis (the duration of the diffusion gradient = 5 ms, the diffusion time = 15 ms) and three b-values (0, 400 and 1400 s/mm-2s), where, &#916; = 15 ms, &#8706; = 5 ms, echo time (TE) = 36 ms, repetition time (TR) = 4000 ms and acquisition time = 7.36 min.</li>
		<li>Obtain the Carr-Purcell-Meiboom-Gill T2 sequence with 12 echoes for T2 quantification, where echo-spacing = 10 ms, TR = 2000 ms and acquisition time = 4.20 min.</li>
		<li>Obtain the Fast Low Angle Shot (FLASH) for T1, where the time from inversion to the first FLASH sequence (T10) is 7.58 ms, with 600 ms increments of 10 inversions up to 5407.58 ms, TR = 5.5 ms, time between inversion pulses (Trelax) = 10 s and acquisition time = 8.20 min.</li>
	</ol>
	</li>
</ol>
3. Image Processing
<ol>
	<li>Computation of relaxometry and ADC maps: Compute qT2, qT1 and ADC maps using Matlab functions provided on University of Bristol website [DOI:10.5523/bris.1bjytiabmtwqx2kodgbzkwso0k], for which the input is a file path to the location of the MRI data.
	<ol>
		<li>For T2 data, apply Hamming filtering in k-space prior to reconstruction of images (or in image domain by convolution, with equivalent results but computationally less efficient). Compute qT2 maps by taking the logarithm of each time series and solving on a voxel-wise basis by linear least-squares (a&#160;bi-exponential fit can also be performed to the T2 decays, but the voxel-wise F-tests tests revealed that voxels within the image for which additional parameters could not be justified).</li>
		<li>For T1 data, apply Hamming filtering in k-space prior to reconstruction of images. Perform T1 fitting according to methods given in reference 23. To deal with the problem of unknown sign (due to the use of magnitude images), the lowest-intensity point may be either excluded, or estimated in the course of fitting with similar results.</li>
		<li>For diffusion-weighted data, apply Hamming filtering by convolution in image domain (this is more straightforward due to the segmented k-space trajectory). Fit ADC maps by the method in13.</li>
	</ol>
	</li>
	<li>Identification of ischemic tissue
	<ol>
		<li>Identify ischemic tissue on reciprocal Dav images (1/Dav) as this provides clear contrast for lesion identification. To generate ischemic volumes of interest (VOI), define ischemic tissue as voxels with values one median absolute deviation above the median value of the whole-brain 1/Dav distribution. To identify homologous regions in the non-ischemic hemisphere, reflect the ischemic VOI about the vertical axis. Manually adjust non-ischemic VOIs to avoid including voxels containing cerebrospinal fluid.</li>
		<li>In order to determine the relationship of qT1 and qT2 with time post MCAO, for each rat and time-point, load the ischemic and non-ischemic VOIs onto qT1 and qT2 maps. Extract mean relaxation times and calculate the percentage difference in qT1 and qT2 between hemispheres (&#916;T1 and &#916;T2) using the following equation: 
		<img alt="Equation" src="/files/ftp_upload/55277/55277eq1.jpg" /> 
		Where Tx is the chosen parameter, qT1 or qT2. <img alt="Equation" src="/files/ftp_upload/55277/55277eq2.jpg" />refers to the mean relaxation time of the ischemic VOI and <img alt="Equation" src="/files/ftp_upload/55277/55277eq3.jpg" /> the mean relaxation time in the non-ischemic VOI. The non-ischemic VOI should be used so that each rat serves as its own control.</li>
		<li>Use the following criteria to identify voxels with elevated qT1 and qT2: any voxels within the ischemic VOI with relaxation times exceeding the median relaxation time of the qT1 or qT2 distribution in the non-ischemic VOI by more than one half-width at half-maximum (HWMH). These criteria mean relaxation times must be in the 95th percentile or higher to be classified as &#39;high&#39;. Use of the median relaxation time of the non-ischemic VOI allows each rat to serve as its own control.</li>
		<li>To picture the spatial distribution of relaxation time changes within regions of decreased diffusion, identify and color code voxels with elevated qT1 or qT2 as well as voxels with both elevated qT1 and qT2 termed &#39;qT1 and qT2 overlap&#39;.</li>
		<li>To determine the size of the lesion according to qT1 and qT2, compute the parameter f (as introduced by Knight et al. 18) from MRI data acquired for each rat and time-point. f1 and f2 represent the number of voxels with high qT1 or qT2 (respectively) as a percentage of the size of the ischemic VOI.
		<ol>
			<li>Use the following equation to calculate f1 and f2: 
			<img alt="Equation" src="/files/ftp_upload/55277/55277eq4.jpg" /> 
			Where <img alt="Equation" src="/files/ftp_upload/55277/55277eq5.jpg" /> refers to the relaxation time (qT1 or qT2), <img alt="Equation" src="/files/ftp_upload/55277/55277eq6.jpg" />refers to the number of &#39;high&#39; relaxation time voxels in the ischemic VOI, <img alt="Equation" src="/files/ftp_upload/55277/55277eq7.jpg" /> is the number of &#39;low&#39; relaxation time voxels in the ischemic VOI and <img alt="Equation" src="/files/ftp_upload/55277/55277eq8.jpg" />, the total number of voxels within the ischemic VOI. Criteria for identifying voxels with elevated qT1 and qT2 are outlined in section 3.2.3. &#39;Low&#39; voxels are voxels with relaxation times less than the median qT1 or qT2 of the non-ischemic VOI by one HWHM. The subtraction of <img alt="Equation" src="/files/ftp_upload/55277/55277eq7.jpg" /> allows for decreases in relaxation times due to ischemia or other pathologies 17.&#160;</li>
			<li>Determine the extent of &#39;qT1&#160;and qT2&#160;overlap&#39; by calculating the volume of overlapping elevated qT1&#160;and qT2&#160;as a percentage of whole brain volumes, hereby referred to as &#39;VOverlap&#39;. Use the following equation: 
			<img alt="Equation" src="/files/ftp_upload/55277/55277eq9.jpg" /> 
			Where, <img alt="Equation" src="/files/ftp_upload/55277/55277eq10.jpg" /> refers to the number of voxels within the ischemic VOI with both &#39;high&#39; qT1 and &#39;high&#39; qT2 and <img alt="Equation" src="/files/ftp_upload/55277/55277eq11.jpg" /> represents the total number of voxels in the whole rat brain. Determine the number of voxels in the rat brain by manually creating a VOI around the whole brain on qT2 relaxometry maps.</li>
		</ol>
		</li>
	</ol>
	</li>
</ol>
4. Verification of Ischemic Lesion with Triphenyletrazolium Chloride (TTC)
<ol>
	<li>Immediately after decapitation, carefully extract the rat brain from the skull. Complete this procedure within 10 min from the time the rat was decapitated.</li>
	<li>Store brains in refrigerated 0.01 M phosphate buffered saline (PBS) before using a rat brain slicer matrix to section the brain into serial 1 mm-thick coronal slices.</li>
	<li>After sectioning, incubate each brain slice in 20 mL PBS containing TTC at 37 &#176;C for 30 min in the dark, as recommended in 24. Although 1% TTC concentration is acceptable, use 0.5% for improved contrast.
	<ol>
		<li>Cover the containers of the sections in foil to keep it dark.</li>
	</ol>
	</li>
	<li>After incubation, remove the TTC solution using a pipette and wash slices in three changes of PBS.</li>
	<li>Immediately photograph slices using a standard light microscope and a digital camera.</li>
</ol>
5. Statistical Analysis
<ol>
	<li>Carry out statistical analysis using Matlab and statistical software.</li>
	<li>Determining the relationship of MR parameters with time
	<ol>
		<li>Perform Pearson&#39;s correlations on pooled rat data to determine the relationship of &#916;T1, &#916;T2, f1 and f2 andVOverlap with time post MCAO.</li>
		<li>For parameters that show a significant linear relationship (p &#60;0.05), perform linear least square regression to determine whether stroke onset time can be predicted by quantifying the parameter of interest. Use the root mean square error (RMSE) to assess the accuracy of onset time estimates.</li>
	</ol>
	</li>
	<li>Quantification of lesion size
	<ol>
		<li>To compare lesion sizes according to different qMRI parameters, conduct one-way related ANOVAs and Fisher&#39;s least significant difference post-hoc on the average number of voxels in the ischemic VOI and the average number of voxels with high qT1 and qT2. Differences are considered significant at p &#60;0.05. If sphericity assumptions are not met per Mauchly&#39;s sphericity test, correct degrees of freedom and significance values according to Greenhouse Geisser estimates.</li>
	</ol>
	</li>
</ol>

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The authors have nothing to disclose.

The current protocol for estimation of stroke onset time in rats uses quantitative diffusion and relaxation time MRI data rather than signal intensities of respective weighted MR contrast images19. Recent evidence points to inferior performance of image intensities in estimating stroke onset time 14,25. In the &#39;diffusion-positive&#39; stroke lesion our MRI protocol provides stroke onset times from qT1 and qT2 MRI data with an accuracy of half an hour or so. It is a general trend that qT2 data outperforms that of qT1. The best accuracy for onset time determination is obtained from the volume of overlapping elevated qT1 and qT2 (Voverlap).
The images in Figure 1 demonstrate that while the reduced diffusion coefficient appears rather uniform, regions with abnormal qT1 and qT2 are heterogeneously scattered within the ischemic lesion. This finding is in accordance with previous observations and is likely due to different sensitivities of these qMRI parameters to pathophysiological changes caused by ischemia 6. This suggests qMRI parameters may be informative of tissue status and supports notions that DWI over-estimates ischemic damage 26. Indeed, recent preclinical evidence points toward the heterogeneity of ischemic damage within diffusion defined lesions 27. Thus, the combination of diffusion, qT1 and qT2 potentially provides information on stroke onset time and tissue status, both of which are clinically useful for treatment decisions regarding patients with unknown onset.
Voverlap and f2 gave the most accurate estimates of stroke onset time. The benefit of quantifying relaxation times is that unlike signal intensities they are insensitive to inherent variations caused by technical factors such as magnetic field inhomogeneities and proton density 6, including the expected magnetic field variation within the ischemic lesion 18. Reduced uncertainty associated with onset time estimates of qT1 and f1 are likely due to the aforementioned bi-phasic response of qT1 to ischemia, which contributes to the shallow slope of the time-dependent qT1 change 8,15,16. The MRI data shown (Figure 2) are in accordance with previous works 13,14, in that the time courses of relaxation time differences between the ischemic and contralateral non-ischemic brain are adequately described by linear functions. It is, however, important to note that the underpinning hydrodynamic changes due to ischemia are not linear 1,18.
The current MRI protocol for stroke time&#160;is demonstrated in rats subjected to permanent ischemia using the Longa et al. procedure 22. In our experience, the Longa et al. procedure fails to induce MCAO in 10-20% of rats, however, as ADC is used to verify presence of ischemia, the experiments can be terminated prematurely. Failure to induce MCAO is often due to imperfect occluder thread. A further factor resulting in experimental failures is that MCAO is a severe procedure causing death of up to 20% of rats during a prolonged MRI session.
The stroke onset timing protocol applies only to permanent ischemia. In rat focal ischemia with reperfusion, the relationship between Dav and qT1 or qT2 will dissociate as Dav&#160;recovers, but may not for qT1 and qT2&#160;depending on duration of ischemia prior to reperfusion 8,28. Additionally, the evolution of ischemic damage is likely to be more variable in stroke patients due to individual differences in factors affecting microcirculation such as age and co-morbidities (e.g., diabetes, hypertension, heart disease). These factors will inevitably influence the time dependence of f1, f2 and Voverlap in human strokes and thus requires investigation in clinical settings.
To conclude, qMRI parameters provide estimates of stroke onset time. Voverlap and f2 provide the most accurate estimates and may also be informative of tissue status. qMRI could therefore be clinically beneficial in terms of aiding treatment decisions for patients with unknown onset time. An issue to be considered here is that the gray-to-white-matter ratio in rat brain is much higher than in humans, and hydrodynamics in these brain tissue types may vary 18. Nevertheless, further investigation into the time dependence of f2, Voverlap and qT2 in hyper acute stroke patients is warranted.

Brain tissue is particularly vulnerable to ischemia due to the high dependence of the oxidative phosphorylation for ATP synthesis and limited energy reserves. Ischemia results in subtle time-dependent ionic changes in intracellular and extracellular spaces that lead to redistribution of brain water pools, release of excitotoxic neurotransmitters and ultimately initiation of destructive processes 1. In focal ischemia, tissue damage spreads beyond the initial core if blood flow is not restored within a certain time frame 2. The time of stroke onset is currently one of the key criteria in clinical decisions for the pharmacotherapy of ischemic stroke, including recanalization by thrombolytic agents 3. Consequently, many patients are automatically ineligible for thrombolytic therapy due to unknown symptom onset time, owing to the stroke occurring during sleep (&#39;wake-up stroke&#39;), lack of witness, or being unaware of symptoms 4,5. A procedure that determines the time of stroke onset is therefore required so that such patients may be considered for thrombolysis.
MRI probes water in vivo. Dynamics of which are severely perturbed by acute ischemic energy failure 6. Most notably, the diffusion of water governed by translational (thermal) motion of water molecules is reduced in the early moments of ischemia due to the energy failure 7. This in turn results in anoxic depolarization of neural cells 8. Diffusion MRI (DWI) has become a gold standard diagnostic imaging modality for acute stroke 9. The DWI signal increases rapidly in response to ischemia allowing ischemic tissue to be identified but does not show any time-dependency during the first few hours of ischemic stroke 10. Likewise, quantitative measures of water diffusion such as the apparent diffusion coefficient (ADC) or the trace of the diffusion tensor (Dav) decrease rapidly in ischemic tissue, but show no relationship with time from stroke onset in animal stroke models 10 and patients 11.
Quantitative MRI (qMRI) relaxation parameters, qT1, qT2 and qT1&#961;, are governed by rotational motion and the exchange of water hydrogen atoms and show complex time-dependent changes in brain parenchyma following ischemic energy failure 6. Such time-dependent changes enabled stroke onset time to be estimated in patients 12 and animal models of ischemia 13,14,15. In rat focal stroke, qT1&#961; increases almost instantaneously after ischemia onset and continues linearly for at least 6 hours 13,14. qT1 relaxation times also increase in a time-dependent fashion in ischemic brain tissue which can be described by two time constants: an initial fast phase followed by a slow phase lasting for hours 8,16. Because of this biphasic increase, the use of qT1 in stroke timing may be more complicated than that of qT1&#961; MRI 15. qT2 relaxation times also show a bi-phasic change in rat focal stroke, whereby there is an initial shortening within the first hour, followed by a linear increase with time 13. The initial shortening can be explained by two parallel running factors including: (i) the buildup of deoxyhemoglobin resulting in the so-called &#39;negative blood oxygenation level dependent effect&#39; and (ii), the shift of extracellular water into the intracellular space 17,18. The time-dependent increase in qT2 is likely due to cytotoxic and/or vasogenic edema with subsequent breakdown of intracellular macromolecular structures 18. Both qT1&#961; and qT2 data provide accurate estimates of stroke onset time in preclinical models 14. qT2 12 and T2-weighted signal intensities 19,20 have also been exploited for stroke onset time estimation in clinical settings.
In addition to hemispheric differences in quantitative relaxation times, the spatial distribution of elevated relaxation times within the ischemic region may also serve as surrogates for stroke onset time 14. In rat models of stroke, regions with elevated qT1&#961;, qT2 and qT1 relaxation times are initially smaller than the diffusion defined ischemic lesion but increase with time 14,15,21. Hence quantification of the spatial distribution of elevated relaxation times as a percentage of the size of the ischemic lesion also enables stroke onset time to be estimated 14,15. Here, we describe the protocol to determine stroke onset time in a rat model of stroke using qMRI parameters.

<table><tbody><tr><td></td><td></td><td>&lt;strong&gt;Magnetic Field Strength&lt;/strong&gt;</td><td>&lt;strong&gt;Operation Frequency&lt;/strong&gt;</td></tr><tr><td>MRI scanner</td><td>Agilent, Santa Clara, CA, USA</td><td>9.4T</td><td>400.13 MHz</td></tr><tr><td>Linear volume transmit RF-coil</td><td>RAPID Biomedical, Rimpar, Germany</td><td>-</td><td>400.13MHz</td></tr><tr><td>Actively decoupled receive coil</td><td>RAPID Biomedical, Rimpar, Germany</td><td>-</td><td>400.13MHz</td></tr><tr><td>Rat head holder</td><td>RAPID Biomedical, Rimpar, Germany</td><td></td><td></td></tr><tr><td>i-Stat handheld blood-gas analyzer</td><td>i-Stat Co, East Windsor, NJ, USA</td><td></td><td></td></tr><tr><td>Pneumatic pillow breathing rate monitor</td><td>SA Instruments Inc, Stony Brook, NY, USA</td><td></td><td></td></tr><tr><td>Rodent rectal temperarure moniring device</td><td>SA Instruments Inc, Stony Brook, NY, USA</td><td></td><td></td></tr><tr><td>&lt;strong&gt;Name&lt;/strong&gt;</td><td>&lt;strong&gt;Company&lt;/strong&gt;</td><td></td><td></td></tr><tr><td>&lt;strong&gt;Chemicals&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>Isoflurane: Attane Vet 1000mg/g</td><td>Piramal Healthcare UK Ltd, Northumberland, UK</td><td></td><td></td></tr><tr><td>2,3,5-Triphenyltetrazolium cholide=TTC</td><td>Sigma-Aldrich, Gillinham, Dorset, UK</td><td></td><td></td></tr></tbody></table>

a magnetic resonance imaging protocol for stroke onset time estimation in permanent cerebral ischemia

MRI provides a sensitive and specific imaging tool to detect acute ischemic stroke by means of a reduced diffusion coefficient of brain water. In a rat model of ischemic stroke, differences in quantitative T1 and T2 MRI relaxation times (qT1 and qT2) between the ischemic lesion (delineated by low diffusion) and the contralateral non-ischemic hemisphere increase with time from stroke onset. The time dependency of MRI relaxation time differences is heuristically described by a linear function and thus provides a simple estimate of stroke onset time. Additionally, the volumes of abnormal qT1 and qT2 within the ischemic lesion increase linearly with time providing a complementary method for stroke timing. A (semi)automated computer routine based on the quantified diffusion coefficient is presented to delineate acute ischemic stroke tissue in rat ischemia. This routine also determines hemispheric differences in qT1 and qT2 relaxation times and the location and volume of abnormal qT1 and qT2 voxels within the lesion. Uncertainties associated with onset time estimates of qT1 and qT2 MRI data vary from &plusmn; 25 min to &plusmn; 47 min for the first 5 hours of stroke. The most accurate onset time estimates can be obtained by quantifying the volume of overlapping abnormal qT1 and qT2 lesion volumes, termed 'Voverlap' (&plusmn; 25 min) or by quantifying hemispheric differences in qT2 relaxation times only (&plusmn; 28 min). Overall, qT2 derived parameters outperform those from qT1. The current MRI protocol is tested in the hyperacute phase of a permanent focal ischemia model, which may not be applicable to transient focal brain ischemia.

Across rats the blood gas profiles were as follows: SO2 95.8 &#177; 3.2%, PaCO2 51.6 &#177; 2.9 mmHg, and pH 7.30 &#177; 0.04.
Typical Dav, qT2 and qT1 images from a central slice of a representative rat at 4 time points post MCAO are shown in the first 3 panels of Figure 1a. Images in the other panels of Figure 1 show the automatically detected ischemic lesion in red and regions within the ischemic lesion with elevated qT1, qT2 and regions with Voverlap are shown in green. Up to 2 h post-MCAO, regions with high qT1 within the ischemic lesion were significantly larger than high qT2 (p &#60;0.01), but converged with time (Figure 1). The ischemic lesion by Dav was also larger than regions of high qT1 (p &#60;0.05) and qT2 (p &#60;0.05) in the first two hours.
The time dependencies of qMRI parameters are shown in Figure 2. All qMRI parameters were significant predictors of time post MCAO (&#916;T1:&#160;R2 = 0.71, &#916;T2:&#160;R2 = 0.75, f1: R2 = 0.53, f2: R2 = 0.82, Voverlap: R2 = 0.87). Based on the RMSE for each parameter, uncertainties associated with estimates of time since stroke onset were &#177; 37 min for &#916;T1, &#177; 28 min for &#916;T2, &#177; 47 min for f1, &#177;34 min for f2, and &#177;25 min for Voverlap. Thus, Voverlap gave the most accurate estimate of time since stroke onset.
TTC staining of brains samples around 6 h after MCAO verified irreversible ischemic damage predominantly in grey matter (Figure 1d).
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/55277/55277fig1.jpg" /> 
Figure 1: Changes in qMRI parameters due to ischemic stroke in an example rat. (a) shows example qMRI images over a 4 h period of ischemia. The first four columns show Dav maps, qT2 maps, qT1 maps and T2 weighted images respectively. Remaining columns show the Dav maps with various representations of the automatically segmented lesions. The automatically detected Dav lesion is shown in column 5 in red. In column 6 the Dav lesion is shown in red with voxels with high qT2 shown in green. In column 7 the Dav lesion is shown in red with high qT1 voxels shown in green. In column 8 the Dav lesion is shown in red with voxels with both elevated qT1 and qT2 (Voverlap) shown in green. (b) shows the distribution of qT2 in the Dav lesion as a function of time post MCAO, as well as the non-lesion qT2 distribution at time zero. (c) shows the corresponding qT1 distributions, the adjacent legend pertaining to both panels (b) and (c). (d) shows a TTC-stained brain slice after the animal was sacrificed at 6 h post-MCAO. <a href="http://cloudflare.jove.com/files/ftp_upload/55277/55277fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/55277/55277fig2.jpg" /> 
Figure 2: The relationships between time post-MCAO and qMRI parameters relevant to the timing of ischemia. (a) shows f1, (b) the f2, (c), Voverlap, (d),&#916;T1 and (e), &#916;T2. Best fit for each parameter (solid red line) and RMSE bars (solid black lines) are shown. Dotted lines represent each of the indivudual 5 rats subjected to MCAO. <a href="http://cloudflare.jove.com/files/ftp_upload/55277/55277fig2large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

Watch this Scientific Journal Video about A Magnetic Resonance Imaging Protocol for Stroke Onset Time Estimation in Permanent Cerebral Ischemia at JoVE.com

A Magnetic Resonance Imaging Protocol for Stroke Onset Time Estimation in Permanent Cerebral Ischemia

A protocol for stroke onset time estimation in a rat model of stroke exploiting quantitative magnetic resonance imaging (qMRI) parameters is described. The procedure exploits diffusion MRI for delineation of the acute stroke lesion and quantitative T1 and T2 (qT1 and qT2) relaxation times for timing of stroke.

MRI provides a sensitive and specific imaging tool to detect acute ischemic stroke by means of a reduced diffusion coefficient of brain water. In a rat ...

a-magnetic-resonance-imaging-protocol-for-stroke-onset-time

Research

JoVE Journal

Neuroscience

14.0K Views.  University of Bristol. Een protocol voor beroerte begin tijd schatting in een rat-model van een beroerte exploitatie van kwantitatieve magnetische resonantie beeldvorming (qMRI) parameters is beschreven. De procedure exploiteert verspreiding MRI voor afbakening van de acute beroerte laesie en kwantitatieve T1 , T2 (qT1 en qT2) ontspanning keer voor timing van een beroerte.

Video: A Magnetic Resonance Imaging Protocol for Stroke Onset Time Estimation in Permanent Cerebral Ischemia

Brain Infarct Segmentation and Registration on MRI or CT for Lesion-symptom Mapping

In lesion-symptom mapping (LSM), brain function is inferred by relating the location of acquired brain lesions to behavioral or cognitive symptoms in a group of patients. With recent advances in brain imaging and image processing, LSM has become a popular tool in cognitive neuroscience. LSM can provide fundamental insights into the functional architecture of the human brain for a variety of cognitive and non-cognitive functions. A crucial step in performing LSM studies is the segmentation of lesions on brains scans of a large group of patients and registration of each scan to a common stereotaxic space (also called standard space or a standardized brain template). Described here is an open-access, standardized method for infarct segmentation and registration for the purpose of LSM, as well as a detailed and hands-on walkthrough based on exemplary cases. A comprehensive tutorial for the manual segmentation of brain infarcts on CT scans and DWI or FLAIR MRI sequences is provided, including criteria for infarct identification and pitfalls for different scan types. The registration software provides multiple registration schemes that can be used for processing of CT and MRI data with heterogeneous acquisition parameters. A tutorial on using this registration software and performing visual quality checks and manual corrections (which are needed in some cases) is provided. This approach provides researchers with a framework for the entire process of brain image processing required to perform an LSM study, from gathering of the data to final quality checks of the results.

Provided here is a practical tutorial for an open-access, standardized image processing pipeline for the purpose of lesion-symptom mapping. A step-by-step walkthrough is provided for each processing step, from manual infarct segmentation on CT/MRI to subsequent registration to standard space, along with practical recommendations and illustrations with exemplary cases.

In lesion-symptom mapping (LSM), brain function is inferred by relating the location of acquired brain lesions to behavioral or cognitive symptoms in a ...

Behavior

Non-invasive Imaging and Analysis of Cerebral Ischemia in Living Rats Using Positron Emission Tomography with 18F-FDG

Stroke is the third leading cause of death among Americans 65 years of age or older1. The quality of life for patients who suffer from a stroke fails to return to normal in a large majority of patients2, which is mainly due to current lack of clinical treatment for acute stroke. This necessitates understanding the physiological effects of cerebral ischemia on brain tissue over time and is a major area of active research. Towards this end, experimental progress has been made using rats as a preclinical model for stroke, particularly, using non-invasive methods such as 18F-fluorodeoxyglucose (FDG) coupled with Positron Emission Tomography (PET) imaging3,10,17. Here we present a strategy for inducing cerebral ischemia in rats by middle cerebral artery occlusion (MCAO) that mimics focal cerebral ischemia in humans, and imaging its effects over 24 hr using FDG-PET coupled with X-ray computed tomography (CT) with an Albira PET-CT instrument. A VOI template atlas was subsequently fused to the cerebral rat data to enable a unbiased analysis of the brain and its sub-regions4. In addition, a method for 3D visualization of the FDG-PET-CT time course is presented. In summary, we present a detailed protocol for initiating, quantifying, and visualizing an induced ischemic stroke event in a living Sprague-Dawley rat in three dimensions using FDG-PET.

Non-invasive Imaging and Analysis of Cerebral Ischemia in Living Rats Using Positron Emission Tomography with 18F-FDG

Brain damage resulting from cerebral ischemia may be non-invasively imaged and studied in rats using pre-clinical positron emission tomography coupled with the injectable radioactive probe, 18F-fluorodeoxyglucose. Further, the use of modern software tools that include volume of interest (VOI) brain templates dramatically increase the quantitative information gleaned from these studies.

Stroke is the third leading cause of death among Americans 65 years of age or older1. The quality of life for patients who suffer from a stroke fails to ...

Medicine

Simultaneous PET/MRI Imaging During Mouse Cerebral Hypoxia-ischemia

Dynamic changes in tissue water diffusion and glucose metabolism occur during and after hypoxia in cerebral hypoxia-ischemia reflecting a bioenergetics disturbance in affected cells. Diffusion weighted magnetic resonance imaging (MRI) identifies regions that are damaged, potentially irreversibly, by hypoxia-ischemia. Alterations in glucose utilization in the affected tissue may be detectable by positron emission tomography (PET) imaging of 2-deoxy-2-(18F)fluoro-&#7429;-glucose ([18F]FDG) uptake. Due to the rapid and variable nature of injury in this animal model, acquisition of both modes of data must be performed simultaneously in order to meaningfully correlate PET and MRI data. In addition, inter-animal variability in the hypoxic-ischemic injury due to vascular differences limits the ability to analyze multi-modal data and observe changes to a group-wise approach if data is not acquired simultaneously in individual subjects. The method presented here allows one to acquire both diffusion-weighted MRI and [18F]FDG uptake data in the same animal before, during, and after the hypoxic challenge in order to interrogate immediate physiological changes.

The method presented here uses simultaneous positron emission tomography and magnetic resonance imaging. In the cerebral hypoxia-ischemia model, dynamic changes in diffusion and glucose metabolism occur during and after injury. The evolving and irreproducible damage in this model necessitates simultaneous acquisition if meaningful multi-modal imaging data are to be acquired.

Dynamic changes in tissue water diffusion and glucose metabolism occur during and after hypoxia in cerebral hypoxia-ischemia reflecting a bioenergetics ...

Performing Permanent Distal Middle Cerebral with Common Carotid Artery Occlusion in Aged Rats to Study Cortical Ischemia with Sustained Disability

Stroke typically occurs in elderly people with a range of comorbidities including carotid (or other arterial) atherosclerosis, high blood pressure, obesity and diabetes. Accordingly, when evaluating therapies for stroke in animals, it is important to select a model with excellent face validity. Ischemic stroke accounts for 80% of all strokes, and the majority of these occur in the territory of the middle cerebral artery (MCA), often inducing infarcts that affect the sensorimotor cortex, causing persistent plegia or paresis on the contralateral side of the body. We demonstrate in this video a method for producing ischemic stroke in elderly rats, which causes sustained sensorimotor disability and substantial cortical infarcts. Specifically, we induce permanent distal middle cerebral artery occlusion (MCAO) in elderly female rats by using diathermy forceps to occlude a short segment of this artery. The carotid artery on the ipsilateral side to the lesion was then permanently occluded and the contralateral carotid artery was transiently occluded for 60 min. We measure the infarct size using structural T2-weighted magnetic resonance imaging (MRI) at 24 hr and 8 weeks after stroke. In this study, the mean infarct volume was 4.5% &#177; 2.0% (standard deviation) of the ipsilateral hemisphere at 24 hr (corrected for brain swelling using Gerriet&#8217;s equation, n = 5). This model is feasible and clinically relevant as it permits the induction of sustained sensorimotor deficits, which is important for the elucidation of pathophysiological mechanisms and novel treatments.

Here we present a protocol to produce permanent distal middle cerebral artery occlusion in elderly female rats with simultaneous occlusion of the carotid arteries to generate large cortical infarcts and sustained deficits. We show confirmation of the lesion size using structural MRI at 24 hr and 8 weeks after stroke.

Stroke typically occurs in elderly people with a range of comorbidities including carotid (or other arterial) atherosclerosis, high blood pressure, ...

Induction of Ischemic Stroke and Ischemia-reperfusion in Mice Using the Middle Artery Occlusion Technique and Visualization of Infarct Area

Cerebrovascular disease is highly prevalent in the global population and encompasses several types of conditions, including stroke. To study the impact of stroke on tissue injury and to evaluate the effectiveness of therapeutic interventions, several experimental models in a variety of species were developed. They include complete global cerebral ischemia, incomplete global ischemia, focal cerebral ischemia, and multifocal cerebral ischemia. The model described in this protocol is based on the middle cerebral artery occlusion (MCAO) and is related to the focal ischemia category. This technique produces consistent focal ischemia in a strictly defined region of the hemisphere and is less invasive than other methods. The procedure described is performed on mice, given the availability of several genetic variants and the high number of tests standardized for mice to aid in the behavioral and neurodeficit evaluation.

We describe a mouse model of stroke induced by the occlusion of the middle cerebral artery using a silicone coated suture. The protocol can be applied to induce permanent occlusion or a temporary ischemia, followed by reperfusion.

Cerebrovascular disease is highly prevalent in the global population and encompasses several types of conditions, including stroke. To study the impact of ...

Transient Middle Cerebral Artery Occlusion Model of Neonatal Stroke in P10 Rats

A number of animal models have been used to study hypoxic-ischemic injury, traumatic injury, global hypoxia, or permanent ischemia in both the immature and mature brain. Stroke occurs commonly in the perinatal period in humans, and transient ischemia-reperfusion is the most common form of stroke in neonates. The reperfusion phase is a critical component of injury progression, which occurs over a period of days to weeks, and of the endogenous response to injury. This postnatal day 10 (p10) rat model of transient middle cerebral artery occlusion (tMCAO) creates a unilateral, non-hemorrhagic focal ischemia-reperfusion injury that can be utilized to study the mechanisms of focal injury and repair in the full-term-equivalent brain. The injury pattern that is produced by tMCAO is consistent and highly reproducible and can be confirmed with MRI or histological analyses. The severity of injury can be manipulated through changes in occlusion time and other methods that will be discussed.

Neonatal stroke is a significant cause of early brain injury requiring a translational model with consistent focal injury patterns and high reproducibility in order to enable study. This study describes the detailed surgical procedure for creating a non-hemorrhagic, unilateral focal ischemia-reperfusion injury in full-term-equivalent rodents.

A number of animal models have been used to study hypoxic-ischemic injury, traumatic injury, global hypoxia, or permanent ischemia in both the immature ...

Optimized Management of Endovascular Treatment for Acute Ischemic Stroke

This manuscript describes a streamlined protocol for the management of patients with acute ischemic stroke, which aims at the minimization of time from hospital admission to reperfusion. Rapid restoration of cerebral blood flow is essential for the outcomes of patients with acute ischemic stroke. Endovascular treatment (EVT) has become the standard of care to accomplish this in patients with acute stroke due to large vessel occlusion (LVO). To achieve reperfusion of ischemic brain regions as fast as possible, all in-hospital time delays have to be carefully avoided. Therefore, management of patients with acute ischemic stroke was optimized with an interdisciplinary standard operating procedure (SOP). Stroke neurologists, diagnostic as well as interventional neuroradiologists, and anesthesiologists streamlined all necessary processes from patient admission and diagnosis to EVT of eligible patients. Target times for every step were established. Actually achieved times were prospectively recorded along with clinical data and imaging scores for all endovascularly treated stroke patients. These data were regularly analyzed and discussed in interdisciplinary team meetings. Potential issues were evaluated and all staff involved was trained to adhere to the SOP. This streamlined patient management approach and enhanced interdisciplinary collaboration reduced time from patient admission to reperfusion significantly and was accompanied by a beneficial effect on clinical outcomes.

The outcome of patients with acute ischemic stroke depends on swift restoration of cerebral blood flow. This protocol aims at optimizing the management of such patients by minimizing peri-procedural timings and rendering the time from hospital admission to reperfusion as short as possible.

This manuscript describes a streamlined protocol for the management of patients with acute ischemic stroke, which aims at the minimization of time from ...

Quantification of Cerebral Perfusion using Laser Speckle Imaging and Infarct Volume using MRI in a Pre-clinical Model of Posterior Circulation Stroke

Background: Basilar artery occlusion (BAO) is a subset of posterior circulation stroke that carries a mortality as high as 90%.&#160; The current clinical standard to diagnose ischemic stroke include computerized tomography (CT), CT angiography and perfusion and magnetic resonance imaging (MRI). Large animal pre-clinical models to accurately reflect the clinical disease as well as methods to assess stroke burden and evaluate treatments are lacking.
Methods: We describe a canine model of large vessel occlusion (LVO) stroke in the posterior circulation, and developed a laser speckle imaging (LSI) protocol to monitor perfusion changes in real time.&#160; We then utilized high b-value DWI (b=1800s/mm2) MRI to increase detection sensitivity. We also evaluated the ability of magnetic resonance angiography (MRA) to assess arterial occlusion and correlate with DSA. Finally, we verified infarct size from apparent diffusion coefficient (ADC) mapping with histology.&#160;
Results:&#160; Administration of thromboembolism occluded the basilar artery as tracked by DSA (n=7).&#160; &#160;LSI correlated with DSA, demonstrating a reduction in perfusion after stroke onset that persisted throughout the experiment, allowing us to monitor perfusion in real time.&#160; DWI with an optimized b-value for dogs illustrated the stroke volume and allowed us to derive ADC and magnetic resonance angiography (MRA) images. The MRA performed at the end of the experiment correlated with DSA performed after occlusion. Finally, stroke burden on MRI correlated with histology.
Conclusions: Our studies demonstrate real time perfusion imaging using LSI of a canine thromboembolic LVO model of posterior circulation stroke, which utilizes multimodal imaging important in the diagnosis and treatment of ischemic stroke.

A canine model of LVO stroke was utilized to develop laser speckle imaging to monitor cerebral perfusion in real-time.&#160; Diffusion-weighted MRI was optimized to image infarct volume utilizing a high b-value, enabling ADC and MRA, correlated with DSA at the time of stroke.&#160; Finally, ADC reconstructions correlated with histological findings.

Background: Basilar artery occlusion (BAO) is a subset of posterior circulation stroke that carries a mortality as high as 90%.&#160; The current clinical ...

Non-Invasive Integrated PAUSAT Whole-Brain Imaging of Ischemic Stroke

Integrated Photoacoustic, Ultrasound, and Angiographic Tomography (PAUSAT) for NonInvasive Whole-Brain Imaging of Ischemic Stroke

Presented here is an experimental ischemic stroke study using our newly developed noninvasive imaging system that integrates three acoustic-based imaging technologies: photoacoustic, ultrasound, and angiographic tomography (PAUSAT). Combining these three modalities helps acquire multi-spectral photoacoustic tomography (PAT) of the brain blood oxygenation, high-frequency ultrasound imaging of the brain tissue, and acoustic angiography of the cerebral blood perfusion. The multi-modal imaging platform allows the study of cerebral perfusion and oxygenation changes in the whole mouse brain after stroke. Two commonly used ischemic stroke models were evaluated: the permanent middle cerebral artery occlusion (pMCAO) model and the photothrombotic (PT) model. PAUSAT was used to image the same mouse brains before and after a stroke and quantitatively analyze both stroke models. This imaging system was able to clearly show the brain vascular changes after ischemic stroke, including significantly reduced blood perfusion and oxygenation in the stroke infarct region (ipsilateral) compared to the uninjured tissue (contralateral). The results were confirmed by both laser speckle contrast imaging and triphenyltetrazolium chloride (TTC) staining. Furthermore, stroke infarct volume in both stroke models was measured and validated by TTC staining as the ground truth. Through this study, we have demonstrated that PAUSAT can be a powerful tool in noninvasive and longitudinal preclinical studies of ischemic stroke.

Author Spotlight: Integrated Photoacoustic, Ultrasound, and Angiographic Tomography (PAUSAT) for NonInvasive Whole-Brain Imaging of Ischemic Stroke  

This work demonstrates the use of a multimodal ultrasound-based imaging platform for noninvasive imaging of ischemic stroke. This system allows for the quantification of blood oxygenation through photoacoustic imaging and impaired perfusion in the brain through acoustic angiography.

Presented here is an experimental ischemic stroke study using our newly developed noninvasive imaging system that integrates three acoustic-based imaging ...

A Model of Transient Cerebral Ischemia by Occlusion of Middle Cerebral Artery

Transient Middle Cerebral Artery Occlusion Model of Stroke

Stroke stands as a major cause of death or chronic disability globally. Nevertheless, existing optimal treatments are limited to reperfusion therapies during the acute phase of ischemic stroke. To gain insights into stroke physiopathology and develop innovative therapeutic approaches, in vivo rodent models of stroke play a fundamental role. The availability of genetically modified animals has particularly propelled the use of mice as experimental stroke models.
In stroke patients, occlusion of the middle cerebral artery (MCA) is a common occurrence. Consequently, the most prevalent experimental model involves intraluminal occlusion of the MCA, a minimally invasive technique that doesn't require craniectomy. This procedure involves inserting a monofilament through the external carotid artery (ECA) and advancing it through the internal carotid artery (ICA) until it reaches the branching point of the MCA. After a 45 min arterial occlusion, the monofilament is removed to allow reperfusion. Throughout the process, cerebral blood flow is monitored to confirm the reduction during occlusion and subsequent recovery upon reperfusion. Neurological and tissue outcomes are evaluated using behavioral tests and magnetic resonance imaging (MRI) studies.

Author Spotlight: Assessing Ischemic Stroke Damage Through Middle Cerebral Artery Occlusion Model 

This protocol describes the model of transient focal cerebral ischemia in mice through intraluminal occlusion of the middle cerebral artery. Additionally, examples of outcome assessment are shown using magnetic resonance imaging and behavioral tests.

Stroke stands as a major cause of death or chronic disability globally. Nevertheless, existing optimal treatments are limited to reperfusion therapies ...

A Magnetic Resonance Imaging Protocol for Stroke Onset Time Estimation in Permanent Cerebral Ischemia

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