Denoising arterial spin labeling perfusion MRI with deep machine learning

PurposeArterial spin labeling (ASL) perfusion MRI is a noninvasive technique for measuring cerebral blood flow (CBF) in a quantitative manner. A technical challenge in ASL MRI is data processing because of the inherently low signal-to-noise-ratio (SNR). Deep learning (DL) is an emerging machine learning technique that can learn a nonlinear transform from acquired data without using any explicit hypothesis. Such a high flexibility may be particularly beneficial for ASL denoising. In this paper, we proposed and validated a DL-based ASL MRI denoising algorithm (DL-ASL).MethodsThe DL-ASL network was constructed using convolutional neural networks (CNNs) with dilated convolution and wide activation residual blocks to explicitly take the inter-voxel correlations into account, and preserve spatial resolution of input image during model learning.ResultsDL-ASL substantially improved the quality of ASL CBF in terms of SNR. Based on retrospective analyses, DL-ASL showed a high potential of reducing 75% of the original acquisition time without sacrificing CBF measurement quality.ConclusionDL-ASL achieved improved denoising performance for ASL MRI as compared with current routine methods in terms of higher PSNR, SSIM and Radiologic scores. With the help of DL-ASL, much fewer repetitions may be prescribed in ASL MRI, resulting in a great reduction of the total acquisition time.     

Quantitation of renal perfusion using arterial spin labeling with FAIR-UFLARE

Quantitative perfusion imaging of human kidneys was performed using arterial spin labeling MRI with a fast spin echo readout-sequence. Perfusion maps of centrally located single slices were obtained in axial and coronal orientations. In ten healthy volunteers, the mean value of perfusion was 213+/-55 mL/(100g min) with a range from 140 to 319 mL/(100g min). These results are in accordance with literature data, considering the fact that FAIR only measures the perfusion component normal to the imaging plane. Intra-individual reproducibility errors of +/-11% were smaller than the natural interindividual variability of renal perfusion (SD = +/- 25%). Perfusion in the cortex was approximately 3-4 times higher compared to the medulla. Considering the relatively high resolution of 2x2x10 mm3, the ability to quantify perfusion, and the lack of ionizing radiation and contrast media, this technique should prove useful in diagnosing renal pathologies that are associated with reductions in tissue perfusion.     

Comparison of pulsed arterial spin labeling encoding schemes and absolute perfusion quantification

Arterial spin labeling (ASL) using magnetic resonance imaging (MRI) is a powerful noninvasive technique to investigate the physiological status of brain tissue by measuring cerebral blood flow (CBF). ASL assesses the inflow of magnetically labeled arterial blood into an imaging voxel. In the last 2 decades, various ASL sequences have been proposed which differ in their ease of implementation and their sensitivity to artifacts. In addition, several quantification methods have been developed to determine the absolute value of CBF from ASL magnetization difference images. In this study, we evaluated three pulsed ASL sequences and three absolute quantification schemes. It was found that FAIR-QUIPSSII implementation of ASL yields 10–20% higher signal-to-noise ratio (SNR) and 18% higher CBF as compared with PICORE-Q2TIPS (with FOCI pulses) and PICORE-QUIPSSII (with BASSI pulses). In addition, quantification schemes employed can give rise to up to a 35% difference in CBF values. We conclude that, although all quantitative ASL sequences and CBF calibration methods should in principle result in the similar CBF values and image quality, substantial differences in CBF values and SNR were found. Thus, comparing studies using different ASL sequences and analysis algorithms is likely to result in erroneous intra- and intergroup differences. Therefore, (i) the same quantification schemes should consistently be used, and (ii) quantification using local tissue proton density should yield the most accurate CBF values because, although still requiring definitive demonstration in future studies, the proton density of blood is assumed to be very similar to the value of gray matter.     

Comparison of multislice and single-slice acquisitions for pulsed arterial spin labeling measurements of cerebral perfusion

Multislice Q2TIPS is a widely used pulsed arterial spin labeling (PASL) technique for efficient and accurate quantification of cerebral blood flow (CBF). Slices are typically acquired inferior to superior from a tagging plane. Superior slices show signal loss greater than the loss expected from blood T1 decay. In order to assess the reasons for this additional signal loss, three single-slice acquisition studies were compared to multislice acquisition (six slices) in healthy volunteers. In Study 1 (n=8), the tagging plane was fixed in location, and the inversion time (TI2) was 1500 ms for each slice. For Study 2 (n=12), the tagging plane was fixed as in Study 1; however, TI2 increased as slices were acquired further from the tagging plane. In Study 3 (n=9), the tagging plane was kept adjacent to the imaging slice, and TI2 was 1500 ms for every slice. Gray matter (GM) and white matter (WM) signal-to-noise ratio (SNR) and CBF were measured per slice. GM SNR from single-slice acquisitions was significantly higher at slices 4-6 in Study 2 and at slices 2-6 in Study 3 compared to multislice acquisitions. Signal loss in distal slices of multislice acquisitions can be attributed to the destruction of tagged bolus in addition to blood T1 decay. If limited brain coverage is acceptable, perfusion images with greater SNR are achievable with limited slices and placement of the tagging region immediately adjacent to the site of interest.     

Arterial spin tagging perfusion imaging of rat brain: dependency on magnetic field strength

Perfusion-weighted imaging (PWI), using the method of arterial spin tagging, is strongly T(1)-dependent. This translates into a high field dependency of the perfusion signal intensity. In order to determine the expected signal improvement at higher magnetic fields we compared perfusion-weighted images in rat brain at 4.7 T and 7 T. Application of PWI to focal ischemia and functional activation of the brain and the use of two different anesthetics allowed the observation of a wide range of flow values. For all these (patho-)physiological conditions switching from 4.7 T to 7 T resulted in a significant increase of mean perfusion signal intensity by a factor of 2.96. The ratio of signal intensities of homotopic regions in the ipsi- and contralateral hemisphere was field-independent. The relative contribution of a) T(1) relaxation time, b) net magnetization, c) the Q-value of the receiver coils and d) the degree of adiabatic inversion to the signal improvement at higher field strength were discussed. It was shown that the main parameters contributing to the higher signal intensity are the lengthening of T(1) and the higher magnetization at the higher magnetic field.     

Blood oxygen level-dependent and perfusion magnetic resonance imaging: detecting differences in oxygen bioavailability and blood flow in transplanted kidneys

Functional magnetic resonance imaging (fMRI) is a powerful tool for examining kidney function, including organ blood flow and oxygen bioavailability. We have used contrast enhanced perfusion and blood oxygen level-dependent (BOLD) MRI to assess kidney transplants with normal function, acute tubular necrosis (ATN) and acute rejection. BOLD and MR-perfusion imaging were performed on 17 subjects with recently transplanted kidneys. There was a significant difference between medullary R2? values in the group with acute rejection (R2?=16.2/s) compared to allografts with ATN (R2?=19.8/s; P=.047) and normal-functioning allografts (R2?=24.3/s;P=.0003). There was a significant difference between medullary perfusion measurements in the group with acute rejection (124.4±41.1 ml/100 g per minute) compared to those in patients with ATN (246.9±123.5 ml/100 g per minute; P=.02) and normal-functioning allografts (220.8±95.8 ml/100 g per minute; P=.02). This study highlights the utility of combining perfusion and BOLD MRI to assess renal function. We have demonstrated a decrease in medullary R2? (decrease deoxyhemoglobin) on BOLD MRI and a decrease in medullary blood flow by MR perfusion imaging in those allografts with acute rejection, which indicates an increase in medullary oxygen bioavailability in allografts with rejection, despite a decrease in blood flow.     

Aberrant resting-state cerebral blood flow and its connectivity in primary dysmenorrhea on arterial spin labeling MRI

PurposeThis study aimed to clarify the resting-state cerebral blood flow alteration patterns induced by primary dysmenorrhea, investigate the relationships between cerebral blood flow alterations and clinical parameters of patients with primary dysmenorrhea, and explore whether brain regions with abnormal cerebral blood flow also feature functional connectivity changes.MethodsArterial spin labeling imaging and clinical parameters were acquired in 42 patients with primary dysmenorrhea and 41 healthy controls during their menstrual phases. Differences in cerebral blood flow were compared between the two groups, and the clusters with significant group differences were selected as the regions of interest for further statistical analyses.ResultsCompared to healthy controls, patients with primary dysmenorrhea exhibited increased cerebral blood flow in the bilateral precuneus, left posterior cingulate cortex, and right rolandic operculum. Among patients with primary dysmenorrhea, we identified a negative correlation between the cerebral blood flow in the right rolandic operculum and the visual analogue score for anxiety, and greater correlation between the functional connectivity in the precuneus/posterior cingulate cortex and the right middle cingulate cortex, and between the right rolandic operculum and the left inferior parietal lobule and the bilateral postcentral gyrus.DiscussionCerebral blood flow abnormalities associated with primary dysmenorrhea were mainly concentrated in the areas comprising the default mode network in primary dysmenorrhea patients, which could be involved in the central mechanism of primary dysmenorrhea. Cerebral blood flow alteration in the rolandic operculum may underlie an anxiety-induced compulsive tendency in patients with primary dysmenorrhea. Investigating the enhanced connectivity among various pain-related brain regions could improve understanding of the onset and development of primary dysmenorrhea.     

Validation study of a pulsed arterial spin labeling technique by comparison to perfusion computed tomography

Abnormalities in cerebral blood flow (CBF) are believed to play a significant role in the development of major neonatal neuropathologies. One approach that would appear ideal for measuring CBF in this fragile age group is arterial spin labeling (ASL) since ASL techniques are noninvasive and quantitative. The purpose of this study was to assess the accuracy of a pulsed ASL method implemented on a 3-T scanner dedicated to neonatal imaging. Cerebral blood flow was measured in nine neonatal piglets, the ASL–CBF measurements were acquired at two inversion times (TI) (1200 and 1700 ms), and CBF was measured by perfusion computed tomography (pCT) for validation. Perfusion CT also provided images of cerebral blood volume, which were used to identify large blood vessels, and contrast arrival time, which were used to assess differences in arterial transit times between gray and white matter. Good agreement was found between gray matter CBF values from pCT (76±1 ml/min per 100 g) and ASL at TI=1700 ms (73±1 ml/min per 100 g). At TI=1200 ms, ASL overestimated CBF (91±2 ml/min per 100 g), which was attributed to substantial intravascular signal. No significant differences in white matter CBF from pCT and ASL were observed (average CBF=60±1 ml/min per 100 g), nor was there any difference in contrast arrival times for gray and white matter (0.95±0.04 and 0.99±0.03 s, respectively), which suggests that the arterial transit times for ASL were the same in this animal model. This study verified the accuracy of the implemented ASL technique and showed the value of using pCT to study other factors that can affect ASL–CBF measurements.     

Spin labeling artery method perfusion MRI study of SPG4 and SCA3/MJD

Background

Spinocerebellar ataxia type 3 (SCA3) and Machado–Joseph disease (MJD) are similar diseases that are often referred to jointly as SCA3/MJD. As the most common autosomal-dominantly inherited subtype of hereditary spastic paraplegia (HSP), HSP4 (or SPG4) has overlapping symptoms with SCA3/MJD, which hinders their diagnoses. Arterial spin labeling (ASL) is a noninvasive, contrast-agent free, magnetic resonance perfusion imaging method used to obtain maps of the cerebral blood flow (CBF). Here, we investigated the diagnostic value of ASL in SCA3/MJD and SPG4 patients.

Methods

A total of 13 SPG4 cases, 38 SCA3/MJD cases (22 onset patients and 16 genetic abnormality-only patients), and 27 healthy volunteers were examined by ASL. Data were processed to obtain the regional CBF (rCBF) and comparatively studied.

Results

In the pons, cerebellar dentate nucleus, and cerebellar cortex, rCBF of the onset SCA3/MJD group was significantly lower than that of the normal control group. In the cerebellar dentate nucleus and cerebellar cortex, the rCBF of the non-onset SCA3/MJD group was significantly lower than that of the control group. In the pons and cerebellar cortex, the rCBF of the onset SCA3/MJD group was significantly lower than that of the SPG4 group.

Conclusions

SCA3/MJD lesions are mainly located in the cerebellum and brainstem. Gray matter and white matter were both involved, although the deep cerebellar nuclei may be the earliest involved region. Cerebellar and brainstem lesions of SCA3/MJD were more severe than those of SPG4. ASL can aid the diagnosis of SCA3/MJD and SPG4.     

Abnormalities of cerebral blood flow in multiple sclerosis: A pseudocontinuous arterial spin labeling MRI study

Arterial spin labeling (ASL) is a noninvasive technique that can measure cerebral blood flow (CBF). To our knowledge, there is no study that examined regional CBF of multiple sclerosis (MS) patients by using this technique. The present study assessed the relationship between clinical presentations and functional imaging data in MS using pseudocontinuous arterial spin labeling (pCASL). Twenty-seven patients with MS and 24 healthy volunteers underwent magnetic resonance imaging and pCASL to assess CBF. Differences in CBF between the two groups and the relationships of CBF values with the T2-hyperintense volume were evaluated. Compared to the healthy volunteers, reduced CBF was found in the bilateral thalami and right frontal region of the MS patients. The volume of the T2-hyperintense lesion was negatively correlated with regional CBF in some areas, such as both thalami. Our results suggest that demyelinated lesions in MS mainly have a remote effect on the thalamus and that the measurement of CBF using ASL could be an objective marker for monitoring disease activity in MS.     

Why perfusion in neonates with congenital heart defects is negative--technical issues related to pulsed arterial spin labeling

Pulsed arterial spin labeling (PASL) perfusion MRI has unique advantages for measuring cerebral blood flow (CBF) in the pediatric population. In neonates with congenital heart defects (CHDs), however, a considerable number of negative CBF values were observed in PASL perfusion images. A set of specific physiological and biophysical conditions were proposed as plausible explanations for this phenomenon, including small body size, low blood flow, prolonged tracer life time (blood T1) and the "shunt" between pulmonary and systemic circulations in CHD. An optimized PASL scheme with a restricted label volume was proposed, and experimental data demonstrated reduced spurious negative values and lower intersubject variability of perfusion measurements in neonates with CHD as compared to standard PASL sequences.     

Absolute quantification of cerebral blood flow: correlation between dynamic susceptibility contrast MRI and model-free arterial spin labeling

Purpose

To compare absolute cerebral blood flow (CBF) estimates obtained by model-free arterial spin labeling (ASL) and dynamic susceptibility contrast MRI (DSC-MRI), corrected for partial volume effects (PVEs).

Methods

CBF was measured using DSC-MRI and model-free ASL (quantitative signal targeting with alternating radiofrequency labeling of arterial regions) at 3 T in 15 subjects with brain tumor, and the two modalities were compared with regard to CBF estimates in normal gray matter (GM) and DSC-to-ASL CBF ratios in selected tumor regions. The DSC-MRI CBF maps were calculated using a global arterial input function (AIF) from the sylvian-fissure region, but, in order to minimize PVEs, the AIF time integral was rescaled by a venous output function time integral obtained from the sagittal sinus.

Results

In GM, the average DSC-MRI CBF estimate was 150±45 ml/(min 100 g) (mean±SD) while the corresponding ASL CBF was 44±10 ml/(min 100 g). The linear correlation between GM CBF estimates obtained by DSC-MRI and ASL was r=.89, and observed DSC-to-ASL CBF ratios differed by less than 3% between GM and tumor regions.

Conclusions

A satisfactory positive linear correlation between the CBF estimates obtained by model-free ASL and DSC-MRI was observed, and DSC-to-ASL CBF ratios showed no obvious tissue dependence.     

Improving cerebral blood flow quantification for arterial spin labeled perfusion MRI by removing residual motion artifacts and global signal fluctuations

Denoising is critical to improving the quality and stability of cerebral blood flow (CBF) quantification in arterial spin labeled (ASL) perfusion magnetic resonance imaging (MRI) due to the intrinsic low signal-to-noise-ratio (SNR) of ASL data. Previous studies have been focused on reducing the spatial or temporal noise using standard filtering techniques, and less attention has been paid to two global nuisance effects, the residual motion artifacts and the global signal fluctuations. Since both nuisances affect the whole brain, removing them in advance should enhance the CBF quantification quality for ASL MRI. The purpose of this paper was to assess this potential benefit. Three methods were proposed to suppress each or both of the two global nuisances. Their performances for CBF quantification were validated using ASL data acquired from 13 subjects. Evaluation results showed that covarying out both global nuisances significantly improved temporal SNR and test-retest stability of CBF measurement. Although the concept of removing both nuisances is not technically novel per se, this paper clearly showed the benefits for ASL CBF quantification. Dissemination of the proposed methods in a free ASL data processing toolbox should be of interest to a broad range of ASL users.     

Balanced steady state free precession for arterial spin labeling MRI: Initial experience for blood flow mapping in human brain,retina, and kidney

We implemented pseudo-continuous ASL (pCASL) with 2D and 3D balanced steady state free precession (bSSFP) readout for mapping blood flow in the human brain, retina, and kidney, free of distortion and signal dropout, which are typically observed in the most commonly used echo-planar imaging acquisition. High resolution functional brain imaging in the human visual cortex was feasible with 3D bSSFP pCASL. Blood flow of the human retina could be imaged with pCASL and bSSFP in conjunction with a phase cycling approach to suppress the banding artifacts associated with bSSFP. Furthermore, bSSFP based pCASL enabled us to map renal blood flow within a single breath hold. Control and test–retest experiments suggested that the measured blood flow values in retina and kidney were reliable. Because there is no specific imaging tool for mapping human retina blood flow and the standard contrast agent technique for mapping renal blood flow can cause problems for patients with kidney dysfunction, bSSFP based pCASL may provide a useful tool for the diagnosis of retinal and renal diseases and can complement existing imaging techniques.     

Biexponential analysis of intravoxel incoherent motion in calf muscle before and after exercise: Comparisons with arterial spin labeling perfusion and T2

PurposeThis study aimed to clarify exercise-induced changes in intravoxel incoherent motion (IVIM) parameters obtained from diffusion-weighted imaging (DWI) of the calf muscle, as well as the relationships between IVIM parameters, perfusion, and water content in muscle tissue.Materials and methodsThirteen healthy volunteers underwent IVIM-DWI, arterial spin labeling (ASL), and multi-echo spin-echo T₂ mapping of the right calf on a 3.0-T magnetic resonance imaging scanner before and after performing dorsiflexion exercise. From the data, we derived the perfusion-related diffusion coefficient (D^⁎), perfusion component fraction (F), blood flow parameter (FD^⁎), and restricted diffusion coefficient (D) in the tibialis anterior muscle. The muscle blood flow (MBF) and transverse relaxation time (T₂) were also calculated from the ASL and multi-echo spin-echo data, respectively. We compared the parameters measured before and after exercise and assessed the relationship of each IVIM-derived perfusion parameter (D^⁎, F, and FD^⁎) with MBF and each diffusion parameter (D and ADC) or F with T₂.ResultsNotably, all these parameters were significantly increased after exercise. Before exercise, the FD^⁎ exhibited a significant positive correlation with the MBF, whereas no significant correlation was observed between D^⁎ or F and MBF. After exercise, both D^⁎ and FD^⁎ exhibited significant positive correlations with MBF, whereas F was not significantly correlated with MBF. Additionally, D was significantly correlated with T₂ after exercise, but not before exercise. No significant correlations were found between ADC and T₂ either before or after exercise.ConclusionsThe IVIM analyses before and after exercise enable the simultaneous evaluation of exercise-induced changes in perfusion and water diffusion in the muscle and increases the body of information on muscle physiology.     

Pulsed arterial spin labeling perfusion imaging at 3 T: estimating the number of subjects required in common designs of clinical trials

Pulsed arterial spin labeling (PASL) is an increasingly common technique for noninvasively measuring cerebral blood flow (CBF) and has previously been shown to have good repeatability. It is likely to find a place in clinical trials and in particular the investigation of pharmaceutical agents active in the central nervous system. We aimed to estimate the sample sizes necessary to detect regional changes in CBF in common types of clinical trial design including (a) between groups, (b) a two-period crossover and (3) within-session single dosing. Whole brain CBF data were acquired at 3 T in two independent groups of healthy volunteers at rest; one of the groups underwent a repeat scan. Using these data, we were able to estimate between-groups, between-session and within-session variability along with regional mean estimates of CBF. We assessed the number of PASL tag-control image pairs that was needed to provide stable regional estimates of CBF and variability of regional CBF across groups. Forty tag-control image pairs, which take approximately 3 min to acquire using a single inversion label delay time, were adequate for providing stable CBF estimates at the group level. Power calculations based on the variance estimates of regional CBF measurements suggest that comparatively small cohorts are adequate. For example, detecting a 15% change in CBF, depending on the region of interest, requires from 7-15 subjects per group in a crossover design, 6-10 subjects in a within-session design and 20-41 subjects in a between-groups design. Such sample sizes make feasible the use of such CBF measurements in clinical trials of drugs.     

Test-retest reliability and reproducibility of long-label pseudo-continuous arterial spin labeling

PurposeArterial spin labeling MRI can quantify the cerebral blood flow (CBF) without exogenous tracer. However, the variation of arterial transit time across different brain regions introduces bias for measuring local CBF, especially for those subjects with long arterial transit time (ATT). Long post-labeling delay (PLD) or multi-PLD methods could mitigate the problem of heterogenous ATT at the expense of the signal-to-noise ratio (SNR). Long-label ASL might address the low SNR problem by increasing the amount of labeled arterial blood. Thus, we hypothesized that with the same relatively long PLD, long-label pCASL may be more robust and reproducible than standard-label pCASL in population with potentially prolonged ATT. The purpose of the study was to investigate the reliability and reproducibility of long-label pCASL in the whole brain and vascular regions of interest in an elderly population, compared with standard-label pCASL.MethodTwenty adult volunteers (14 males, 6 females; age, 56.6 ± 17.2 years) were scanned twice on one 3.0 T scanner by standard-label pCASL (label duration (LD) = 1500 ms, PLD = 2000 ms) and long-label pCASL (LD = 3500 ms, PLD = 2000 ms). The intraclass correlation coefficient (ICC), within-subject coefficient of variation (wsCV), random noise and signal coefficient of variation(CoV) were used to assess global and regional reliability and reproducibility. Measurement agreement and difference were compared in different brain regions using correlation coefficient plots and Bland-Altman plots respectively.ResultsCBF value measured by long-label pCASL was overall higher than standard-label pCASL in all ROIs. Long-label pCASL had higher ICC than standard-label pCASL in most ROIs, and lower wsCV, random noise and CoV in all ROIs. Regardless of ASL method used, anterior circulation flow territories (ICC, 0.93–0.97; wsCV, 0.03–0.06) had higher CBF reliability and reproducibility than posterior circulation flow territories (ICC, 0.89; wsCV, 0.06–0.08). In all ROIs, the correlation analysis showed higher test-retest agreement (r_long-label > r_{standard-label}) and the Bland-Altman plots demonstrated lower measurement difference in long-label pCASL.ConclusionThe study demonstrated good reliability and reproducibility of long-label pCASL in anterior brain regions in the elderly population. To further improve CBF quantification in a long-ATT population while proper PLD is already used, increasing the label duration may help.     

Small angle neutron scattering and spin labeling of human ceruloplasmin

Small angle neutron scattering evidence of intermolecular correlations between cerulo plasmin units in anaqueous medium is provided. By the same technique, the radius of gyration of the globular biomolecule has been calculated to be 33 ± 3 Å. This value was found to agree very well with that measured by the authors with a spin labeling approach.     

An automated image-processing strategy to analyze dynamic arterial spin labeling perfusion studies. Application to human skeletal muscle under stress

Arterial spin labeling (ASL) perfusion measurements allow the follow-up of muscle perfusion with high temporal resolution during a stress test. Automated image processing is proposed to estimate perfusion maps from ASL images. It is based on two successive analyses: at first, automated rejection of the image pairs between which a large displacement is detected is performed, followed by factor analysis of the dynamic data and cluster analysis to classify pixels with large signal variation characteristic of vessels. Then, after masking these "vascular" pixels, factor analysis and cluster analysis are further applied to separate the different muscles between low or high perfusion increase, yielding a functional map of the leg. Data from 10 subjects (five normal volunteers and five elite sportsmen) had been analyzed. Resulting time perfusion curves from a region of interest (ROI) in active muscles show a good accordance whether extracted with automated processing or with manual processing. This method of functional segmentation allows automated suppression of vessels and fast visualization of muscles with high, medium or low perfusion, without any a priori knowledge.     

Ocular integrity following manganese labeling of the visual system for MRI

Injection of manganese into the eye will enhance the contrast of visual system neuronal pathways imaged by MRI (MEMRI). The present study was undertaken to determine the effect of a range of MnCl₂ doses upon the integrity of various ocular structures. Anesthetized mice received ocular anterior chamber injections of 50–500 nmol of MnCl₂. One week later, the eyes were fixed, embedded in paraffin, sectioned, and stained with hematoxylin and eosin. Additional animals received 50 nmol of MnCl₂ injected into the anterior chamber and were later imaged using T1-weighted 7 T MRI. Following 500 and 300 nmol MnCl₂, the corneal stroma and endothelium were degenerated, the anterior chamber contained a dense fibrin matrix with extensive inflammatory cell infiltration, a plaque often formed on the anterior lens, and significant retinal degeneration was observed. Following 100 nmol MnCl₂, retinal preservation of ocular structures was significantly better than at higher doses. In addition, there was no difference from vehicle control retina in cell counts within the ganglion cell layer, or in the width of the inner nuclear layer or outer nuclear layer. Also, there was no difference in the thickness of the inner plexiform layer. However, there was thinning of the peripheral outer plexiform layer, as well as in the outer segment layer. Visual system elements labeled in MRI of mice that received 100 nmol MnCl₂ included the retina, optic nerve, lateral geniculate nucleus, and superior colliculus. The preservation of ganglion cell layer cell counts and inner plexiform layer thickness following 100 nmol MnCl₂ suggests there was negligible injury to RGCs following this dose. These results support using 100 nmol MnCl₂ in mouse eyes for in vivo assessment of the integrity of RGC projections to target neurons in the brain.