Abstract
Background
The role of imaging in autoimmune encephalitis (AIE) remains unclear, and there are limited data on the utility of magnetic resonance imaging (MRI) to diagnose, treat, or prognosticate AIE.
Purpose
To evaluate whether MRI is a diagnostic and prognostic marker for AIE and assess its efficacy in distinguishing between various AIE subtypes.
Material and Methods
We analyzed data from 96 AIE patients from our prospective autoimmune registry. MRI sequences examined were FLAIR, diffusion, SWI, T2WI, ASL, and contrast enhancement. Short-term outcomes were measured using the Modified Rankin Scale (mRS) at discharge; long-term outcomes were assessed with the Functional Independence Measure (FIM) at 6 months.
Results
MRI confirmed AIE in cases of new-onset seizures (82.1%, P < 0.001) and dementia (100%, P = 0.02). Antibody-negative AIE exhibited significant multifocal FLAIR abnormalities compared to antibody-positive cases (P = 0.002). LGI1 and CASPR2 encephalitis frequently involved the mesial temporal region (P = 0.004), while ASL revealed hyperperfusion of the contralateral basal ganglia in faciobrachial dystonic seizures (P = 0.016). GAD65 encephalitis predominantly affected the cerebellum (P = 0.002), and NMDA encephalitis showed contrast enhancement in five cases (P = 0.045). MRI was not useful for predicting short-term outcomes but was associated with long-term outcomes; specifically, a normal MRI was linked to a better long-term outcome in 47.8% of patients (P = 0.035), and resolution of abnormalities correlated with a favorable FIM score (>54) in 76.7% (P = 0.016).
Conclusion
MRI is valuable for early detection of seizures or dementia as initial manifestations of AIE and for differentiating AIE subtypes. Follow-up MRI is significant in predicting long-term outcomes.
Introduction
In the past decade, there has been a dramatic rise in the identification and characterization of autoimmune encephalitis, driven by heightened awareness and advances in research. The California Encephalitis Project revealed that anti-NMDAR (N-methyl D-aspartate receptor) encephalitis is four times more prevalent than encephalitis caused by Herpes simplex virus 1, West Nile virus, or Varicella Zoster virus (1,2).
Autoimmune encephalitis (AIE) needs to be considered in any patient with a subacute onset of rapidly progressive (within 3 months) working memory impairment, altered mentation, or psychiatric symptoms, particularly if accompanied by at least one of the following: new focal neurological deficits; unexplained seizures; cerebrospinal fluid (CSF) pleocytosis; or magnetic resonance imaging (MRI) features indicative of encephalitis, after excluding alternative causes (3). Although detecting autoantibodies through cell-based immunoassays or immunoblotting is the most specific diagnostic tool, many autoimmune encephalitis cases are antibody-negative (4). Previous studies on imaging findings in AIE associated with surface antigens have shown that MRI findings may vary widely, ranging from normal to increased T2 signal intensities, often in the mesial temporal region (5). However, there has also been reports of involvement beyond the limbic system, including other lobes, the basal ganglia, cerebellum, brainstem, spinal cord, and multifocal abnormalities (6,7). The utility of MRI for diagnosing, treating, or prognosticating AIE has not been critically analyzed so far.
The aim of the present study was to describe MRI findings in patients with antibody-positive (non-paraneoplastic) and antibody-negative AIE at a tertiary care center in India. In doing so, we sought to address the following research questions, which remain unresolved: the utility of one or multiple MRI scans for diagnosing and differentiating between the various subtypes of AIE; and in management, the role of MRI in predicting short- and long-term outcomes for patients with AIE.
Material and Methods
We collected data from patients enrolled in our prospective AIE registry, which has been operational since 2013. The registry includes cases of antibody-positive and antibody-negative AIE diagnosed between 2013 and 2018. Patient selection was based on the International Encephalitis Consortium Diagnostic Criteria for Encephalitis and Encephalopathy of Presumed Infectious or Autoimmune Etiology (8) Approval was obtained from the ethics committee of Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCT/IEC/714). The procedures used in this study adhere to the tenets of the Declaration of Helsinki.
The exclusion criteria were infectious causes of encephalitis and other differential diagnoses, such as primary central nervous system angiitis, Bickerstaff's brainstem encephalitis, acute disseminated encephalomyelitis, Rasmussen's encephalitis, underlying malignancy, septic encephalopathy, metabolic encephalopathy, Hashimoto's encephalopathy, drug toxicity, cerebrovascular disease, neoplastic disorders, Creutzfeldt-Jakob disease, rheumatologic disorders (e.g. lupus, sarcoidosis), Reye’s syndrome (in children), mitochondrial diseases, and inborn errors of metabolism. These exclusion criteria were based on clinical findings and appropriate investigations.
As part of the protocol for our prospective registry, all patients underwent testing for serum and cerebrospinal fluid (CSF) antibodies to neuronal surface antigens and non-paraneoplastic antibodies. The autoimmune panel included a combination of NMDA, LGI1, CASPR2, GABABR1/B2, and AMPA1&2. For autoimmune encephalitis antibody testing, we used a fixed cell-based assay with HEK293 transfected cells (Euroimmun, Lübeck, Germany). Serum samples were diluted to 1:10, and CSF samples were tested neat (undiluted).
Our paraneoplastic panel included amphiphysin, CV2, PNMA2 (Ma2/Ta), Ri, Yo, Hu, SOX1, Recoverin, Titin, Zic4, Tr, and GAD65. Paraneoplastic antibodies were detected in serum using a commercially available immunoblot kit (Euroimmun, Lübeck, Germany) at a 1:101 dilution.
Patients underwent 3-T MRI scans (Discovery MR 750W; GE Healthcare, Milwaukie, USA), which were reviewed by two experienced neuroradiologists. The MRI sequences analyzed included T1-weighted (T1W), T2-weighted (T2W), 3D fluid attenuation inversion recovery (FLAIR), diffusion-weighted imaging (DWI), apparent diffusion coefficient (ADC), susceptibility-weighted imaging (SWI), magnetic resonance spectroscopy (MRS), arterial spin labeling (ASL), and T1 volumetric interpolated breath-hold examination (VIBE)/T1 blood-rapid volumetric acquisition (BRAVO) (post-contrast gradient sequences). We evaluated the follow-up MRI for resolution, volume loss, and cortical laminar necrosis.
Short-term outcomes were assessed using the modified Rankin Scale (mRS) at discharge, and long-term outcomes were assessed using the Functional Independence Measure (FIM) (9) at a 6-month follow-up. The follow-up period was uniform for all patients up to 6 months. An mRS score >3 and FIM score <54 was considered to have a poor outcome.
Statistical analysis
Demographic data and variables were analyzed; proportions were used for categorical variables and means with standard deviation for continuous variables. Bivariate analysis was performed using the Chi-square test for proportions. Unpaired t-tests and Mann–Whitney U-tests were used to analyze continuous variables, and the Shapiro–Wilk test was used to assess normality. The association between MRI and outcome was analyzed, and multivariate regression was carried out to evaluate the role of MRI in predicting outcomes. Variables with a P value < 0.1 were included in the multivariate regression model. A P value < 0.05 was considered statistically significant. The statistical analysis was performed using SPSS Statistics for Windows Statistics version 21.0 (IBM Corp., Armonk, NY, USA).
Results
Clinical characteristics
Of the 5459 patients admitted to the ward and intensive care unit during the study period, 96 (1.7%) were diagnosed with AIE, of which 59 (61.5%) patients were antibody positive. The mean age of the cohort was 28 ± 10 years (age range = 4–79 years). Among the antibody-positive cases, the majority were positive for anti-NMDA antibodies followed by anti CASPR2, LGI1, GAD65, and anti-glycine in that order. Seizures were the most common clinical presentation (including status epilepticus), followed by neuropsychiatric manifestations, involuntary movements, dementia, and Isaac's syndrome (Table 1).
Demographic, clinical, and imaging variables.
Values are given as n (%) or mean ± SD.
ASL, arterial spin labeling; FLAIR, fluid attenuation inversion recovery; MRI, magnetic resonance imaging.
Diagnostic role of MRI in AIE
MRI was found to be the primary diagnostic tool for patients with AIE with initial clinical presentation of new-onset seizures or rapidly progressive dementia. However, in patients who presented with status epilepticus or neuropsychiatric manifestations, MRI served only as an ancillary investigation. In these cases, AIE was diagnosed and treatment was initiated before MRI (Table 2).
Role of MRI in diagnosis of AIE.
AIE, autoimmune encephalitis; MRI, magnetic resonance imaging.
*Chi-square test.
MRI findings in AIE
MRI was carried out in all 96 patients, of which 61 (63.5%) had FLAIR abnormalities. Among these, majority patients showed bilateral involvement. The distribution of FLAIR abnormalities was predominantly involvement of multiple lobes, followed by involvement of mesial temporal, cerebellar, insula, basal ganglia, and parietal lobe, in that order (Table 1).
Diffusion restriction was observed in 17 (17.7%) patients, T2 shine-through in the ADC was seen in 18 (18.8%), and contrast enhancement was noted in 9 (9.4%) patients. SWI sequences did not show blooming. ASL hyperperfusion was noted in basal ganglia, mesial temporal region, and was also multifocal (Table 1). Follow-up MRI was available for 45 (46.8%) patients. Of these, resolution was noted in the majority, followed by volume loss and cortical laminar necrosis (Table 2).
MRI in antibody-positive versus antibody-negative cases
On comparing imaging findings between antibody-positive and antibody-negative cases, we noted a significantly higher prevalence of multifocal FLAIR abnormalities (Fig. 1) in antibody-negative cases (n = 19, 79.2%) than antibody-positive cases (n = 13, 37.8%) (P = 0.002). Follow-up MRI showed resolution in 15 (83.3%) antibody-positive cases compared to 14 (51.9%) antibody-negative cases (P = 0.015). No significant differences were found between the two groups with regard to other MRI parameters (Table 3).

Antibody negative encephalitis: (a) Axial FLAIR images; (b, c) axial DWI and ADC shows multiple gyriform swelling in the form of cortical and subcortical white matter hyperintensity in bilateral insula and frontotemporal region. These areas appear to be ADC hyperintense consistent with facilitated diffusion or edema. (d) T2* MR perfusion image shows high perfusion in left insulotemporal region suggestive of more cerebral blood flow due to active inflammation. ADC, apparent diffusion coefficient; DWI, diffusion-weighted imaging; FLAIR, fluid attenuation inversion recovery; MR, magnetic resonance.
Comparison of MRI characteristics in antibody positive and antibody negative patients.
Values are given as n (%).
FLAIR, fluid attenuation inversion recovery; MRI, magnetic resonance imaging.
MRI findings relevant to various antibody-positive subtypes
MRI findings relevant to the various antibody subtypes are summarized in Table 3. NMDA encephalitis (see Fig. 2) showed contrast enhancement in 5 (13.2%) cases (P = 0.045). In addition, the T2 shine-through effect was less evident in patients with NMDA encephalitis (n = 5, 13.2%; P = 0.026) when compared to other etiologies.

NMDA encephalitis: (a, b) axial FLAIR and T2 images show gyral swelling and hyperintensity of right cerebral hemisphere, left posterior temporal, and perirolandic regions; (c) diffusion restriction in the above regions; (d) post-contrast leptomeningeal enhancement in the affected areas. FLAIR, fluid attenuation inversion recovery.
Patients with CASPR2 and LGI1 encephalitis (Fig. 3) had a higher prevalence of mesial temporal hyperintensities (n = 9, 75%; P = 0.004), which were bilateral and symmetric in the majority (n = 5, 56%; P = 0.019), compared to other conditions. ASL hyperperfusion of the contralateral basal ganglia (Fig. 4) was noted in three cases of LGI1 and CASPR2 encephalitis with prototype faciobrachial dystonic seizures (FBDS) (P = 0.016) (Fig. 5).

LGI1 encephalitis: subacute phase (3-month follow-up); (a) axial FLAIR images and (b) post-contrast T1 images showing symmetric FLAIR hyperintensity with atrophy of bilateral limbic region with no contrast enhancement. FLAIR, fluid attenuation inversion recovery.

CASPR2 encephalitis: (a) axial T2W image shows asymmetric hyperintensity involving bilateral caudate and lentiform nucleus with patchy involvement of cingulate and left posterior temporal lobe; (b) DWI and (c) ADC show restricted diffusion of caudate and lentiform nucleus; (d) ASL shows asymmetric hyperperfusion of left caudate and insular-perisylvian region in a patient presenting with faciobrachial dystonic seizures. ADC, apparent diffusion coefficient; ASL, arterial spin labeling; DWI, diffusion-weighted imaging; T2W, T2-weighted.

Representative MR images of a case of LGI1 positive AIE at baseline and 6-month follow-up. Baseline: (a) axial FLAIR depicting hyperintensities in bilateral anteromedial temporal lobes, bilateral hippocampi, basifrontal regions, anterolateral basal ganglia; (b) axial T2W depicting hyperintensities in bilateral anteromedial temporal lobes, insular cortices, cingulate, bilateral hippocampi, anterolateral basal ganglia; (c) axial DWI showing restriction of rim of insular cortices, bilateral cingulate; (d) ASL showed no perfusion abnormalities; (e) axial T1 contrast-enhanced images showed no enhancement. Follow-up at 6 months: (f) axial FLAIR image shows follow-up atrophy of medial temporal lobes, decrease in hyperintensities in other regions; (g) axial T2 image shows a decrease in temporal lobe hyperintensities in bilateral anteromedial temporal lobes, insular cortices, and cingulate; (h) axial DWI depicting decreased diffusion restriction of rim of insular cortices and cingulate region on follow-up; (i) axial T1 contrast-enhanced images showed no enhancement. ADC, apparent diffusion coefficient; AIE, autoimmune encephalitis; ASL, arterial spin labeling; DWI, diffusion-weighted imaging; FLAIR, fluid attenuation inversion recovery; MR, magnetic resonance.
GAD65 antibody-mediated encephalitis had a propensity for cerebellar involvement (Fig. 6), with FLAIR hyperintensities in the cerebellum evident in 2 of 4 (50%) cases (P = 0.002). The single patient with anti-glycine antibody-mediated encephalitis showed multifocal hyperintensities on MRI.

GAD encephalitis: (a) axial and coronal FLAIR images shows patchy areas of hyperintensity in bilateral cerebellar hemispheres and vermis showing GAD cerebellitis; (b) representative images of another patient – axial FLAIR images depicting the bilateral hippocampal hyperintensities and gliotic changes in left parietal operculum and left inferior parietal lobule. FLAIR, fluid attenuation inversion recovery.
Short- and long-term outcomes in patients with AIE
At discharge, 71 (74%) patients had a mRS score of 0–2, while 25 (26%) had a mRS score of >3. At the last follow-up, 64 (67%) patients had a FIM score of ≥54 and 32 (33%) had a FIM score of <54.
MRI as a prognostic marker in AIE
On assessing the MRI parameters for their utility in predicting short-term outcome, no statistical significance was noted. However, in evaluating MRI and its association with long-term outcome (Table 4), the presence of a normal MRI in 11 (47.8%) patients (P = 0.035) and resolution of MRI abnormalities in 23 (76.7%) patients with a FIM score >54 (P = 0.016) were noted to be statistically significant. Multivariate regression analysis also indicated that a normal MRI (P = 0.001) and resolution of MRI changes (P = 0.02), particularly in antibody-positive patients (P = 0.037), were associated with a better outcome (FIM >54), suggesting a definitive role for MRI as a prognostic marker.
MRI as a predictor of short- and long-term outcomes.
Values are given as n (%).
*Modified Rankin Scale.
Chi-square test.
Functional independence measure.
Discussion
Our study involved a large cohort of patients with both antibody-positive and antibody-negative autoimmune encephalitis (AIE). The clinical presentations in these patients were varied, and a broad range of differential diagnoses were considered. We investigated the role of MRI as a diagnostic and prognostic marker in AIE and analyzed its ability to differentiate between various subtypes. In resource-limited settings, MRI can be expensive and labor-intensive, particularly for patients with AIE with acute presentation as recurrent seizures and behavioral abnormalities. However, the Antibody Prevalence in Epilepsy (APE) and Response to Immunotherapy in Epilepsy (RITE) scores, which include MRI findings as one of the components, highlight the role of MRI in the diagnosis of autoimmune epilepsy and evaluating response to immunotherapy even before antibody testing or in antibody-negative patients (10). This reiterates the importance of MRI in the diagnosis, management, and the prognosis of AIE.
We found that MRI plays an essential diagnostic role in patients with AIE presenting with new-onset seizures and rapidly progressive dementia. For new-onset seizures, in spite of similar MRI changes in post-ictal states (e.g. T2 signal abnormalities or diffusion restriction in gray or white matter) (11) and can mimic changes in infectious encephalitis, low-grade tumors, drug-induced toxicity, autoimmune encephalitis should still be considered if MRI findings include focal (more common in antibody-positive cases) or multifocal (more common in antibody-negative cases) FLAIR hyperintensities restricted to gray matter of limbic or extra-limbic regions, often with gyral swelling and without diffusion restriction in most cases. In rapidly progressive dementia, MRI findings, such as propensity for the limbic system and multifocal hyperintensities without diffusion restriction, suggest AIE and help exclude other causes like Creutzfeldt-Jakob disease, which has characteristic findings like cortical ribboning (12).
We identified specific MRI findings associated with each AIE subtype. Leptomeningeal enhancement was a prominent feature for NMDA encephalitis (Fig. 2). Previous studies showed that NMDA encephalitis often has a para-infectious trigger and the severity of neuropsychiatric manifestations associated with anti-NMDA receptor autoantibodies depends on blood–brain barrier integrity (13–15). A substantial proportion (42.1%) of patients with anti-NMDA positive encephalitis had either normal MRI or non-specific findings involving multiple regions, such as the mesial temporal lobe, cerebellum, insula, and parietal lobe. This is consistent with prior studies where MRI was normal in 21%–89% of patients (16–18). In addition, the T2 shine-through effect was less prevalent in NMDA encephalitis than in other etiologies. There are reports of posterior reversible encephalopathy syndrome due to autoimmune etiology associated with CASPR2 and LGI1 antibodies, the resultant vasogenic edema produces a T2 shine-through effect on MRI (19). In LGI1 and CASPR2-related encephalitis (Fig. 3), bilateral symmetric mesial temporal hyperintensities were observed, consistent with previous findings (20,21). Both LGI1 and CASPR2 are expressed in the hippocampus and limbic system, and thereby explain the predilection of these areas (22). ASL hyperperfusion of the contralateral basal ganglia (Fig. 4) was noted in three cases with LGI1-related encephalitis presenting with FBDS, which aligns with prior reports of perfusion, diffusion, or FLAIR abnormalities in the basal ganglia (23–26). This suggests a network hypothesis involving cortical and subcortical areas, with seizures typically originating in the temporal lobes and potentially spreading to the basal ganglia.
Anti-GAD65 antibody-positive cases (Fig. 6) showed a predilection for cerebellar involvement. Prior studies showed association of anti-GAD65 positivity with limbic encephalitis involving the mesial temporal lobes (27). Cerebellar atrophy was found in 8 of 14 patients with cerebellar ataxia who were anti-GAD65 positive earlier (28). Our study's novel finding of cerebellar involvement can be attributed to the high density of GAD-containing axon terminals in the cerebellum (29).
Our study also addressed antibody-negative autoimmune encephalitis, a diagnostic dilemma with scarce data. In patients with encephalitis of non-infectious etiology who test antibody-negative but are steroid-responsive, the presence of bilateral mesial temporal hyperintensities on T2-weighted/FLAIR MRI is highly suggestive of an immune-mediated disorder (4). Our findings showed a significantly higher prevalence of multifocal FLAIR abnormalities in antibody-negative cases and less resolution on follow-up MRI, indicating worse outcome when compared to antibody-positive cases. This expands the diagnostic armamentarium for detecting antibody-negative autoimmune encephalitis. Based on our data, the presence of normal MRI with resolution of FLAIR abnormalities on follow-up is a potential prognostic marker for long-term outcome. The greater resolution observed in antibody-positive cases compared to antibody-negative cases may be ascribed to the delay in diagnosis and initiation of immunomodulatory therapy in antibody-negative patients.
The present study has some limitations. These include the retrospective nature of the study and the need for high patient cooperation to minimize movement artefacts, resulting in ASL being performed in only 23 patients. The number of cases with anti-GAD (n = 4) and anti-glycine (n = 1) mediated encephalitis was limited, and follow-up MRI was available for only 45 patients. The follow-up MRI was also not obtained at a uniform time for all the patients.
Despite these limitations, our study highlights the role of MRI as both a diagnostic and prognostic marker in AIE. We developed an algorithm to assist in identifying specific AIE subtypes based on characteristic MRI findings (Fig. 7).

Utility of MRI in diagnosis of AIE. Alternate etiologies: primary central nervous system angiitis, Bickerstaff's brainstem encephalitis, acute disseminated encephalomyelitis, Rasmussen's encephalitis, underlying malignancy, septic encephalopathy, metabolic encephalopathy, Hashimoto's encephalopathy, drug toxicity, cerebrovascular disease, neoplastic disorders, Creutzfeldt-Jakob disease, rheumatologic disorders (e.g. lupus, sarcoidosis), Reye's syndrome (in children), mitochondrial diseases, and inborn errors of metabolism.
In conclusion, autoimmune encephalitis is primarily diagnosed based on clinical suspicion, with MRI providing crucial diagnostic clues to exclude alternative causes. MRI aids in the early detection of AIE, particularly in patients with seizures or dementia. The location of MRI abnormalities can be useful in differentiating between various AIE subtypes despite significant overlap. The resolution of MRI changes on follow-up is associated with a favorable long-term outcome.
Footnotes
Acknowledgments
We express our profound gratitude to Chandrasekharan Kesavadas, Neuroradiologist, and Rajalakshmi Poyuran, Neuropathologist, for their invaluable assistance in the methodology. Their expertise and guidance have been instrumental in the successful completion of this work
Declaration of conflicting interests
The authors declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.
Funding
This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors
