Gloria J. Guzman, MD, MSc Christopher Owen, MA Dan Marcus, PhD Russ Hornbeck, MCSC Matthew Smyth, MD, FAANS, FACS, FAAP Tammie Lee Benzinger, MD, PhD

Financial Disclosures Gloria Guzman, Christopher Owen, Dan Marcus, Russ Hornbeck, Matthew Smyth : None Tammie Lee Benzinger: Over 10k: She participates in clinical trials sponsored by Eli Lilly, Avid Radiopharmaceuticals, and Roche. and research funding from Avid Radiopharmaceuticals (current) Less 10k: Advisory Board membership for Eli Lilly (2011 She also reports providing expert testimony and receiving compensation from Kujawaski & Associates (2011)

PURPOSE

To prepare an educational exhibit on the workflow for volumetric MRI quantification in patients with Alzheimer’s dementia, multiple sclerosis and in medically intractable epilepsy

APPROACH/ METHODS

What is volumetric imaging? Technique used to assess volumetry of brain regions or whole brain volume after acquisition of high resolution MR images for the delineation of anatomical boundaries Most frequently used sequences are T1, T2 and proton density MR scanners are either 1.5 Tesla (T) or 3T systems. 3T systems offer higher resolution of tissue contrast (i.e. increased visualization of the borders between grey matter and white matter and cerebrospinal fluid)

Why is volumetry important? Early in the course of dementia, it is difficult to distinguish between dementia due to Alzheimer’s Disease (AD) versus other, potentially treatable causes of dementia, such as normal pressure hydrocephalus (NPH). Tools that more accurately diagnose early manifestations of this disease, such as hippocampal volumetry, are critical in patient management. It is also useful as a quantitative measure of disease progression Likewise, evaluation of general whole brain atrophy in Multiple Sclerosis (MS) patients can identify those that present with subtle or no clinical symptoms. These patients could benefit from early aggressive treatment if they demonstrate quantifiable and progressive brain volume loss. It is also useful as a quantitative measure of disease progression Finally, focal cortical dysplasia (FCD) and other cortical anomalies can be difficult lesions to identify radiographically. These patients have medically intractable epilepsy that significantly affects their quality of life. Surgical excision of these lesions results in marked improvement to complete resolution of the epileptic episodes. A color-coded volumetric map that can easily demarcate abnormal cortical areas would have a significant impact on patient management and outcomes

How is volumetry processed? The FreeSurfer software suite is an MRI-based brain imaging software package used in functional brain mapping that facilitates the visualization of the different anatomical regions of the brain cortex Contains both volume based and surface based analysis which can be used for the reconstruction of topologically correct and geometrically accurate models of both the gray/white matter and pial surfaces Surfaces used in conjunction with segmentation can be used for measuring cortical thickness, surface area and folding, and for computing inter-subject registration based on the pattern of cortical folds

Processing of volumetric map for MS and AD MR scans are moved to the Radiology supercomputer for parcelation and segmentation via the FreeSurfer software suit Whole brain, gray matter, and white matter volume are calculated and normalized via a comparison of subject intracranial volume to intracranial volume of a supernormal cohort (called ICV or eTIV in FreeSurfer) After normalization, the large ROI's are compared to a loess regression weighted against age generated with the supernormal cohort. Standard deviations and percentiles of specific subjects are calculated from the aforementioned loess regression. Subjects can be displayed longitudinally one a graph to show changes of volume over time with respect to the loess regression

MR scans are moved to the Radiology supercomputer for parcelation and segmentation via the FreeSurfer software suit Thickness values for each vertex on the pial layer are extracted from FreeSurfer assessor files, and normalized against the supernormal group A weighted loess regression is generated for every vertex in the FreeSurfer surface using the supernorm data set, and the z-score (number of standard deviations away from the mean) is calculated for the vertices of a subject's surface Processing of MRI volumetric map for FCD

The resulting z-scores are stored in a text file generated by the R-script and then converted to mgh (a file format created by Massachusetts General Hospital), which in this case is an "overlay" for the FreeSurfer suite An overlay can then be displayed on the patient's gray matter surface using freeview or tksurfer, and images generated from the z-score map The images can then be compared to what can be seen though tkmedit. In tkmedit, we look at the areas of the brain that have abnormal values in our z-score map to ensure that the z-scores are not due to errors in the surface themselves, rather than being a reflection of physiology

Example of adapted FreeSurfer using “R” coding program for AD For normalizing the supernormal group and generating a reference graph: #Find linear model between ROI and ICV hippLeftReg = lm(super$Left_Hippocampus_volume~super$IntraCranialVol) #Get head size (ICV) corrected hippocampal volume super$corrHippLeftVolume = (super$Left_Hippocampus_volume - hippLeftReg$coefficients[2]*(super$IntraCranialVol-mean(super$IntraCranialVol))) #Smooth population data with loess (weighted regression) smoothHippLeftFit = loess(super$corrHippLeftVolume~super$Age,degree=1,span=0.7) #Generate graph represeting Supernormal Data smoothHippLeftPred = predict(smoothHippLeftFit,newdata=43:90,se=TRUE) For normalizing the patient's data: #Calculate corrected hippocampal volume for patient data using the linear model already created normHippLeftVolume = all$Left_Hippocampus[all$Session==eval(parse(text=paste("\"",Subject_number,"\"",sep ="")))] normCorrHippLeftVolume = normHippLeftVolume - hippLeftReg$coefficients[2]*(all$IntraCranialVol[all$Session==eval(parse(text=paste("\" ",Subject_number,"\"",sep="")))]-mean(super$IntraCranialVol))

Normalization of data For MS and AD: The Super-Norm cohort is composed of scans from individuals who have tested cognitively normal in the Cognitive Dementia Rating (CDR 0) and have normal biomarker Mean Cortical Binding Potential (MCBP<0.18) or other normal cerebrospinal fluid (CSF) markers for at least three years after the included data For FCD: The normal children’s cohort is composed of patients from ages 4 to 15 who have had normal MRI brain scans at Saint Louis Children’s Hospital

FreeSurfer map

FreeSurfer map quality control Example of how the pial surface can extend into dura, and how you can fix it by editing brainmask.mgz

FINDINGS/DISCUSSION

CASES

Multiple sclerosis (MS)

52 year-old female with relapsing remitting MS currently on Aubagio. Visual evaluation on anatomical MR of volume loss is abnormal, but not strikingly so Multiple sclerosis CASE 1 - MS 2014

52 year-old female with relapsing remitting MS currently on Aubagio. Visual evaluation on anatomical MR is not strikingly abnormal. However, patient has advanced symptoms. She is unable to walk without assistance of a walker, and can only do so for 5 feet. Whole brain volume in the 2 nd percentile for age, very advanced compared to expected from visual qualitative evaluation CASE 1 - MS

52 year old, right-handed, Caucasian female with a history of relapsing remitting multiple sclerosis that was diagnosed in Significant visual atrophy between 2007 (top) and 2014 (bottom) Multiple sclerosis CASE 2 - MS 2014

52 year-old female with relapsing remitting MS currently on Aubagio. Visual evaluation demonstrates significant interval atrophy between 2007 and On whole brain volume evaluation done in 2014, brain volume is in the 9 th percentile for her age CASE 2 - MS

51 year old female, initially diagnosed in 2006 at age 42. She presents with worsening progression in number and size of T2/FLAIR hyperintense lesions. Patient was changed from Tysabri. She began Tecfidera in January This was begun, after failing Aubagio based on active MRI lesions. Below is MRI from 2015 (top) and 2014 (bottom) showing increase in size of left periventricular lesion (blue arrows) CASE 3 - MS

51 year old female, initially diagnosed in 2006 at age 42 year old. She presents with worsening progression in number and size of T2/FLAIR hyperintense lesions. Below is whole brain volumetry curve showing how the patient’s total brain volume is 2 standard deviations below the mean, at the 2 nd percentile CASE 3 - MS

Alzheimer’s Disease (AD)

74 year-old female. Presented at age 64, had nursing as a profession. Her mother died of AD at age 70 with disease onset at age 64. Patient’s initial complaint is of “word-finding difficulties”, has a clinical dementia rating score (CDR) of 0 and mini mental state examination (MMSE) score of 30. At age 70 has CDR of 0.5 and MMSE of 29. At age 74 has CDR of 1 and MMSE of 23. MRI Brain at age 74 shows moderate aging changes, see below CASE 1 - AD 2014

74 year-old female. Presented at age 64, had nursing as a profession. Her mother died of AD at age 70 with disease onset at age 64. Patient’s initial complaint is of “word-finding difficulties”, and at presentation has a clinical dementia rating (CDR) of 0 and mini mental state examination (MMSE) score of 30. At age 70 has CDR of 0.5 and MMSE of 29. At age 74 has CDR of 1 and MMSE of 23. Below is her volumetry graph demonstrating increasing loss of hippocampal volume, with more than 2 standard deviations below the mean: 1 st percentile on right and 0 th percentile on left CASE 1 - AD

69 year-old male with no family history of AD. Presented to our institution at age 62 with memory loss, was an aerospace engineer forced to retire by age 60, with initial onset of symptoms at age 57. At age 62 had a CDR of 0.5 and MMSE of 30. By age 63 had a CDR of 1 and MMSE of 27. Remained CDR 1 through age 68 with MMSE of 24 and by age 69 had CDR of 2 and MMSE of 19. By visual evaluation, loss of whole brain volume and hippocampal volume between 2009 and CASE 2 - AD

69 year-old male with no family history of AD. Presented to our institution at age 62 with memory loss, was an aerospace engineer forced to retire by age 60, with initial onset of symptoms at age 57. At age 62 had a CDR of 0.5 and MMSE of 30. By age 63 had a CDR of 1 and MMSE of 27. Remained CDR 1 through age 68 with MMSE of 24 and by age 69 had CDR of 2 and MMSE of 19. Below is volumetry graph demonstrating increasing loss of hippocampal volume, with more than 2 standard deviations below the mean: 2nd percentile on right and 1st percentile on left CASE 2 - AD

73 year-old female. Presented at age 70, had nursing as a profession in early youth and then was a home- maker after having children. Paternal history of AD at age 72 with death at age 79. Patient’s initial complaint is of problems with memory and has a clinical dementia rating (CDR) of 0.5 and mini mental state examination (MMSE) score of 28 at age 70. At age 73 has a CDR of 0.5 and MMSE of 28. Initially diagnosed with early amnesic disorder versus depression. Visually, there is decrease in volume between 2012 and CASE 3 - AD

73 year-old female. Presented at age 70, had nursing as a profession in early youth and then was a home-maker after having children. Paternal history of AD at age 72 with death at age 79. Patient’s initial complaint is of problems with memory and has a clinical dementia rating (CDR) of 0.5 and mini mental state examination (MMSE) score of 28 at age 70. At age 73 has a CDR of 0.5 and MMSE 28. Initially diagnosed with early amnesic disorder versus depression. Although there is no change in CDR or MMSE, there is decline of hippocampal volume bilaterally. Also note that even though the hippocampal volume is normal for age, IT IS DECREASING. During 2014 clinical visit, definite diagnosis of AD made, discarding diagnosis of depression CASE 3 - AD

68 year old male with right occipital infarct (blue arrow) presents with new onset memory loss after the stroke. Evaluation to discriminate between vascular dementia or AD. Initial read of chronic right occipital stroke, no other notable findings on original report EXTRA RELATED CASE 2014

68 year old male with right occipital infarct presents with new onset memory loss after the stroke. Evaluation to discriminate between vascular dementia or AD. Initial read of chronic right occipital stroke, no other notable findings. Images below show significant asymmetric atrophy of the right hippocampus (blue arrow) compared to the left, not noted on the original report. The occipital infarct extended anteriorly to include right hippocampus. An addendum added to the report once the volumetric data was available, which shows 2 nd percentile right and 34 th percentile left hippocampal volume EXTRA RELATED CASE

Focal Cortical Dysplasia (FCD)

13-year-old boy who has been suffering from medically refractory seizures since the first grade. He typically has clusters of seizures, better or partially controlled with a combination of Dilantin or Topamax. During the seizures, he abruptly begins yelling and moves his right arm and leg in a disorganized fashion. The seizures are associated with drowsiness but can occur in the daytime. He has some delays in language and development, but is at regular school. Imaging demonstrates focal cortical thickening in the right frontal lobe (superior frontal sulcus), with correlated area of decreased radiotracer uptake on PET-Brain CASE 1 - FCD

13-year-old boy who has been suffering from medically refractory seizures since the first grade. Cortical thickening identified with the help of PET BRAIN. He has had a comprehensive evaluation by our multidisciplinary epilepsy center culminating in a recommendation for surgery for a probable right frontal lobe onset with or without invasive electrode monitoring. Cortical volumetric mapping demonstrates lesion in red, as a region of increased thickening compared to adjacent normal cortex CASE 1 - FCD

Patient is an otherwise healthy, 11-year-old boy who had the onset of seizures at age 5. His seizures occur approximately once per month, but they can cluster with several in a month and he also went one period of two years with no seizures. He has been trialed on the number of anticonvulsant medications and has been evaluated by our Multidisciplinary Epilepsy Center including MRI, PET scan, and neuropsychological testing and interictal and ictal video EEG evaluation. Imaging shows cortical thickening at the right frontal lobe (superior and middle frontal gyrus) with correlated area of decreased radiotracer uptake on PET-Brain) CASE 2 - FCD

Patient is an otherwise healthy, 11-year-old boy who had the onset of seizures at age 5. He has been trialed on the number of anticonvulsant medications and has been evaluated by our Multidisciplinary Epilepsy Center including MRI, PET scan, and neuropsychological testing and interictal and ictal video EEG evaluation. Imaging shows cortical thickening at the right frontal lobe (superior and middle frontal gyrus) with correlated area of decreased radiotracer uptake on PET-Brain). Cortical volumetric mapping demonstrates lesion in red, as a region of increased thickening compared to adjacent normal cortex CASE 2 - FCD

SUMMARY

In summary Volumetric imaging can be a powerful quantitative tool for diagnosis and follow-up assessment of multiple neurological conditions, among them Alzheimer’s Disease, Multiple Sclerosis, and Focal Cortical Dysplasia Useful information is acquired from single point data, but more importantly, from longitudinal data that allows evaluation of disease progression that may be too subtle to assess clinically or by anatomical imaging alone

Where can I find this software? FreeSurfer can be downloaded for free at: AndInstall The “R” code used to produce these volumetric maps will be made available shortly in the open source website GitHub.com. As well, they can be acquired from Christopher Owen from our NeuroImaging Lab at:

References Barkovich AJ. "Current concepts of polymicrogyria. "Neuroradiology” 2010: 52(6), Free SL, Bergin, PS, Fish DR, et al. Methods for normalization of hippocampal volumes measured with MR. “American Journal of Neuroradiology” 1995: 16(4), Cleveland, WS. Robust locally weighted regression and smoothing scatterplots. “Journal of the American statistical association” 1979: 74(368), Buckner, RL, Head D, Parker J, et al. A unified approach for morphometric and functional data analysis in young, old, and demented adults using automated atlas-based head size normalization: reliability and validation against manual measurement of total intracranial volume. “Neuroimage” 2004:23(2),

Thank you for your attention!