na-mic national alliance for medical image computing lesion classification in lupus update h....

NA-MICNational Alliance for Medical Image Computing http://na-mic.org

Lesion Classification in Lupus Update

H. Jeremy Bockholt

DBP2, MIND

National Alliance for Medical Image Computing http://na-mic.org

Background and Significance

• Systemic lupus erythematosus (SLE) is an autoimmune disease affecting multiple tissues, including the brain

– the facial rash of some people with lupus looked like the bite or scratch of a wolf ("lupus" is Latin for wolf and "erythematosus" is Latin for red). patients may feel weak and fatigued, have muscle aches, loss of appetite, swollen glands, and hair loss, sometimes have abdominal pain, nausea, diarrhea, and vomiting.

• Estimates of SLE prevalence range from 14.6-372 per 105

– About 1.5 million americans, 90% diagnosed are female

• Neuropsychiatric SLE (NPSLE), a term that subsumes the neurologic and psychiatric complications of SLE, occurs in up to 95% of SLE patients

• While MRI often reveals distinct white matter abnormalities in active NPSLE, the pathologic processes underlying these lesions, whether purely autoimmune or vascular (e.g., hemostasis), are unknown


Aims of the RO1 Study

• Test hypotheses concerning the possible thrombotic or embolic origin of white matter brain lesions in NPSLE

• Examine whether the incidence of lesions correlates with either levels of thrombosis markers or emboli in the blood or a potential source of emboli in the heart

• Examine whether overall lesion load or the levels of particular classes of lesion correlate with cognitive function


Background and Objective

• Critical to understanding the etiology of brain lesions in NPSLE will be the accurate measurement of their location, size, and time course.

• Lupus brain lesions are known to vary in MRI intensity and temporal evolution and include acute, chronic, and resolving cases.

• Monitoring the time course of image intensity changes in the vicinity of lesions, therefore, may serve to classify them based on their temporal characteristics.

• Major objective of this DBP will be the evaluation of existing tools and the development new tools using the NA-MIC kit for the time series analysis of brain lesions in lupus. As a roadmap initiative we are currently engaged in an end-to-end tutorial for lesion analyses in Slicer 3.


The MIND Institute / UNMThe Analysis of Brain Lesions in Neuropsychiatric Systemic Lupus Erythematosis

INVESTIGATORS:H. Jeremy Bockholt, MINDCharles Gasparovic, UNMSteve Pieper, IsomicsRoss Whitaker, UtahGuido Gerig, UtahMarcel Prastawa, UtahKilian Pohl, BWHBrad Davis, KitwareCONSULTANTS:Vincent Magnotta, UIOWAVince Calhoun, MIND, UNMPROGRAMMER:Mark Scully, MIND

BACKGROUND:• NPSLE is an autoimmune disorder that

causes neurological and psychiatric complications

• Afflicted patients have distinct white matter lesions that vary over time

• To understand the etiology of brain lesions in NPSLE, accurate measurement of lesion location, size, and time course must be achieved

AIMS:

• Create an end-to-end tutorial in the NA-MIC kit for lesion analyses in NPSLE

• Using the NA-MIC kit, create a time series analysis tool for brain lesions found in NPSLE

DATA:

• MRI sequences T1, T2, and FLAIR


Example NPSLE Lesion

Hypointense on T1 Hyperintense T2 Hyperintense on FLAIR


Challenges

• Lesion trace bronze standard will be manual traces done by expert rater– What happens if automated analyses

find broader range of lesions not visible to human

• Co-registration of T1, T2, FLAIR– Small lesions can be mostly edges and

suffer from partial voluming– Geometric distortion across sequences


Summary of MRI Protocol

• The MRI data in the roadmap initiative are collected on both a 1.5T Siemens Sonata scanner using an 8-channel head coil or 3.0T Siemens Trio using a 12-channel head coil. We plan to collect 5 patients and 5 controls with baseline and 6 month follow-up scans.

Scanner Contrast Sequence TR TE TI Vox Time1.5T T1 FLASH 12 4.76 . 1.1x1.1x1.5mm 6m32s

T2 FSE 9040 64 . 1.1x1.1x1.5mm 6m2sFLAIR FSE 1000 105 2500 1.1x1.1x1.5mm 9m2s

3.0T T1 MEMPR 2530 1.64 . 1.0x1.0x1.0mm 6m3sT2 MUGLER 3200 447 . 1.0x1.0x1.0mm 7m8s

FLAIR MUGLER 6000 105 2500 1.0x1.0x1.0mm 9m2s


Roadmap

• Process baseline 5 lupus + 5 control data-sets – EM Segment within Slicer 3– Marcel Prastawa custom/ITK– Magnotta BRAINS/ITK– Manual identification of lesions


Progress to Date

• Participation in Jan 2008 Programming Week– Training

• EM Segmenter• Plugins for Slicer3• DBP Engineers Lunch• Batchmake

• Participation in June 2007 Programming Week– Training

• Slicer 3• KWWidgets• ITK


Progress

• Successful build of slicer3 from svn repository on Mac G4/G5 OS 10.4 environment

• Becoming comfortable with the NA-MIC and feel confident on

• Initial EM Segment results– Working with Brad and Killian, we have run a

lupus and control subject successfully

• Prastawa/Gerig results– Working with Marcel and Guido, we have an

initial result, including lesion segmentation


Jan 08 to June 08 Workplan

• Jan: Finish Data collection of 5 patients and 5 controls for roadmap tutorial

• Feb: Establish final criteria for lesion definitions and final manual traces for roadmap data-set

• Mar/April: Write up methods paper including Brad/Killian/others as co-authors

• April/May: apply methods to clinical sample (n=40)

• June: Finish Data 6 month follow-up visits


Future

• Work with Kilian on tumor growth project– This will give us a head start on the

longitudinal lesion analysis phase of this DBP

na-mic national alliance for medical image computing lesion classification in lupus update h....

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