All Hands Meeting 2005 MRI Calibration Update Morphometry BIRN

mBIRN: MRI Calibration Goals Overview Optimize reproducibility T1/T2/DTI MRI derived metrics: Quantitative characterization (sequence/vendor/field effects) Develop/test correction methods for improved reproducibility First: work at specific sites (MGH, Duke, JHU, UCSD) Then: human traveling phantoms, multiple mBIRN sites Dissemination of results Acquisition protocol recommendations MRI Calibration data Software tools for distortion correction

Timeline from mBIRN MRI Calibration StagesCore 1 Calibration TasksYear 1Year 2Year 3Year 4Year 5 I Structural MRI Calibration B1 inhomogeneity correction B0 inhomogeneity correction Online motion correction Gradient distortion (new sites, 1.5T and 3T) Calibration of FSE (PD, T2, FLAIR) Healthy and lesion brain tissue modeling Diffusion MRI Calibration Base sequences effects (EPI & Spiral) SNR, spatial resolution and b-factor effects Gradient encoding direction effects Plan calibration for additional imaging methods that support research other than AD/depression II Extension to methods for research other than AD/depression Distribution and support of Stage I methods

Evaluation of distortion correction from gradient non-linearities (MGH, mBIRN) Status: Manuscript in press Evaluation of MRI system upgrade effects (MGH, BWH) Sonata -> Avanto (Siemens 1.5T, MGH) Status: all data acquired, analysis Trio -> Trio TIM (Siemens 3T, MGH) Status: pre-upgrade data acquired A -> B (GE 3T, BWH) Status: pre-upgrade acquisition ongoing Evaluation of T1/PD/T2* multi-contrast sequences for morphometry (MGH) Metrics: image intensity, cortical thickness and subcortical volumes reproducibility Acquisition variables: imaging sequence (MP-RAGE, SEF, MEF), MRI Vendor (GE, Siemens), main field strength (1.5T, 3T), system version Analyses variables: cross-sectional/longitudinal, smoothing effects Status: Data acquired, thickness reproducibility paper submitted, subcortical analyses ongoing Evaluation of lesion reproducibility from T1/T2 multi-contrast sequences (Duke) Acquisition: test-retest (within 6 months), 1.5T, 3T, 4T Subjects: choose from previously scanned elderly subjects with vascular lesions Analysis: automated segmentation pipeline will be used Status: identified pool of 75 subjects, recruited and scanned 3, each at 3T once, one twice at 3T. mBIRN Calibration: Progress Outline Multi-contrast structural MRI Reproducibility Studies

Uncorrected ImagesCorrected Images Siemens Sonata (1.5T) Siemens AC88 (7T) mBIRN Calibration: sample unwarping results

Evaluation of distortion correction from gradient non-linearities (MGH, mBIRN) Status: Paper written, reviewed, now in press Evaluation of MRI system upgrade effects (MGH, BWH) Sonata -> Avanto (Siemens 1.5T, MGH) Status: all data acquired, analysis Trio -> Trio TIM (Siemens 3T, MGH) Status: pre-upgrade data acquired A -> B (GE 3T, BWH) Status: pre-upgrade acquisition ongoing Evaluation of T1/PD/T2* multi-contrast sequences for morphometry (MGH) Metrics: image intensity, cortical thickness and subcortical volumes reproducibility Acquisition variables: imaging sequence (MP-RAGE, SEF, MEF), MRI Vendor (GE, Siemens), main field strength (1.5T, 3T), system version Analyses variables: cross-sectional/longitudinal, smoothing effects Status: Data acquired, thickness reproducibility paper submitted, subcortical analyses ongoing Evaluation of lesion reproducibility from T1/T2 multi-contrast sequences (Duke) Acquisition: test-retest (within 6 months), 1.5T, 3T, 4T Subjects: choose from previously scanned elderly subjects with vascular lesions Analysis: automated segmentation pipeline will be used Status: identified pool of 75 subjects, recruited and scanned 3, each at 3T once, one twice at 3T. mBIRN Calibration: Progress Outline Multi-contrast structural MRI Reproducibility Studies

mBIRN Calibration: sample Sonata-Avanto upgrade results (MP-RAGE) Global Thickness: Group results (lh) Global thickness Sonata-Sonata Sonata-Avanto Avanto-Avanto Thickness variability maps: Group results (lh)

Evaluation of distortion correction from gradient non-linearities (MGH, mBIRN) Status: Paper written, reviewed, now in press Evaluation of MRI system upgrade effects (MGH, BWH) Sonata -> Avanto (Siemens 1.5T, MGH) Status: all data acquired, analysis Trio -> Trio TIM (Siemens 3T, MGH) Status: pre-upgrade data acquired A -> B (GE 3T, BWH) Status: pre-upgrade acquisition ongoing Evaluation of T1/PD/T2* multi-contrast sequences for morphometry (MGH) Metrics: image intensity, cortical thickness and subcortical volumes reproducibility Acquisition variables: imaging sequence (MP-RAGE, SEF, MEF), MRI Vendor (GE, Siemens), main field strength (1.5T, 3T), system version Analyses variables: cross-sectional/longitudinal, smoothing effects Status: Data acquired, thickness reproducibility paper submitted, subcortical analyses ongoing Evaluation of lesion reproducibility from T1/T2 multi-contrast sequences (Duke) Acquisition: test-retest (within 6 months), 1.5T, 3T, 4T Subjects: choose from previously scanned elderly subjects with vascular lesions Analysis: automated segmentation pipeline will be used Status: identified pool of 75 subjects, recruited and scanned 3, each at 3T once, one twice at 3T. mBIRN Calibration: Progress Outline Multi-contrast structural MRI Reproducibility Studies

Advantages: Less B0 distortion and intensity variation than MP-RAGE (due to high bandwidth) Enables estimation of tissue parameters (T1, PD, T2*) (two flip angle acquisitions) CNR subcortical structures better than MP-RAGE (more accurate segmentations) mBIRN Calibration: sample multi-echo FLASH results Disadvantages: Not standard, currently only on a few Siemens sites Gray/white matter CNR lower than MP-RAGE MEF flip 5 0 (PD) MEF flip 30 0 (T1)

Optimal image can be synthesized from original echo images for better visualization of subcortical structures External Pallidum Internal Pallidum Thalamus To help skull-stripping mBIRN Calibration: sample multi-echo FLASH results Enlarged inset

mBIRN Calibration: sample multi-echo FLASH results MEF provides higher CNR for subcortical structures W: White Matter G: Gray Matter H: Hippocampus A: Amygdala T: Thalamus V: Lateral Ventricle I: Inf. Lat. Ventricle C: Caudate P: Pallidum Successive improvements in hippocampus volume reproducibility Cortical thickness reproducibility THE GOOD THE NOT SO GOOD

Evaluation of distortion correction from gradient non-linearities (MGH, mBIRN) Status: Manuscript in press Evaluation of MRI system upgrade effects (MGH, BWH) Sonata -> Avanto (Siemens 1.5T, MGH) Status: all data acquired, analysis Trio -> Trio TIM (Siemens 3T, MGH) Status: pre-upgrade data acquired A -> B (GE 3T, BWH) Status: pre-upgrade acquisition ongoing Evaluation of T1/PD/T2* multi-contrast sequences for morphometry (MGH) Metrics: image intensity, cortical thickness and subcortical volumes reproducibility Acquisition variables: imaging sequence (MP-RAGE, SEF, MEF), MRI Vendor (GE, Siemens), main field strength (1.5T, 3T), system version Analyses variables: cross-sectional/longitudinal, smoothing effects Status: Data acquired, thickness reproducibility paper submitted, subcortical analyses ongoing Evaluation of lesion reproducibility from T1/T2 multi-contrast sequences (Duke) Acquisition: test-retest (within 6 months), 1.5T, 3T, 4T Subjects: choose from previously scanned elderly subjects with vascular lesions Analysis: automated segmentation pipeline will be used Status: identified pool of 75 subjects, recruited and scanned 3, each at 3T once, one twice at 3T mBIRN Calibration: Progress Outline Multi-contrast structural MRI Reproducibility Studies

Evaluation of DTI derived diffusion anisotropy reproducibility (JHU, Duke) Effects of SNR, # of gradient directions, b-value, TE (JHU) Status: Acquisition and preliminary analyses for SNR and number of gradients done. Acquisition for b-value and TE effects on going Distortion correction for DTI, not based on phase-map data (JHU) Status: Manuscript in progress. Ongoing preparation of software tool distribution Direction-dependent distortion correction (phase-map) for multiple platforms (Duke) Status: Manuscript validating the method (GE scanner) in press Method ported to Siemens. Correction code ported to C++. Integration with JHU’s reproducibility work ongoing mBIRN Calibration: Progress Outline Multi-contrast structural MRI Reproducibility Study

mBIRN Calibration: sample DTI results Distortion corrections with phase-maps for each diffusion-encoding direction Fractional anisotropy variability maps: effect of number of diffusion encoding directions

Scanner Upgrade Calibration Protocol: Status: available in Software: i) Gradient non-linearities distortion correction code Status: needs license Ii) Distortion correction code for DTI (Bo and eddy currents effects) Iii) Siemens/GE DTI pulse sequence extensions compatible with (ii) Status: finishing paperwork MRI data: i) multi-site mBIRN calibration study (5 subjects, 5 sites, 2 visits) Status: de-identify and DB Ii) DTI calibration data (2 subjects scanned multiple times) Status: agree on data format Manuscripts: Gradient unwarping (in press) Cortical thickness reproducibility (submitted) Bo and eddy current correction for DTI (in press) mBIRN Calibration: Progress Outline Dissemination ( )

StagesCore 1 Calibration TasksYear 1Year 2Year 3Year 4Year 5 I Structural MRI Calibration B1 inhomogeneity correction B0 inhomogeneity correction Online motion correction Gradient distortion (new sites, 1.5T and 3T) Calibration of FSE (PD, T2, FLAIR) Healthy and lesion brain tissue modeling Gone Diffusion MRI Calibration Base sequences effects (EPI & Spiral) SNR, spatial resolution and b-factor effects Gradient encoding direction effects Gone Traveling human phantom study combining all of above Gone Plan calibration for additional imaging methods that support research other than AD/depression Gone II Extension to methods for research other than AD/depression Distribution and support of Stage I methods mBIRN Calibration: Future Most projects are progressing well Projects in yellow below need added attention Define who will lead the coordination of this effort going forward

mBIRN Calibration: Future Next issues include: Agree on how to put closure on Phase I B1 inhomogeneity correction evaluation Motion correction Start planning traveling phantom study Agree on T1/T2/DTI single-session multi-site protocol Agree on sites that should be included Agree on preliminary protocol tests with local subjects at participating sites Agree on plan for traveling human phantoms Start planning calibration for additional imaging methods E.g., in support for pediatrics, MS, HIV neuroimaging research Define who will lead the coordination of this effort going forward