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Core 3-1.2 DBP Dartmouth Data

NA-MIC National Alliance for Medical Image Computing http://na-mic.org. Core 3-1.2 DBP Dartmouth Data. Brain Imaging Laboratory Departments of Psychiatry and Radiology, Dartmouth Medical School Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire

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Core 3-1.2 DBP Dartmouth Data

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  1. NA-MIC National Alliance for Medical Image Computing http://na-mic.org Core 3-1.2 DBP Dartmouth Data Brain Imaging Laboratory Departments of Psychiatry and Radiology, Dartmouth Medical School Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire New Hampshire Hospital, Concord, New Hampshire http://synapse.hitchcock.org

  2. Sample of six healthy controls with complete multi-modality data series (GE 1.5T LX scanner): • - SPGR T1-weighted Volume and T2 Axial Series • - Diffusion Tensor Series • Functional MRI Recognition Task • Goal: provide template for reading DHMC data formats and test of de-identification and upload Initial Dartmouth MRI Data Set

  3. Raw MRI Data: SPGR T1 Volume • Acquisition plane: coronal • Slice Thickness: 1.5 mm (no skip) • Number of Slices: 124 • TR: 25 ms • TE: 3 ms (min) • FOV: 24 cm • NEX: 1 • Scan Matrix: 256 x 256 • Image Matrix: 256 x 256 • Voxel Dim: 0.9375 x 0.9375 x 1.5 mm • Acquisition Time: 10 min 18 sec • Format: DICOM

  4. Raw MRI Data: T2 Series • Acquisition plane: axial • Slice Thickness: 3.0 mm (no skip) • Number of Slices: 48 • TR: 3000 ms • TE: 25 ms • FOV: 24 cm • NEX: 1 • Scan Matrix: 256 x 256 • Image Matrix: 256 x 256 • Voxel Dim: 0.9375 x 0.9375 x 3.0 mm • Acquisition Time: 4 min 12 sec • Format: DICOM

  5. Raw MRI Data: DTI Series • Acquisition: Single-shot spin-echo EPI • Acquisition Plane: axial • Slice Thickness: 3 mm (no skip) • Number of Slices: 36 • TR / TE / NEX: 8000 ms / minimum / 4 • FOV: 24 cm • Scan Matrix: 128 x 128 • Image Matrix (Vox Dim): 256 x 256 (0.9375 x 0.9375 x 3) • Number of Diffusion Directions: 12 (plus 2 w/o diffusion) • Diffusion Weighting (b-value) 800 s/mm2 • Total Number of Images: 504 (14 images per slice) • Acquisition Time: 7 min 28 sec • Formats: DICOM & post-processed

  6. Raw MRI Data: fMRI Time Series • Task: Auditory-Verbal Event-Related Recognition (ER-RECOG) • Acquisition Sequence: single shot gradient echo EPI • Acquisition Plane: sagittal (interleaved) • Slice Thickness: 5 mm (no skip) • Number of Slices: 29 • TR / TE / FA / NEX: 2500 ms / 40 ms / 90 / 1 • FOV: 24 cm • Scan Matrix: 64 x 64 • Image Matrix (Vox Dim) 64 x 64 (3.75 x 3.75 x 5 mm) • Repetitions: 144 • Acquisition Time: 6 min. • Reconstruction: off-line using epirecon (P file) • Preprocessing: Analyze format, then SPM99

  7. Dartmouth Data: Plans & Next Steps • Advanced Imaging Center: Philips Achieva 3Ts (4/05 & 9/05) • Schizophrenia Data Sets • - SPGR volumes • - Labeled frontal subregions • - Labeled hippocampus • - fMRI Semantic activation • Healthy Controls • - Larger series • - Multiple modalities (fMRI, DTI) • - Labeled medial temporal regions • Data from other clinical populations: bipolar, PTSD, MCI/AD

  8. Hippocampal Shape Analysis B. Orthogonal views of the hippocampal template. A 3D ROI was constructed for each subject’s hippocampi. All ROIs were registered and scaled to a standard volume and then warped to the template. A. The hippocampus was manually traced in an oblique coronal plane along its long axis with reference to markers placed in orthogonal sections. C. Surface renderings of the 3D model of the symmetric hippocampal template in several arbitrary rotations reflect shape information. Saykin et al, NeuroImage13(6): S1096

  9. Example: DTI and SPGR-Registered FA Map registered to SPGR volume Segmented SPGR T1 volume SPGR T1 volume

  10. fMRI of Normal Memory Circuitry Working Memory: 2-back Task Semantic Memory: Category and Function Exemplar Tasks Johnson et al, Aging, Neuropsychology & Cognition (2001) McAllister et al, Neurology (1999)

  11. Clinical fMRI Studies of Memory Example of neuropharmacological application of fMRI. Treatment by group interaction in MCI patients after donepezil Saykin et al, Brain, July 2004 McDonald & Saykin (in press)

  12. Rules for accessing and using the data • Documented IRB training (human subject protection) • Data sharing (do not transfer data to other people) • Data source study/publication acknowledgement • Grant acknowledgements • NIGHS/NI - U54 GM 072977 to Ron Kikinis • NIH – R01 AG19771 and R01 CA101318 to Saykin for healthy control data • NARSAD grants to Flashman and Saykin for schizophrenia data* * upload pending • Contact us for help with any questions

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