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Software Overview

Software Overview. 1) Installation 2) Scanning Procedure 3) File organization 4) Segmentation 5) Unfolding 6) Importing data into HFM toolbox 7) Demarcation 8) Analysis in Flat Space. Before you begin. Read all of the following: Zeineh et. al. NeuroImage 11(6):668-83, 2000

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Software Overview

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  1. Software Overview 1) Installation 2) Scanning Procedure 3) File organization 4) Segmentation 5) Unfolding 6) Importing data into HFM toolbox 7) Demarcation 8) Analysis in Flat Space

  2. Before you begin ... Read all of the following: • Zeineh et. al. NeuroImage 11(6):668-83, 2000 • Zeineh et. al. The Anatom. Record: New Anatomist 265:111-120, 2001 • Zeineh et. al. Science Jan 24:299(5606) 577-80, 2003 • Amaral & Insausti 1990. Hippocampal formation. In The Human Nervous System (G. Praxinos, Ed.), pp. 711–755. Academic Press, San Diego • Duvernoy, H. M. 1998. The Human Hippocampus: Springer, Berlin. • Insausti et. al. Am. J. Neuroradiol. 19: 659–671.

  3. Instructions http://airto.loni.ucla.edu/BMCweb/HowTo/Hippocampus/

  4. Requirements • PC: segmentation • UNIX: MATLAB • patience, forttude, + computer skills

  5. I. Installation • PC: download mrGray - segmentation program. http://white.stanford.edu/~brian/mri/segmentUnfold.htm

  6. I. Installation • UNIX: download, gunzip, and untar 5 files http://sourceforge.net/projects/mtl-unfolding/ • HFM Main Module • Stanford Unfolding Code (Brian Wandell) • Stanford mrLoadRet Visualization Utility • Image utilities • Example data

  7. I. Installation • UNIX: download updated image utilities • Automated Image Registration (AIR) http://bishopw.loni.ucla.edu/ • imconvert (UCLA image conversion utility) http://airto.loni.ucla.edu/BMCweb/SharedCode/ImgLib/imconvert.c.html http://airto.loni.ucla.edu/BMCweb/SharedCode/SharedSoftware.html#Anchor-UCLA-35829 • Compile everything • Make data directories and links • Test with the sample data

  8. I. Installation • Sign up for the mailing list! http://lists.sourceforge.net/mailman/listinfo/mtl-unfolding-help

  9. II. Scanning - Structural • Need high in-plane resolution (512 x 512) for less than 0.5 mm in plane pixel size • Go perpendicular to hippocampal long axis • Get as many structural slices as possible • An adjunct 3-D volume can help discern sulci

  10. II. Scanning - Functional • Also need high in-plane resolution (128 x 128 minimum) for less than 1.5 mm pixel size • Alignment with structural slices is most important - get them coplanar to make it easy • If acquired in different planes, will need accurate 3D alignment via AIR / SPM / other tools.

  11. III. File Organization • For each subject, 4 main directories • raw - all fxnal aw data goes in here • segment - all structural data for segmentation • air - motion correction for fxnal data • loadret - it all gets synthesized here

  12. IV. Segmentation

  13. IV. Segmentation White CSF Gray 1) Segment white matter Anterior 1) PHG 2) FG 3) lat. vent. 4) fornix Posterior

  14. IV. Segmentation White CSF Gray 2) Segment CSF Anterior 5) hippocampal and collateral sulci 6) adjacent vessels/cisterns 7) boundaries - encapsulate segmentation in 3D Posterior

  15. White CSF Gray IV. Segmentation Especially for white matter: 1) smooth transitions 2) thicken boundaries (all >= size 1 fxnal voxel) 3) eliminate topological errors 3) Interpolate segmentation

  16. White CSF Gray IV. Segmentation 4) Grow out layers of gray matter

  17. V. Unfolding Use the matlab unfolding routine to computationally stretch gray matter mesh so it is uniplanar, then compress all planes or layers onto one. • Select a seed pixel in the subiculum, enter in data parameters • The algorithm does the rest!

  18. VI. Importing data into HFM • Imports: • Raw Structural Data • Unfolded MTLs • Motion Corrected Fxnal Dat

  19. VI. Importing data into HFM • Enter parameters • # slices, # of fxnal runs • image sizes

  20. VI. Importing data into HFM • Roughly align structurals w/ functionals

  21. VI. Importing data into HFM • Import all fMRI time series

  22. VI. Importing data into HFM • Finely align fMRI with structurals

  23. VII. Demarcating the MTL • Boundaries can be created using ROI generation tools and stored in one of 12 slots for each hemisphere.

  24. VII. Demarcating the MTL 1 3 2 1. Select the boundary, 2. Draw, 3. Store

  25. VII. Demarcating the MTL • You can project the boundary to flat space (smaller projection is better).

  26. VII. Demarcating the MTL 1) Locate the 1st slice where HC head starts - this divides anterior and posterior HC • This corresponds to the boundary between ERC/PRC and PHG • Mark this boundary from ERC vertex to FG (12)

  27. VII. Demarcating the MTL 2) Locate the slice with the hippocampal feet in it (pez), likely next slice anterior • Anterior to this boundary, CA 1, 2, 3, and DG are all present and indistinguishable • Mark this boundary from the superior tip of CA 1 all the way medially (10)

  28. VII. Demarcating the MTL 3) Mark these posterior boundaries • Medial Fusiform Vertex - lateral startpoint of CoS (1) • CoS - depth of collateral sulcus (2) • Sub : PHG - most medial point of PHG (4) • CA 1 : Sub - medial termination of HC body (7) • CA23DG : CA 1 - 45º off HC body/fissure (8) 8 7 4 8 2 7 1 1 2 4

  29. VII. Demarcating the MTL Shift with CoS depth 4) Mark these anterior boundaries • PRC : FG - lateral startpoint of CoS (1) • CoS - depth of collateral sulcus (3) • ERC : PRC - medial startpoint of CoS (5) • Sub : ERC - medial/superior vertex of PHG (6) • CA 1 : Sub - inferior to middle of HC head (7) • CA23DG : CA 1 - 45º off HC body/fissure (8) 1 3 8 5 6 7 8 7 3 6 5 1

  30. VII. Demarcating the MTL 5) Demarcations can all be projected to flat space 6) Smooth boundaries can be automatically fit!

  31. VIII. Analysis - Images Paradigm Correlation Analysis Need: paradigm file Generate from your behavioral paradigm, smooth by HRF

  32. 1. Create correlation map ... 3.Adjust threshold 2. View the phase map increase decrease

  33. Color enhance activations VIII. Analysis - Images Export to photoshop! Make it snazzy! Superimpose boundaries

  34. VIII. Analysis - ROI ROI analysis • create ROIs • edit as necessary

  35. VIII. Analysis • plot ROI timeseries

  36. VIII. Analysis • Export all timeseries to spreadsheet

  37. Time Series for Subregions Sustained Late Activation No Activation CA 2, 3, DG CA 1 Parahippocampal Fusiform Subiculum Entorhinal

  38. Future Releases • Hippocampal Flat Template • Warping • Automated Segmentation

  39. Acknowledgements UCLA Medical Scientist Training Program NIH National Research Service Award Ahmanson Foundation Pierson-Lovelace Foundation Brain Mapping Medical Research Organization Tamkin Foundation Alma and Nick Robson Norma and Lyn Lear Jennifer Jones-Simon UCLA School of Medicine Neuropsychiatric Institute Department of Neurology Susan Bookheimer Stephen Engel John Mazziotta Barbara Knowlton Joaquin Fuster Itzhak Fried Charles Wilson Mark Cohen Paul Thompson Bernice Wenzel Gary Small Roger Woods Arthur Toga Russ Poldrack Paul Rodriguez

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