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

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Presentation on theme: "Software Overview 1) Installation 2) Scanning Procedure 3) File organization 4) Segmentation 5) Unfolding 6) Importing data into HFM toolbox 7) Demarcation."— Presentation transcript:

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

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

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

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

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. Select the boundary, 2. Draw, 3. Store 1 2 3

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 Mark this boundary from the superior tip of CA 1 all the way medially (10) Anterior to this boundary, CA 1, 2, 3, and DG are all present and indistinguishable

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 2 1 8 7 42 1

29 VII. Demarcating the MTL 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) 8 7 6 5 3 8 7 6 5 3 1 1 Shift with CoS depth

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

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

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 SustainedLate ActivationNo Activation Parahippocampal Fusiform CA 2, 3, DGCA 1 SubiculumEntorhinal

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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