software overview 1) installation 2) scanning procedure 3) file organization 4) segmentation 5)...

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• 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.

Instructionshttp://airto.loni.ucla.edu/BMCweb/HowTo/Hippocampus/

Requirements

• PC: segmentation

• UNIX: MATLAB

• patience, forttude, + computer skills

I. Installation• PC: download mrGray - segmentation

program.http://white.stanford.edu/~brian/mri/segmentUnfold.htm

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

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

I. Installation• Sign up for the mailing list!

http://lists.sourceforge.net/mailman/listinfo/mtl-unfolding-help

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

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.

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

IV. Segmentation

IV. Segmentation

1) Segment white matter

Anterior

Posterior

WhiteCSFGray

1) PHG

2) FG

3) lat. vent.

4) fornix

IV. Segmentation

2) Segment CSF

Anterior

Posterior

WhiteCSFGray

5) hippocampal and collateral sulci

6) adjacent vessels/cisterns

7) boundaries - encapsulate segmentation in 3D

IV. Segmentation3) Interpolate segmentation White

CSF

Gray

Especially for white matter:1) smooth transitions2) thicken boundaries (all >= size 1 fxnal voxel)3) eliminate topological errors

IV. Segmentation4) Grow out layers of gray matter White

CSF

Gray

V. UnfoldingUse 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!

VI. Importing data into HFM

Imports:

• Raw Structural Data

• Unfolded MTLs

• Motion Corrected Fxnal Dat

VI. Importing data into HFM• Enter parameters

– # slices, # of fxnal runs– image sizes

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

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

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

VII. Demarcating the MTL

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

VII. Demarcating the MTL

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

1

23

VII. Demarcating the MTL

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

VII. Demarcating the MTL1) 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)

VII. Demarcating the MTL2) 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

VII. Demarcating the MTL3) 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

421

87421

VII. Demarcating the MTL4) 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)

87

65

387

653

1

1

Shift withCoSdepth

VII. Demarcating the MTL5) Demarcations can all be projected to flat space

6) Smooth boundaries can be automatically fit!

VIII. Analysis - ImagesParadigm Correlation Analysis

Need: paradigm file

Generate from your behavioral paradigm, smooth by HRF

3.Adjust threshold

increase

decrease

1. Create correlation map ...

2. View the phase map

VIII. Analysis - ImagesMake it snazzy!Color

enhance activations

Superimpose boundaries

Export to photoshop!

VIII. Analysis - ROIROI analysis• create ROIs

• edit as necessary

VIII. Analysis• plot ROI timeseries

VIII. Analysis• Export all timeseries to spreadsheet

Time Series for Subregions

Sustained Late Activation No Activation

Parahippocampal

Fusiform

CA 2, 3, DG CA 1

Subiculum Entorhinal

Future Releases

• Hippocampal Flat Template

• Warping

• Automated Segmentation

AcknowledgementsUCLA Medical Scientist Training

ProgramNIH 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