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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 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
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
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.


Instructions
Instructions

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


Requirements
Requirements

  • PC: segmentation

  • UNIX: MATLAB

  • patience, forttude, + computer skills


I installation
I. Installation

  • PC: download mrGray - segmentation program.

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


I installation1
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 installation2
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 installation3
I. Installation

  • Sign up for the mailing list!

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


Ii scanning structural
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
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
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 segmentation1
IV. Segmentation

White

CSF

Gray

1) Segment white matter

Anterior

1) PHG

2) FG

3) lat. vent.

4) fornix

Posterior


Iv segmentation2
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


Iv segmentation3

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


Iv segmentation4

White

CSF

Gray

IV. Segmentation

4) Grow out layers of gray matter


V unfolding
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!


Vi importing data into hfm
VI. Importing data into HFM

  • Imports:

  • Raw Structural Data

  • Unfolded MTLs

  • Motion Corrected Fxnal Dat


Vi importing data into hfm1
VI. Importing data into HFM

  • Enter parameters

    • # slices, # of fxnal runs

    • image sizes


Vi importing data into hfm2
VI. Importing data into HFM

  • Roughly align structurals w/ functionals


Vi importing data into hfm3
VI. Importing data into HFM

  • Import all fMRI time series


Vi importing data into hfm4
VI. Importing data into HFM

  • Finely align fMRI with structurals


Vii demarcating the mtl
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 mtl1
VII. Demarcating the MTL

1

3

2

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


Vii demarcating the mtl2
VII. Demarcating the MTL

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


Vii demarcating the mtl3
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)


Vii demarcating the mtl4
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)


Vii demarcating the mtl5
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


Vii demarcating the mtl6
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


Vii demarcating the mtl7
VII. Demarcating the MTL

5) Demarcations can all be projected to flat space

6) Smooth boundaries can be automatically fit!


Viii analysis images
VIII. Analysis - Images

Paradigm Correlation Analysis

Need: paradigm file

Generate from your behavioral paradigm, smooth by HRF


1. Create correlation map ...

3.Adjust

threshold

2. View the phase map

increase

decrease


Viii analysis images1

Color enhance activations

VIII. Analysis - Images

Export to photoshop!

Make it snazzy!

Superimpose boundaries


Viii analysis roi
VIII. Analysis - ROI

ROI analysis

  • create ROIs

  • edit as necessary


Viii analysis
VIII. Analysis

  • plot ROI timeseries


Viii analysis1
VIII. Analysis

  • Export all timeseries to spreadsheet


Time Series for Subregions

Sustained

Late Activation

No Activation

CA 2, 3, DG

CA 1

Parahippocampal

Fusiform

Subiculum

Entorhinal


Future releases
Future Releases

  • Hippocampal Flat Template

  • Warping

  • Automated Segmentation


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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