Transcript Differential Activity Within the Human Medial Temporal Lobe During

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.
Instructions
http://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/mtlunfolding-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
White
CSF
Gray
1) PHG
2) FG
3) lat. vent.
4) fornix
Posterior
IV. Segmentation
2) Segment CSF
Anterior
White
CSF
Gray
5) hippocampal
and collateral
sulci
6) adjacent
vessels/cisterns
7) boundaries encapsulate
segmentation in
3D
Posterior
IV. Segmentation
3) Interpolate segmentation
Especially for white matter:
1) smooth transitions
2) thicken boundaries (all >= size 1 fxnal voxel)
3) eliminate topological errors
White
CSF
Gray
IV. Segmentation
4) Grow out layers of gray matter
White
CSF
Gray
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
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
3
2
1. Select the boundary, 2. Draw, 3. Store
VII. Demarcating the MTL
• You can project the
boundary to flat
space (smaller
projection is better).
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 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 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
1
2
4
7
8
7
4
2
1
VII. Demarcating the MTL
4) Mark these anterior boundaries
•
•
•
•
•
•
PRC : FG - lateral startpoint of CoS (1) Shift
with
CoS
CoS - depth of collateral sulcus (3)
depth
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
5 6
7
8
8
3
1
7
6
5
VII. Demarcating the MTL
5) Demarcations can all be projected to flat
space
6) Smooth boundaries can be automatically fit!
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 - Images
Color
enhance
activations
Make it snazzy!
Export to photoshop!
Superimpose
boundaries
VIII. Analysis - ROI
ROI analysis
• create ROIs
• edit as necessary
VIII. Analysis
• plot ROI timeseries
VIII. Analysis
• Export all timeseries to spreadsheet
Time Series for Subregions
Sustained
Parahippocampal
Fusiform
Late Activation
No Activation
CA 2, 3, DG
CA 1
Subiculum
Entorhinal
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