software overview
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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• 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
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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
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