Mark Dow

 Mark's MRI gradient at skin surface, direction color-coded skin surface rendering unwrapped, from MRI data Brodmann labelled rendered brain human brain, rendered from Colin27T1, link to Human mid-brain, link to axial MRI slices of various contrasts, link to axial MRI slices of various contrasts, link to axial MRI slices of various contrasts, link to axial MRI slices of various contrasts, link to axial MRI slices of various contrasts, link to  MNI ICBM  color rendered top MNI ICBM color sagital medial  Pell spirals similarity tiling link Brigid's cross tilings, link to Thue-Morse sequence tiling link Thue-Morse cube, link to Three symbol symmetric systems with two terminating rules, link to Minimal arrays with all combinations, link to T2 slice through cochlea skin surface after masking of noise, MRI  render, stereo pairSierpinski curves

Research Assistant
Brain Development Lab, University of Oregon

e-mail: dow [at] uoregon.edu
*cell*541-954-6780**


Research
Cross modal plasticity
Segmentation software tools for neuroimaging
Far peripheral human vision
My BDL and LCNI stuff, publications, presentations, etc.

Geek art, geometric images and algorithms
My deviantArt gallery
Simple recursive systems and fractal patterns
Example volume and slice renderings
Example animations
Universal motifs, tilings, knits, weaves and chains

Geek software
Video motion estimation and quantification, estimating frame to frame motion in video files
Space Software, volumetric data manipulation and visualization
Scale Space Edges software, edge detection

My other stuff, some of
Other projects
Mark's photos
Family and Friends
Miscellaneous

Other people's great stuff


Research

MT test-retest repeatability
Functionally active areas during viewing of moving images compared to a static image. The alternating green and yellow spots highlight significant activity in the middle-temporal (V5/MT) regions, on the left and right near the back of the brain, during two fMRI scans separated by several months. This gives a sense of how spatially specific and repeatable  fMRI can be, at least for some classes of neuronal activity.
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    I work on software for image and functional MRI time series analysis, and am involved with fMRI studies involving human tactile-visual processing, visual spatial attention and retinotopy.

Cross-modal Plasticity

     This fMRI and ERP study examines how different sensory modalities, such as hearing, vision and touch, interact in the human brain, and how these interactions are shaped by external factors in environment and internal factors such as attention.

Segmentation software tools for neuroimaging

    These include 3-D surface extraction and segmentation algorithms, and volume navigation and editing tools that provide a framework for semi-automatic region of interest generation and landmark specification. The approach we are developing is based on edge/surface detection using Gaussian derivative filters, over-segmentation, and hierarchical region combination. The goal is to quickly identify primary surfaces, landmarks, and other image based features, and to use maps of these features to inform segmentation or parcellation of 3-D images.

Far peripheral human vision

    These fMRI experiments are designed to investigate the organization, operation, and plasticity of cortical areas involved in visual processing at large (20-80 degree) eccentricities. We use light guiding fibers to present flashing stimuli at peripheral locations during functional imaging. Retinotopically mapped visual areas and areas that preferentially respond to peripheral visual stimulation are identified. We are investigating the extent and organization of these visual areas, and how they are modulated by spatial attention. Comparison of hearing and congenitally deaf adults results will elucidate how visual cortical networks are modified and modulated by different auditory experience.


Geek art, geometric images and the algorithms that generate them


My deviantArt gallery
I, phone, link to Sodium cherry, link to Pattern and process, link to Circling the square, link to Polyquads tiling, link to Squirms tiling, link to

Simple recursive systems and fractal patterns
Pell spirals tesselation link Bar rotation similarity motifs Brain Frieze

Thue-Morse sequence tilings
Thue-Morse sequence tiling link Thue-Morse cube, link to Three bars motifs, link to Thue-Morse mesh tiling Thue-Morse X tiling, link to Thue-Morse diag1 tiling, link to Thue-Morse  dual twist tiling, link to Thue-Morse half-diagonal tiling, link to Thue-Morse half-diagonal shaded tiling, link to


2x2 4-rotation cyclic L-systems

2x2 symmetric L-systems
 Three symbol symmetric systems with two terminating rules, link to Five symbol symmetric systems with two terminating rules, link to Five symbol symmetric systems with two terminating rules, link to Five symbol symmetric systems with two terminating rules, link to Seven symbol symmetric systems with two terminating rules, link to Square wave quarter-twist system, link to Square waves system, link to
Brigid's cross tessellations
Brigid's octomino Thue-Morse tesselations link Brigid's cross similarity tilings, link to Brigid's cross similarity tiling thumbnail Brigid's pyramids articulated thumbnail Brigid's pyramid spiral face thumbnail

Pell spirals

Oak cubes and hexagonal tilings
48-Meta-Cube, link to

Binary fractal images

Mobius bands and tilings

Logarithmic spirals, waves and tilings
Logarithmic spirals, waves and tilings, link to Orthologia, link to

About Mark's fractal geek art

Space Software example volume and slice renderings
Quail chick rendered from MRI, link to Four knot 1, link to virion structure rendering, link to
Space Software example animations
Human brain, blended Brodmann area coloring, link to Virion_structure_animations, link to
Universal motifs, tilings, knits, weaves and chains
Squeel motif Diagonal braid tilings, link to mixed braids, link to
Squeel tessellations
squeel tesselations link

Directional edge contrast motion illusion comparison

Rattling boundary illusion
Rattling boundary illusion, link to

Minimal arrays containing all sub-array combinations of symbols
Minimal arrays with all combinations, link to Minimal arrays with all combinations, link to

miscellaneous MRI related images

brain art fodder

Geek art in Oregon

Geek software

Video motion estimation and quantification


video motion estimation MATLAB tools for estimating frame to frame motion in video files.

        Video motion software download, description, code, and examples

Space Software


MRI Space software animation Free volume navigation, visualization, and editing software (MS Windows). In active development, in collaboration with Greg Scott.

Space software download, description, and examples

Scale Space Edges software

eye edges from MRI data, Scale Space Edges

MATLAB tools for 2-D edge extraction and segmentation.

        Scale Space Edges download, description, code, and examples


Presentations, papers, posters, teaching materials, etc.

Emergence of the neural network for reading in five-year-old beginning readers of different levels of pre-literacy abilities: An fMRI study
Yoshiko Yamada, Courtney Stevens, Mark Dow, Beth A. Harn, David J. Chard and Helen J. Neville
NeuroImage, Volume 57, Issue 3, 1 August 2011, Pages 704-713
...
Following 3 months of kindergarten and, for AR children, supplemental reading instruction, OT children showed left-lateralized activation in the temporo-parietal region, whereas AR children showed bilateral activation and recruitment of frontal regions including the anterior cingulate cortex. These data suggest that typical reading development is associated with initial recruitment and subsequent disengagement of right hemisphere homologous regions while atypical reading development may be associated with compensatory recruitment of frontal regions.

Arithmetical Self-Similarity (seminar slides)
Mark Dow, Jörg Endrullis, Dimitri Hendriks, Jan Willem Klop
Streams Seminar, Nijmegen, April 20, 2010

What is the underlying construction for scale-invariant sequences? We determine the arithmetical self-similarity of several classes of streams. What is their relation to fractals: is scale-invariance a sufficient criterion for turtle drawings to converge to a fractal curve?

BOLD localization of short visual events (seminar slides)
Mark Dow
LCNI science meeting, February 2005


An edge based image segmentation method (poster)
Mark Dow, Ray Nunnally
ISMRM 2004 conference, [abstract .doc]

Neuroscience, disease progression and clinical trial studies, using MRI and other imaging modalities, benefit from unbiased and repeatable image feature quantification. We describe a general method for segmentation of 2-D images that reduces the burden of manual region of interest (ROI) selection while increasing repeatability. The method uses an objective edge definition and edge linking criteria to over-segment an image, and hierarchical clustering of the resulting elemental segments. The algorithms have been tested on a range of imagery, and are suitable for several MRI tissue segmentation purposes. The algorithms do not require thresholds that are image or image modality dependant, and can be extended to 3-D for segmentation and feature extraction tasks, such as landmark identification.


Human retinotopic mapping of the far periphery (poster)
Greg Scott, Mark Dow, Helen Neville
Society for Neuroscience 2003 conference

We used fMRI to map cortical areas sensitive to visual stimuli in the far periphery. Discrete flashing light stimuli at eccentricities of 2-80° presented in each visual field quadrant of one eye induced a BOLD response in cortical visual areas. By tracing these activations at increasing eccentricities, several retinotopic paths were delineated for each visual field quadrant. Some of these regions can be identified with known visual areas by their spatial arrangement and mirroring of neighboring representations.Cortical distance between activation locations of spatially adjacent stimuli were estimated. This provides a measure of the cortex used as a function of eccentricity, for each identified visual area.

Measuring the earth's shape: Maximum solar elevation observations, through space and time (seminar slides, .ppt)
Mark Dow, Ansel Dow
Road trip report at Brain Development Lab
[print/high res. version:  .ppt (32 MB)]


Dressed basis for highly excited molecular vibrations (.pdf)
Michael E. Kellman, Mark W. Dow, and Vivian Tyng
J. Chem. Phys. 118, 9519 (2003)

[The following abstract is the way a theoretical chemist would describe how the vibrations of a water molecule (stretching an bending of bonds between the atoms of H2O) might be modeled. While we often know how molecules behave experimentally by spectrum analysis, there is no easy way to predict the complexities without some simplifiing model that retains the richness of interactions.]

Starting from a multiresonance spectroscopic Hamiltonian fit by Baggott to experimental levels of H2O, an approximate Hamiltonian is devised using a prediagonalized “dressed” zero-order basis, within which a residual, effective single-resonance coupling operator acts. The dressed basis incorporates many of the effects of nonintegrability, while the effective resonance furnishes much of the simplicity of integrable systems. Numerical tests are performed for two distinct dressed bases, in which different resonance operators are chosen as the residual effective coupling. Excellent agreement with the energies and eigenvectors of the exact system is obtained for each of the two dressed bases.

miscellaneous, BDL and LCNI

Psych 607 class resources , winter 2004
LCNI resources
LCNI historical
MATLAB class, summer 2008

Some of my other stuff

Other projects

inordinate detail, a blog including current Programmers Anonymous notes, miscellaneous references and some project details.
Programmers Anonymous, an informal programming class I lead (currently way out of date)
Thermodynamic entropy and information, their relationship as I understand it
Dense Image Space, photographic/software project, in process
Math background, discrete math, math topics that are not in pre-college curriculum but should be
Meso-scale materials
Virions
Virion and virus structure, mechanics and dynamics references
P-22_virion_structure
EMD-1220 rendering notes
Test renderings of the P22 virion EMD-1220 data set
Worthington's mercury droplet splash animation
Phase-locked oscillator clock
Point cloud to mesh
Apollo moon stereo pairs
Stereo pairs of the moon
Stereo pair smooth disparity reversal

Miscellaneous

Internet Black Hole Discovered, computer fiction science journalism (inspired by Sean Michael Ragan's fiction science)
0-bit for Brie, a laptop's obituary
Fronto Temperal Dementia (FTD) and tau V337M FTDP-17 information and references

Mark's photos

Walk on N. Fork of M. Fork Willamette River, 2-15-09
Doug's photos on the same walk

pics, Kristen and Jasper-Jon's wedding
Kristen and Jasper's wedding, link to

Yellowstone, August 2009
   

Family and friends

Wayne Dow's web site, my dad's personal, family and family history material
pics, Yoshiko's party 6/06
Tonn Nua, the group my son Ansel makes music with
Tonn Nua, link to


Other people's great stuff 

Science is Beauty, thumbnails
The Geometry Junkyard
Sean Michael Ragan, great ideas

deviantART, great art, searchable. Here are a few of my favorites.
Mathematical imagery, Jos Leys
The Brain From Top To Bottom, tour of human brain functional neuroanatomy
fMRI 4 Newbies, tutorials
Tatjana van Vark's instuments, particularly her The Harmonium for mechanical Fourier analysis and synthesis
Making Art the Otto Lange Way (I recommend subscribing to the blog through email)

Some great free software

World Wind, virtual spherical navigation
MRIcron, Chris Rorden's free, great volume display software
IrfanView,  Irfan Skiljan's free, great 2-D image software
Nvu, free, great web page generation, web authoring software
Google Desktop, hard drive indexed search
MRIConvert, Jolinda Smith's free, great GUI batch DICOM file conversion program

Some great books

Walden, Henry David Thoreau
John McPhee, everything written by
The Human use of Human Beings, Norbert Weiner
A Study of Spashes, A. M. Worthington