ChepkwonyChatterjee: Difference between revisions

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== Background ==
== Background ==


Human vision science has been generally defined based on the presence of four types of photopigments in the retina: rods and three types of cones. Rods are responsible for peripheral vision under scotopic and mesopic lighting conditions. Rods are generally not associated with color vision. The cones on the other hand are present in the foveal region and are responsible for color vision. The L,M,S cones are sensitive to different wavelength ranges of light.  
Human vision science has been generally defined based on the presence of four types of photopigments in the retina: rods and three types of cones. Rods are responsible for peripheral vision under scotopic and mesopic lighting conditions. Rods are generally not associated with color vision. The cones on the other hand are present in the foveal region and are responsible for color vision under photopic conditions. The L,M,S cones are sensitive to different wavelength ranges of light.  


There has been a recent discovery [http://www.jneurosci.org/content/20/2/600.full] of another type of non-rod non-cone photopigment in the human retina, and this is melanopsin present in the specialized ganglion cells of the retina. Melanopsin in the retina has been studied to the extent that its primary function has been determined to be signaling changes in ambient light levels to the brain throughout the day for unconscious visual reflexes, such as pupillary constriction, and regulating a number of daily behavioral and physiological rhythms, collectively called circadian rhythms. It has been suspected that Melanopsin may play some role in the human visual system as well. The role of melanopsin in color vision and temporally varying light intensity patterns is an emerging research area.
There has been a recent discovery [http://www.jneurosci.org/content/20/2/600.full] of another type of non-rod non-cone photopigment in the human retina, and this is melanopsin present in the specialized ganglion cells of the retina. Melanopsin in the retina has been studied to the extent that its primary function has been determined to be signaling changes in ambient light levels to the brain throughout the day for unconscious visual reflexes, such as pupillary constriction, and regulating a number of daily behavioral and physiological rhythms, collectively called circadian rhythms. It has been suspected that Melanopsin may play some role in the human visual system as well. The role of melanopsin in color vision and temporally varying light intensity patterns is an emerging research area.
<br>


== MNI space ==
To understand the role of Melanopsin in the human visual system, researchers need a setup for conducting psychophysical experiments. The goal of our project was to build such a device which makes it easy to carry out such experiments.


MNI is an abbreviation for [http://en.wikipedia.org/wiki/Montreal_Neurological_Institute Montreal Neurological Institute].
== High Level Device Specifications ==


= Methods =
== Measuring retinotopic maps ==
Retinotopic maps were obtained in 5 subjects using Population Receptive Field mapping methods [http://white.stanford.edu/~brian/papers/mri/2007-Dumoulin-NI.pdf Dumoulin and Wandell (2008)]. These data were collected for another [http://www.journalofvision.org/9/8/768/ research project] in the Wandell lab. We re-analyzed the data for this project, as described below. 


=== Subjects ===
Subjects were 5 healthy volunteers.


=== MR acquisition ===
== Methods ==
Data were obtained on a GE scanner. Et cetera.


=== MR Analysis ===
== Results ==
The MR data was analyzed using [http://white.stanford.edu/newlm/index.php/MrVista mrVista] software tools.


==== Pre-processing ====
All data were slice-time corrected, motion corrected, and repeated scans were averaged together to create a single average scan for each subject. Et cetera.


==== PRF model fits ====
== Conclusions ==
PRF models were fit with a 2-gaussian model.


==== MNI space ====
== References ==
After a pRF model was solved for each subject, the model was trasnformed into MNI template space. This was done by first aligning the high resolution t1-weighted anatomical scan from each subject to an MNI template. Since the pRF model was coregistered to the t1-anatomical scan, the same alignment matrix could then be applied to the pRF model. <br>
Once each pRF model was aligned to MNI space, 4 model parameters - x, y, sigma, and r^2 - were averaged across each of the 6 subjects  in each voxel.


Et cetera.


= Results - What you found =
== Retinotopic models in native space ==
Some text. Some analysis. Some figures.
== Retinotopic models in individual subjects transformed into MNI space ==
Some text. Some analysis. Some figures.
== Retinotopic models in group-averaged data on the MNI template brain ==
Some text. Some analysis. Some figures. Maybe some equations.
=== Equations===
If you want to use equations, you can use the same formats that are use on wikipedia. <br>
''See wikimedia help on  [http://meta.wikimedia.org/wiki/Help:Displaying_a_formula formulas] for help.'' <br>
This example of equation use is copied and pasted from [http://en.wikipedia.org/wiki/Discrete_Fourier_transform wikipedia's article on the DFT].
The [[sequence]] of ''N'' [[complex number]]s ''x''<sub>0</sub>, ..., ''x''<sub>''N''−1</sub> is transformed into the  sequence of ''N'' complex numbers ''X''<sub>0</sub>, ..., ''X''<sub>''N''−1</sub> by the DFT according to the formula:
:<math>X_k = \sum_{n=0}^{N-1} x_n e^{-\frac{2 \pi i}{N} k n} \quad \quad k = 0, \dots, N-1</math> 
           
where i is the imaginary unit and <math>e^{\frac{2 \pi i}{N}}</math>  is a primitive N'th [[root of unity]]. (This expression can also be written in terms of a [[DFT matrix]]; when scaled appropriately it becomes a [[unitary matrix]] and the ''X''<sub>''k''</sub> can thus be viewed as coefficients of ''x'' in an [[orthonormal basis]].)
The transform is sometimes denoted by the symbol <math>\mathcal{F}</math>, as in <math>\mathbf{X} = \mathcal{F} \left \{ \mathbf{x} \right \} </math> or <math>\mathcal{F} \left ( \mathbf{x} \right )</math> or <math>\mathcal{F} \mathbf{x}</math>. 
The '''inverse discrete Fourier transform (IDFT)''' is given by
:<math>x_n = \frac{1}{N} \sum_{k=0}^{N-1} X_k e^{\frac{2\pi i}{N} k n} \quad \quad n = 0,\dots,N-1.</math>
== Retinotopic models in group-averaged data projected back into native space ==
Some text. Some analysis. Some figures.
= Conclusions =
Here is where you say what your results mean.
= References - Resources and related work =
References


Software
Software


= Appendix I - Code and Data =
== Appendix I - Code and Data ==


==Code==
===Code===
[[File:CodeFile.zip]]
[[File:CodeFile.zip]]


==Data==
===Data===
[[File:DataFile.zip | zip file with my data]]
[[File:DataFile.zip | zip file with my data]]


= Appendix II - Work partition (if a group project) =
== Appendix II - Work partition (if a group project) ==
Brian and Bob gave the lectures. Jon mucked around on the wiki.

Revision as of 21:34, 17 March 2012


LED Flicker system design

Background

Human vision science has been generally defined based on the presence of four types of photopigments in the retina: rods and three types of cones. Rods are responsible for peripheral vision under scotopic and mesopic lighting conditions. Rods are generally not associated with color vision. The cones on the other hand are present in the foveal region and are responsible for color vision under photopic conditions. The L,M,S cones are sensitive to different wavelength ranges of light.

There has been a recent discovery [1] of another type of non-rod non-cone photopigment in the human retina, and this is melanopsin present in the specialized ganglion cells of the retina. Melanopsin in the retina has been studied to the extent that its primary function has been determined to be signaling changes in ambient light levels to the brain throughout the day for unconscious visual reflexes, such as pupillary constriction, and regulating a number of daily behavioral and physiological rhythms, collectively called circadian rhythms. It has been suspected that Melanopsin may play some role in the human visual system as well. The role of melanopsin in color vision and temporally varying light intensity patterns is an emerging research area.

To understand the role of Melanopsin in the human visual system, researchers need a setup for conducting psychophysical experiments. The goal of our project was to build such a device which makes it easy to carry out such experiments.

High Level Device Specifications

Methods

Results

Conclusions

References

Software

Appendix I - Code and Data

Code

File:CodeFile.zip

Data

zip file with my data

Appendix II - Work partition (if a group project)

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