Choose one project among the ones listed here. For each project the name of one or several mentors is given. You will have to arrange with your mentor how to install the software on your computer, get access to the sample data set , or get access to computers at the RCBI to be able to carry your project. You should declare which project you will work on by Nov 2^nd and no later than Nov 9^th and get going right away!

PS: there is a possibility of making you own project if you wish to do so. You will first have to hand in a detailed outline of your project and get it approved by the instructors before you can proceed. If you wish to do so, please hand the outline of you project to the instructors on November 2^nd.

(1) Using VolumeOne package to process a set of Siemens brain data. Discuss merits and drawbacks in functions of the package. How does it compare with some other packages you may know of? Are you aware of methods of analysis that cannot be achieved with this software? http://www.volume-one.org

(2) Search literature for analytical expressions for various diffusion anisotropy indices. Then estimate their sensitivities to the signal-to-noise ratio of the diffusion tensor eigen values, based on which these anisotroic indices are calculated. Which index is more sensitive at high anisotropic level, which is more sensitive at low anisotropic level?

(3) Discuss an aspect of DTI or diffusion imaging in general that is not covered in lectures (Hint: remaining issues, limitations of methods, or new biomedical applications).

(4) List your references.

Note: Quantitative analysis is expected. You can complete all tasks, or expand fully on one among (1)-(3), and include in your writing sections with motivation, analysis, figures, discussion, and conclusion.

(1) Design an Inversion-recovery pulse sequence

- derive (or find in literature) the expression for signal dependence on sequence parameters TR, TE, TI;

- use brain GM and WM T1/T2, plot how the contrast between GM/WM changes as a function of TI.

- if we want to get rid of signal from CSF, what should be the value for TI (this is the basis for FLAIR: Fluid-Attenuation Inversion Recovery)?

- Bonus: can you see how to obtain images showing only WM signal?

(2) Evaluate the relationship between the "soft" RF pulse waveshapes and the frequency excitation profile. Following evolution of longitudinal and transverse magnetization via Bloch equation during a sinc pulse, and plot magnetizations as functions of slice-selection location, after a

- 90° pulse;

- 180° pulse.

(Can use tools such as Stanford toolbox Bloch Equation simulation by Brian Hargreaves http://www-mrsrl.stanford.edu/~brian/blochsim/ )

(3) Select an imaging method that is NOT covered in lectures, and present it in terms of

- contrast mechanism;

- dependence of signal on imaging/tissue parameters;

- SNR or any important characteristics.

(4) List your references.

(1) Define Brain segmentation and state in brief it’s application to fmri studies

(2) Outline the steps involved in Image segmentation using FSL

http://www.fmrib.ox.ac.uk/fsl

(3) Perform Gray matter /white matter segmentation on the given Siemens datasets using

-Parametric

-Non-parametric approaches

List the merits and demerits of the 2 approaches and support them with your results. (figures required)

(4) Perform statistics on the output GM/WM masks and calculate the total no. of voxels, mean intensity, std dev for each

(5) Discuss the possibility of using multiple sequence types (T1&T2) at a single voxel to perform segmentation along with its advantages and disadvantages.

(6). List your references.

(1) Retinotopy Paradigm:

- Draw a basic visual field map with corresponding retinotopy showing horizontal and vertical meridian organization in early visual area V1.

- Define the cortical magnification factor.

- Explain the retinotopy paradigm. In what is it different to block or event-related designs?

- Discuss the limits of the experimental setup. In particular, what are the parameters on the magnet that would influence the resolution of the retinotopic map.

- Bonus: How can you design the experimental stimulus to improve the SNR?

(2) Data Analysis

- Download data and install mrVista (contact aguidon@rcbi.rochester.edu for installation or use RCBI machines)

- Read mrVista manual: http://white.stanford.edu/~sweta/VistaLab/Manual/mrvista.html

- Follow RCBI manual for retinotopic mapping step-by-step to obtain hand-delineated areas and a 3d-reconstructed overlay. Determine which type of stimulus was used to get this result (Rotating wedge or expanding rings?)

(3) List your references.

Mentor: Aaron Newman, Jennifer Vannest

(1) Work through web-based tutorials to learn to analyze a cognitive fMRI experiment using FSL software.

http://www.fmrib.ox.ac.uk/fslcourse/

or locally they are mirrored at http://rcbi.rochester.edu/analysis/

(2) Apply them to the real data we provide. There are 2 datasets — one from a block-design fMRI experiment and one from an event-related design.

(3) Critically evaluate the results from the above analysis in terms of possible source of errors and neuroscience implications.

(4) List your references.

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