Sara

Back to Psych 204B Projects 2012

Background

You can use subsections if you like. Below is an example of a retinotopic map. Or, to be precise, below will be an example of a retinotopic map once the image is uploaded. To add an image, simply put text like this inside double brackets 'MyFile.jpg | My figure caption'. When you save this text and click on the link, the wiki will ask you for the figure.

Below is another example of a reinotopic map in a different subject.
Figure 2

Once you upload the images, they look like this. Note that you can control many features of the images, like whether to show a thumbnail, and the display resolution.

Figure 3

MNI space

MNI is an abbreviation for Montreal Neurological Institute.

Methods

Subjects

Five individuals diagnosed with MDD and five non-depressed control subjects were included in the study. All participants were females between the ages of 18 and 59. The Structured Clinical Interview for the DSM-IV was administered to all participants to assess current and lifetime diagnoses for anxiety, mood, psychotic symptoms, alcohol and substance use, somatoform, and eating disorders. Participants who met DSM-IV criteria for current MDD were included in the MDD group; exclusion criteria included substance abuse within the prior 6 months and co-occurring psychosis and/or mania. Participants with no current or past Axis I disorder, and who were not taking any psychotropic medications, were included in the control (CTL) group. Exclusion criteria for the CTL group included prior substance abuse problems and previous use of psychotropic medications.

MR Acquisition

Blood-oxygen level-dependent (BOLD) data were acquired with a 3 Tesla (T) strength General Electric Signa MR scanner (Milwaukee, Wisconsin), using a gradient echo EPI sequence (37 axial slices; field of view [FOV]=224mm, slice thickness=3.2mm, gap=0mm, repetition time [TR]=2000, echo time [TE]=30ms, flip angle [FA]=77°). A structural T1-weighted volume (186 sagittal slices, FOV=240mm, slice thickness=0.9mm, gap=0mm, TR=6200, TE=230, FA=12°) was performed following BOLD scanning runs. Head movement was minimized by using foam cushions.

MR Analysis

The MR data was analyzed using FSL 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

PRF models were fit with a 2-gaussian model.

MNI space

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.
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

Accept Task

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.
See wikimedia help on formulas for help.
This example of equation use is copied and pasted from wikipedia's article on the DFT.

The sequence of N complex numbers x₀, ..., x_N−1 is transformed into the sequence of N complex numbers X₀, ..., X_N−1 by the DFT according to the formula:

$X_k=\sum _{n=0}^{N-1}{x}_n{e}^{-\frac{2\pi i}{N}kn}k=0,\dots ,N-1$

where i is the imaginary unit and $e^{\frac{2\pi i}{N}}$ 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_k can thus be viewed as coefficients of x in an orthonormal basis.)

The transform is sometimes denoted by the symbol $ℱ$, as in $𝐗=ℱ\left\{𝐱\right\}$ or $ℱ\left(𝐱\right)$ or $ℱ𝐱$.

The inverse discrete Fourier transform (IDFT) is given by

$x_n=\frac{1}{N}\sum _{k=0}^{N-1}{X}_k{e}^{\frac{2\pi i}{N}kn}n=0,\dots ,N-1.$

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

Appendix I - Code and Data

Code

File:CodeFile.zip

Data

zip file with my data