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= Differences Between Spin-Echo and Gradient-Echo Imaging =
= Differences Between Spin-Echo and Gradient-Echo Imaging =
Spin-Echo and Gradient-Echo imaging are two different methods of obtaining fMRI data that vary along various dimensions: the pulse sequence used to generate and obtain the signal, signal-to-noise ratio, and sensitivity to large blood vessels, to name a few.
Spin-Echo and Gradient-Echo imaging are two popular methods of obtaining fMRI data that vary along various dimensions: the pulse sequence used to generate and obtain the signal, signal-to-noise ratio, and sensitivity to large blood vessels, to name a few. This study examines the differences between the two by looking at a data set from the VISTA lab. Overall differences in signal-to-noise, areas of high and low signal, and distortions are examined. Furthermore, hV4 and other areas of visual cortex are considered and compared between the two types of scans.
<br>
 
Note that this is a project template. Other styles are possible. For example, you could use [http://white.stanford.edu/teach/index.php/Main_Page#Multiple_page_format a multiple page format].
*Note: another goal of this study was to familiarize the author (who has no experience viewing fMRI data) with fMRI data, analysis techniques, software, and different types of data.


= Background =
= Background =
== Retinotopic maps ==
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.
<br>
[[File:Example.jpg | Figure 1]]


Below is another example of a reinotopic map in a different subject.
===Gradient-Echo Imaging===
<br>
Gradient-Echo images are generated by an applied gradient-followed by an RF pulse sequence to excite slices one by one and collect data from each. Gradient-Echo images have a stronger overall signal than Spin-Echo images and the overall signal-to-noise ratio is higher. However, Gradient-Echo images are prone to large distortions from large blood vessels, sinuses, and other inhomogeneities.
[[File:Example2.jpg | 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.
===Spin-Echo Imaging===
[[File:Example3.jpg |thumb|300px|center| Figure 3]]
Spin-Echo images are generated by a 180-degree pulse following the applied gradient. This pulse realigns the dephasing spins and gives another shot at capturing data. Spin-Echo images are weaker in signal and signal-to-noise ratio than Gradient-Echo images. However, Spin-Echo images should be less sensitive to distortions from large blood vessels and sinuses.
<br>


== MNI space ==
===Vessel Distortions===
Spin-Echo imaging can be used to refocus the loss of phase coherence and eliminate the large-vessel signal. For smaller vessels, the gradient changes rapidly over space relative…Loss of phase coherence cannot be recovered by Spin-Echo imaging (from Huettel et al. text).


MNI is an abbreviation for [http://en.wikipedia.org/wiki/Montreal_Neurological_Institute Montreal Neurological Institute].
===Purpose===
Although Gradient-Echo images have a stronger overall signal and signal-to-noise ratio and generally show more in most brain regions, Spin-Echo images are theorized to avoid distortions due to large blood vessels and inhomogeneities. The hope of this study was to find areas in which Spin-Echo images could reveal things in visual cortex that Gradient-Echo could not. For example, areas like hV4...


= Methods =
= Methods =
== Measuring retinotopic maps ==
The data were obtained from Jon Winawer through VISTA lab.  
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 ===
Data were obtained on a GE scanner. Et cetera.


=== MR Analysis ===
=== MR Analysis ===
The MR data was analyzed using [http://white.stanford.edu/newlm/index.php/MrVista mrVista] software tools.  
The MR data were analyzed using [http://white.stanford.edu/newlm/index.php/MrVista mrVista] software tools. Features used included correlation analyses, traveling wave analyses, mean maps, phase-projected coherence maps, and time series plots.
 
==== 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 ====
=== Pre-processing ===
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>
All data were slice-time corrected, motion corrected, and repeated scans were averaged together to create a single average scan for each subject. Pre-processing was done by Jon.
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 =


[[File:Slices.jpg |thumb|300px|center| (Figure 1) Slice Origin]]


= Results - What you found =
[[File:V1-V3_tSeries.jpg |thumb|300px|left| (Figure 4) Raw Time Series of Areas V1-V3 (bilateral)]] [[File:Right_hV4_Average.jpg |thumb|300px|right| (Figure 6) Average Time Series of Right hV4]]


== Retinotopic models in native space ==
[[File:V1-V3_Average_tSeries.jpg |thumb|300px|left| (Figure 5) Average Time Series of Areas V1-V3 (bilateral)]] [[File:Right_hV4_Single_Cycle.jpg |thumb|300px|right| (Figure 7) Single Cycle of Right hV4]]
Some text. Some analysis. Some figures.


== Retinotopic models in individual subjects transformed into MNI space ==
[[File:Gradient_vs._Spin.jpg |thumb|500px|center| (Figure 2) Gradient-Echo vs. Spin-Echo]]
Some text. Some analysis. Some figures.


== Retinotopic models in group-averaged data on the MNI template brain ==
[[File:GradientSpinMajorDistortions.jpg |thumb|500px|center| (Figure 3) Major Distortions in Gradient-Echo vs. Spin-Echo]]
Some text. Some analysis. Some figures.


[[File:Sinus_ROI.jpg |thumb|400px|center| (Figure 8) Sinus ROI and nearby visual cortex]]


== Retinotopic models in group-averaged data projected back into native space ==
[[File:Gradient_Echo_FFT.jpg |thumb|400px|left| (Figure 9) Gradient-Echo FFT]]
Some text. Some analysis. Some figures.
[[File:Spin_Echo_FFT.jpg |thumb|400px|center| (Figure 10) Spin-Echo FFT]]


= Conclusions =
= Conclusions =


Here is where you say what your results mean.
==Overall==
 
At first glance, one notices the difference in overall signal and signal-to-noise between the two scans as indicated by the brighter colors in the Gradient-Echo scan and the greater contrast between areas of signal areas of no signal (Figure 2). Another striking difference is seen in the type of distortions caused by the ear canals in the Gradient-Echo (absence of signal in that area) and the Spin-Echo ("bubbles" of signal built up over that area) scans (Figure 3). Furthermore, the phase, as shown by the FFT of each scan, of the two signals is right in-sync, with both peaking at the same time (Figures 9 & 10).
= References - Resources and related work =
 
References
 
Software
 
= Appendix I - Code and Data =
 
==Code==
[[Media:MyCodeZipFile.zip | zip file with code]]
 
==Data==
[[Media:MyDataZipFile.zip | zip file with my data]]
 
= Appendix II - Work partition (if a group project) =
Brian and Bob gave the lectures. Jon mucked around on the wiki.
 
 
= Test Equations =
 
''This is a test of equation use on our wiki. The text below is copied and pasted from [http://en.wikipedia.org/wiki/Discrete_Fourier_transform wikipedia's article on the DFT]''
 
==Definition==
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>
The next thing to note is the overall similarity in signal and phase between the Spin-Echo and Gradient-Echo signals for V1-V3 (Figures 4 & 5). One also notices that the Spin-Echo scan has a much lower overall signal throughout. Though the Spin-Echo scans have a weaker signal, they seem to reflect similar data for most areas of visual cortex (analyses of cortex other than V1-V3 not shown). In areas like the ear canals where the distortions produced differ in character, Spin-Echo imaging doesn't do a better job either.


A simple description of these equations is that the complex numbers <math>X_k</math> represent the amplitude and phase of the different sinusoidal components of the input "signal" <math>x_n</math>.  The DFT computes the <math>X_k</math> from the <math>x_n</math>, while the IDFT shows how to compute the <math>x_n</math> as a sum of sinusoidal components <math>(1/N) X_k e^{\frac{2\pi i}{N}k n}</math> with [[frequency]] <math>k/N</math> cycles per sample. By writing the equations in this form, we are making extensive use of [[Euler's formula]] to express sinusoids in terms of complex exponentials, which are much easier to manipulate. In the same way, by writing <math>X_k</math> in [[Complex_number#Polar_form|polar form]], we immediately obtain the sinusoid amplitude <math>A_k</math> and phase <math>\phi_k</math> from the [[complex argument|complex modulus and argument]] of <math>X_k</math>, respectively:
==hV4==
In the areas of interest, specifically left and right hV4 near the sinus, Spin-Echo imaging did no better than Gradient-Echo imaging in gathering a coherent signal from hV4. Furthermore, surrounding areas have distortions in Spin-Echo scans which are absent in Gradient-Echo scans (Figure 8). It seems that Spin-Echo scans, at least in this case, provide no useful additional information about hV4.


:<math>A_k = |X_k| = \sqrt{\operatorname{Re}(X_k)^2 + \operatorname{Im}(X_k)^2},</math>
==Implications==
:<math>\varphi_k = \arg(X_k) = \operatorname{atan2}\big( \operatorname{Im}(X_k), \operatorname{Re}(X_k) \big).</math>
Further research might examine other methods of obtaining functional data in this region (e.g. different pulse sequences). Also, other regions of the brain remain to be examined. Perhaps there are areas of (visual and non-visual) cortex in which Spin-Echo scans offer a distinct advantage.


Note that the normalization factor multiplying the DFT and IDFT (here 1 and 1/''N'') and the signs of the exponents are merely conventions, and differ in some treatments. The only requirements of these conventions are that the DFT and IDFT have opposite-sign exponents and that the product of their normalization factors be 1/''N''.  A normalization of <math>1/\sqrt{N}</math> for both the DFT and IDFT makes the transforms [[unitary matrix|unitary]], which has some theoretical advantages, but it is often more practical in numerical computation to perform the scaling all at once as above (and a unit scaling can be convenient in other ways).
= References =


(The convention of a negative sign in the exponent is often convenient because it means that <math>X_k</math> is the amplitude of a "positive frequency" <math>2\pi k/N</math>. Equivalently, the DFT is often thought of as a [[matched filter]]: when looking for a frequency of +1, one correlates the incoming signal with a frequency of −1.)
Software: [http://white.stanford.edu/newlm/index.php/MrVista mrVista]


In the following discussion the terms "sequence" and "vector" will be considered interchangeable.
Winawer J, Horiguchi H*, Sayres R*, Amano K, Wandell BA. (In Press) Mapping hV4 and ventral occipital cortex: The venous eclipse. Journal of Vision.

Latest revision as of 21:33, 9 December 2009

Back to Psych 204 Projects 2009

Differences Between Spin-Echo and Gradient-Echo Imaging

Spin-Echo and Gradient-Echo imaging are two popular methods of obtaining fMRI data that vary along various dimensions: the pulse sequence used to generate and obtain the signal, signal-to-noise ratio, and sensitivity to large blood vessels, to name a few. This study examines the differences between the two by looking at a data set from the VISTA lab. Overall differences in signal-to-noise, areas of high and low signal, and distortions are examined. Furthermore, hV4 and other areas of visual cortex are considered and compared between the two types of scans.

  • Note: another goal of this study was to familiarize the author (who has no experience viewing fMRI data) with fMRI data, analysis techniques, software, and different types of data.

Background

Gradient-Echo Imaging

Gradient-Echo images are generated by an applied gradient-followed by an RF pulse sequence to excite slices one by one and collect data from each. Gradient-Echo images have a stronger overall signal than Spin-Echo images and the overall signal-to-noise ratio is higher. However, Gradient-Echo images are prone to large distortions from large blood vessels, sinuses, and other inhomogeneities.

Spin-Echo Imaging

Spin-Echo images are generated by a 180-degree pulse following the applied gradient. This pulse realigns the dephasing spins and gives another shot at capturing data. Spin-Echo images are weaker in signal and signal-to-noise ratio than Gradient-Echo images. However, Spin-Echo images should be less sensitive to distortions from large blood vessels and sinuses.

Vessel Distortions

Spin-Echo imaging can be used to refocus the loss of phase coherence and eliminate the large-vessel signal. For smaller vessels, the gradient changes rapidly over space relative…Loss of phase coherence cannot be recovered by Spin-Echo imaging (from Huettel et al. text).

Purpose

Although Gradient-Echo images have a stronger overall signal and signal-to-noise ratio and generally show more in most brain regions, Spin-Echo images are theorized to avoid distortions due to large blood vessels and inhomogeneities. The hope of this study was to find areas in which Spin-Echo images could reveal things in visual cortex that Gradient-Echo could not. For example, areas like hV4...

Methods

The data were obtained from Jon Winawer through VISTA lab.

MR Analysis

The MR data were analyzed using mrVista software tools. Features used included correlation analyses, traveling wave analyses, mean maps, phase-projected coherence maps, and time series plots.

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. Pre-processing was done by Jon.

Results

(Figure 1) Slice Origin
(Figure 4) Raw Time Series of Areas V1-V3 (bilateral)
(Figure 6) Average Time Series of Right hV4
(Figure 5) Average Time Series of Areas V1-V3 (bilateral)
(Figure 7) Single Cycle of Right hV4
(Figure 2) Gradient-Echo vs. Spin-Echo
(Figure 3) Major Distortions in Gradient-Echo vs. Spin-Echo
(Figure 8) Sinus ROI and nearby visual cortex
(Figure 9) Gradient-Echo FFT
(Figure 10) Spin-Echo FFT

Conclusions

Overall

At first glance, one notices the difference in overall signal and signal-to-noise between the two scans as indicated by the brighter colors in the Gradient-Echo scan and the greater contrast between areas of signal areas of no signal (Figure 2). Another striking difference is seen in the type of distortions caused by the ear canals in the Gradient-Echo (absence of signal in that area) and the Spin-Echo ("bubbles" of signal built up over that area) scans (Figure 3). Furthermore, the phase, as shown by the FFT of each scan, of the two signals is right in-sync, with both peaking at the same time (Figures 9 & 10).

The next thing to note is the overall similarity in signal and phase between the Spin-Echo and Gradient-Echo signals for V1-V3 (Figures 4 & 5). One also notices that the Spin-Echo scan has a much lower overall signal throughout. Though the Spin-Echo scans have a weaker signal, they seem to reflect similar data for most areas of visual cortex (analyses of cortex other than V1-V3 not shown). In areas like the ear canals where the distortions produced differ in character, Spin-Echo imaging doesn't do a better job either.

hV4

In the areas of interest, specifically left and right hV4 near the sinus, Spin-Echo imaging did no better than Gradient-Echo imaging in gathering a coherent signal from hV4. Furthermore, surrounding areas have distortions in Spin-Echo scans which are absent in Gradient-Echo scans (Figure 8). It seems that Spin-Echo scans, at least in this case, provide no useful additional information about hV4.

Implications

Further research might examine other methods of obtaining functional data in this region (e.g. different pulse sequences). Also, other regions of the brain remain to be examined. Perhaps there are areas of (visual and non-visual) cortex in which Spin-Echo scans offer a distinct advantage.

References

Software: mrVista

Winawer J, Horiguchi H*, Sayres R*, Amano K, Wandell BA. (In Press) Mapping hV4 and ventral occipital cortex: The venous eclipse. Journal of Vision.

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