Alex - Revision history

imported>Psych204B at 03:42, 16 March 2012

2012-03-16T03:42:00Z

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	[[File:TravelingWaveIllustration.png‎\|thumb\|~~300px~~\|center\| Figure 1: Traveling Wave Method for creating retinotopic field maps in occipital cortex. Referred to Wandell et al. 2007 for more details. ]]		[[File:TravelingWaveIllustration.png‎\|thumb\|500px\|center\| Figure 1: Traveling Wave Method for creating retinotopic field maps in occipital cortex. Referred to Wandell et al. 2007 for more details. ]]


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	[[File:Parietal_rois_silver.png‎\|thumb\|~~300px~~\|center\| Figure 3: Topographic Maps Parietal Cortex from Silver and Kastner 2009]]		[[File:Parietal_rois_silver.png‎\|thumb\|400px\|center\| Figure 3: Topographic Maps Parietal Cortex from Silver and Kastner 2009]]

imported>Psych204B at 03:41, 16 March 2012

2012-03-16T03:41:26Z

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	= References =		= References =

	Bressler DW, Silver MA (2010) Spatial attention improves reliability of fMRI retinotopic mapping signals in occipital and parietal cortex. NeuroImage		Bressler DW, Silver MA (2010) Spatial attention improves reliability of fMRI retinotopic mapping signals in occipital and parietal cortex. NeuroImage

	Brian A. Wandell, Serge O. Dumoulin, Alyssa A. Brewer, Visual Field Maps in Human Cortex, Neuron, Volume 56, Issue 2, 25 October 2007		Brian A. Wandell, Serge O. Dumoulin, Alyssa A. Brewer, Visual Field Maps in Human Cortex, Neuron, Volume 56, Issue 2, 25 October 2007

	Brian A. Wandell, Jonathan Winawer, Imaging retinotopic maps in the human brain, Vision Research, Volume 51, Issue 7, 13 April 2011		Brian A. Wandell, Jonathan Winawer, Imaging retinotopic maps in the human brain, Vision Research, Volume 51, Issue 7, 13 April 2011
	Engel SA, Rumelhart DE, Wandell BA, Lee AT, Glover GH, Chichilnisky EJ, Shadlen MN(1994) fmri of human visual cortex. Nature 369:525.
			Engel SA, Rumelhart DE, Wandell BA, Lee AT, Glover GH, Chichilnisky EJ, Shadlen MN(1994) fmri of human visual cortex. Nature 369:525

	Silver MA, Kastner S (2009) Topographic maps in human frontal and parietal cortex. Trends in Cognitive Sciences		Silver MA, Kastner S (2009) Topographic maps in human frontal and parietal cortex. Trends in Cognitive Sciences

imported>Psych204B at 03:40, 16 March 2012

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	= References =		= References =
			Bressler DW, Silver MA (2010) Spatial attention improves reliability of fMRI retinotopic mapping signals in occipital and parietal cortex. NeuroImage
	~~Engel SA~~, ~~Rumelhart DE, Wandell BA, Lee AT, Glover GH, Chichilnisky EJ, Shadlen MN~~(~~1994~~) ~~fmri~~ of ~~human visual~~ cortex. ~~Nature 369:525.~~

	Brian A. Wandell, Serge O. Dumoulin, Alyssa A. Brewer, Visual Field Maps in Human Cortex, Neuron, Volume 56, Issue 2, 25 October 2007		Brian A. Wandell, Serge O. Dumoulin, Alyssa A. Brewer, Visual Field Maps in Human Cortex, Neuron, Volume 56, Issue 2, 25 October 2007
	Brian A. Wandell, Jonathan Winawer, Imaging retinotopic maps in the human brain, Vision Research, Volume 51, Issue 7, 13 April 2011		Brian A. Wandell, Jonathan Winawer, Imaging retinotopic maps in the human brain, Vision Research, Volume 51, Issue 7, 13 April 2011
			Engel SA, Rumelhart DE, Wandell BA, Lee AT, Glover GH, Chichilnisky EJ, Shadlen MN(1994) fmri of human visual cortex. Nature 369:525.
			Silver MA, Kastner S (2009) Topographic maps in human frontal and parietal cortex. Trends in Cognitive Sciences

imported>Psych204B at 03:39, 16 March 2012

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	= Background =		= Background =

	Many cortical areas have a one to one mapping between visual field and cortical location (Bressler and Silver 2010). A natural way to explore this is to have a stimulus that traverses the visual field in some fashion, and then do some type of correlation analysis between visual field location and brain activity. Engel et al. ~~(1993,~~1994,~~1997)~~ were one of the first experimenters to develop a continuos stimuli covers all of the visual space. They showed that by using a traveling wave analysis for a rotating wedge and moving concentric circles stimuli, the visual field maps could be produced in occipital cortex. Figure 1, taken from Wandell et al. 2007 illustrates this method.		Many cortical areas have a one to one mapping between visual field and cortical location (Bressler and Silver 2010). A natural way to explore this is to have a stimulus that traverses the visual field in some fashion, and then do some type of correlation analysis between visual field location and brain activity. Engel et al. 1994, were one of the first experimenters to develop a continuos stimuli that covers all of the visual space for an fMRI experiment. They showed that by using a traveling wave analysis for a rotating wedge and moving concentric circles stimuli, the visual field maps could be produced in occipital cortex. Figure 1, taken from Wandell et al. 2007 illustrates this method.


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	= References =		= References =

			Engel SA, Rumelhart DE, Wandell BA, Lee AT, Glover GH, Chichilnisky EJ, Shadlen MN(1994) fmri of human visual cortex. Nature 369:525.

			Brian A. Wandell, Serge O. Dumoulin, Alyssa A. Brewer, Visual Field Maps in Human Cortex, Neuron, Volume 56, Issue 2, 25 October 2007
			Brian A. Wandell, Jonathan Winawer, Imaging retinotopic maps in the human brain, Vision Research, Volume 51, Issue 7, 13 April 2011

imported>Psych204B at 03:33, 16 March 2012

2012-03-16T03:33:14Z

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	[[File:Rois.002.jpg \| thumb\|500px\|center\| Figure 6: Dorsal Visual Field Maps ]]		[[File:Rois.002.jpg \| thumb\|500px\|center\| Figure 6: Dorsal Visual Field Maps ]]

			V2d is defined by continuing dorsally from V1 in the Calcarine sulcus. V2d and V3d were a bit tricky to identify since the reversals were not as marked as in other areas. V3dAB follows V3d by going red to blue, then IPS0 by going blue to red.

	[[File:Rois.003.jpg \| thumb\|500px\|center\| Figure 7: Parietal Maps ]]		[[File:Rois.003.jpg \| thumb\|500px\|center\| Figure 7: Parietal Maps ]]

			In this subject the parietal field maps are not as clear as the ventral ones. But some of the reversals can still be seen in these areas. Continuing dorsally from IPS0 a red reversal is observed to start IPS1. The start of IPS2 is a bit tricky since there wasn't too much signal. However, maps continue dorsally and this subject showed a very clear SPL1.

	= Conclusions =		= Conclusions =

	~~Here~~ is where ~~you say what your results mean~~.		The goal of this project was to receive training in how to do retinotopy/ attenotopy using mrVista. I defined a total of 15 maps in ventral visual cortex and in parietal cortex. There is definitely an element of judgement when defining these maps as must of the boundaries are defined by approximating where one thinks the reversal takes place. Moreover, these maps are highly variable across subjects and a good amount of experience is needed in order to be consistant in defining these maps. Nonetheless, I must admit that it is very cool seeing and defining these maps, and also to see how the brain organizes what we observe. Special thanks to Kevin Weiner who helped at every step, from obtaining the data getting everything running, to checking that the ROI's made were not in frontal cortex.

	~~= References - Resources~~ and ~~related work =~~

	~~References~~

	~~Software~~

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

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

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

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

imported>Psych204B at 03:10, 16 March 2012

2012-03-16T03:10:27Z

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	[[File:Rois.003.jpg \| thumb\|500px\|center\| Figure 7: Parietal Maps ]]		[[File:Rois.003.jpg \| thumb\|500px\|center\| Figure 7: Parietal 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.~~
	~~<br>~~
	~~[[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.~~
	~~[[File:Example3.jpg \|thumb\|300px\|center\| Figure 3]]~~
	~~<br>~~

	~~== MNI space ==~~

	~~MNI is an abbreviation for [http://en.wikipedia.org/wiki/Montreal_Neurological_Institute Montreal Neurological Institute].~~

	~~= 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 ===~~
	~~Data were obtained on a GE scanner. Et cetera.~~

	~~=== MR Analysis ===~~
	~~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 ====~~
	~~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. <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.~~

imported>Psych204B at 03:09, 16 March 2012

2012-03-16T03:09:28Z

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	[[File:Rois.001.jpg \| thumb\|500px\|center\| Figure 5: Ventral Visual Field Maps ]]		[[File:Rois.001.jpg \| thumb\|500px\|center\| Figure 5: Ventral Visual Field Maps ]]

	Figure 5 shows the maps produced using this procedure in ventral visual cortex. Starting in V1, moving dorsally a blue contrast reversal is seen and ~~that~~ marks the start of V2		Figure 5 shows the maps produced using this procedure in ventral visual cortex. Starting in V1, moving dorsally a blue contrast reversal is seen, indicating the end of that hemifield and the marks the start of V2d. The distinction between V2 and V3 is not as marked, but it is there. From V3d there is a clear blue and then red reversal, which marks the start of V4. After V4; VO1, VO2, PHC1 and PHC2 can be easily identified. Also from VO1 all the ROI's follow the colateral sulcus.

	[[File:Rois.002.jpg \| thumb\|500px\|center\| Figure 6: Dorsal Visual Field Maps ]]		[[File:Rois.002.jpg \| thumb\|500px\|center\| Figure 6: Dorsal Visual Field Maps ]]

imported>Psych204B at 03:02, 16 March 2012

2012-03-16T03:02:52Z

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	[[File:Rois.001.jpg \| thumb\|500px\|center\| Figure 5: Ventral Visual Field Maps ]]		[[File:Rois.001.jpg \| thumb\|500px\|center\| Figure 5: Ventral Visual Field Maps ]]

	Figure 5 shows the maps produced using this procedure in ventral visual cortex.		Figure 5 shows the maps produced using this procedure in ventral visual cortex. Starting in V1, moving dorsally a blue contrast reversal is seen and that marks the start of V2

	[[File:Rois.002.jpg \| thumb\|500px\|center\| Figure 6: Dorsal Visual Field Maps ]]		[[File:Rois.002.jpg \| thumb\|500px\|center\| Figure 6: Dorsal Visual Field Maps ]]

imported>Psych204B at 02:45, 16 March 2012

2012-03-16T02:45:06Z

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	=Analysis and Results=		=Analysis and Results=

	Visual field maps were defined following Wandell et al. 2007 definitions. Briefly, a visual field area should: 1) represent a substantial portion of the visual field, 2) it must do so in an orderly fashion, 3) the basic features should be consistant within subjects. Starting from V1 (easily identified by the Calcarine Sulcus) contrast reversals are followed dorsally and ventrally to define the rest of the maps. ~~Figure 5 shows~~ the ~~maps produced using this procedure in ventral visual cortex~~.		Visual field maps were defined following Wandell et al. 2007 definitions. Briefly, a visual field area should: 1) represent a substantial portion of the visual field, 2) it must do so in an orderly fashion, 3) the basic features should be consistant within subjects. Starting from V1 (easily identified by the Calcarine Sulcus) contrast reversals are followed dorsally and ventrally to define the rest of the maps. The results are shown in the following figures.

			[[File:Rois.001.jpg \| thumb\|500px\|center\| Figure 5: Ventral Visual Field Maps ]]

	~~[[File:Rois.001.jpg \| thumb\|500px\|center\|~~ Figure 5~~: Ventral Visual Field Maps ]]]]~~		Figure 5 shows the maps produced using this procedure in ventral visual cortex.

	[[File:Rois.002.jpg \| thumb\|500px\|center\| Figure 6: Dorsal Visual Field Maps ]]]]		[[File:Rois.002.jpg \| thumb\|500px\|center\| Figure 6: Dorsal Visual Field Maps ]]

	[[File:Rois.003.jpg \| thumb\|500px\|center\| Figure 7: Parietal Maps ]]]]		[[File:Rois.003.jpg \| thumb\|500px\|center\| Figure 7: Parietal Maps ]]

imported>Psych204B at 02:43, 16 March 2012

2012-03-16T02:43:53Z

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	[[File:Rois.001.jpg \| thumb\|~~300px~~\|center\| Figure 5: Ventral Visual Field Maps ]]]]		[[File:Rois.001.jpg \| thumb\|500px\|center\| Figure 5: Ventral Visual Field Maps ]]]]

	[[File:Rois.002.jpg \| thumb\|~~300px~~\|center\| Figure 6: Dorsal Visual Field Maps ]]]]		[[File:Rois.002.jpg \| thumb\|500px\|center\| Figure 6: Dorsal Visual Field Maps ]]]]

	[[File:Rois.003.jpg \| thumb\|~~300px~~\|center\| Figure 7: Parietal Maps ]]]]		[[File:Rois.003.jpg \| thumb\|500px\|center\| Figure 7: Parietal Maps ]]]]

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	[[File:Rois.001.jpg \| thumb\|~~300px~~\|center\| Figure 5: Ventral Visual Field Maps ]]]]		[[File:Rois.001.jpg \| thumb\|500px\|center\| Figure 5: Ventral Visual Field Maps ]]]]

	[[File:Rois.002.jpg \| thumb\|~~300px~~\|center\| Figure 6: Dorsal Visual Field Maps ]]]]		[[File:Rois.002.jpg \| thumb\|500px\|center\| Figure 6: Dorsal Visual Field Maps ]]]]

	[[File:Rois.003.jpg \| thumb\|~~300px~~\|center\| Figure 7: Parietal Maps ]]]]		[[File:Rois.003.jpg \| thumb\|500px\|center\| Figure 7: Parietal Maps ]]]]