Anthony & Jesse - Revision history

imported>Kweb: /* Methods for Mapping Visual Cortex */

2013-06-04T23:28:50Z

Methods for Mapping Visual Cortex

imported>Kweb: /* Methods for Mapping Visual Cortex */

2013-06-04T23:27:44Z

Methods for Mapping Visual Cortex

← Older revision		Revision as of 23:27, 4 June 2013
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	Decomposing each voxel's timecourse into discrete frequency bands using a Fourier transform allows you to estimate the proportion of variance explained by each signal modulation at each frequency. If a voxel is retinotopic, the frequency with the most energy should be equal to the number of cycles in the experiment. Shown below is the energy at each frequency extracted with the Fourier transform:		Decomposing each voxel's timecourse into discrete frequency bands using a Fourier transform allows you to estimate the proportion of variance explained by each signal modulation at each frequency. If a voxel is retinotopic, the frequency with the most energy should be equal to the number of cycles in the experiment. Shown below is the energy at each frequency extracted with the Fourier transform:

	[[File:Fourier.jpg\|center\|400px]]		[[File:Fourier.jpg\|center\|400px\|thumb\|center\| Figure from [[Mai]]]]]]

	As expected, the peak in this voxel's power spectrum is at 6 cycles, which is equal to the number of cycles in the experiment. This suggests that the voxel is retinotopic but is not informative about the particular eccentritiy (or polar angle) that optimally activates it. To determine the time lag that best explains the data, the 6-cycle sine wave is shifted and the phase shift that generates the best fit to the data is used to estimate the eccentricity (or polar angle) preferred by the voxel. If a voxel prefers foveal stimuli, for example, a small time shift should produce the best fit because foveal rings are presented at the beginning of the cycles in the eccentricity mapping experiment. Then, the same procedure is performed at every voxel, and a similar analysis can be applied to polar angle mapping experiments. To generate a map of polar angle and eccentricity biases, the range of phase shifts is color coded and mapped onto each voxel.		As expected, the peak in this voxel's power spectrum is at 6 cycles, which is equal to the number of cycles in the experiment. This suggests that the voxel is retinotopic but is not informative about the particular eccentritiy (or polar angle) that optimally activates it. To determine the time lag that best explains the data, the 6-cycle sine wave is shifted and the phase shift that generates the best fit to the data is used to estimate the eccentricity (or polar angle) preferred by the voxel. If a voxel prefers foveal stimuli, for example, a small time shift should produce the best fit because foveal rings are presented at the beginning of the cycles in the eccentricity mapping experiment. Then, the same procedure is performed at every voxel, and a similar analysis can be applied to polar angle mapping experiments. To generate a map of polar angle and eccentricity biases, the range of phase shifts is color coded and mapped onto each voxel.

imported>Kweb: /* Phase Encoding */

2013-06-04T23:27:16Z

Phase Encoding

← Older revision		Revision as of 23:27, 4 June 2013
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	The traveling wave of response generated by the ring and wedge stimuli allow you to determine the the most effective eccentricity (or polar angle) for driving a given voxel using a technique known as phase encoding. This use of this technique depends on the ring (or wedge) stimulus sweeping across each location in the visual field once in each cycle of the stimulus. Therefore, voxels that are part of a visual field map should illustrate six peaks in their response over the course of a run containing six cycles. The fact that different eccentricities (or polar angles) are sampled at different times in the cycle allows you to determine the particular degree of eccentricity (or polar angle) that most strongly activates each voxel. For example, imagine this were the timecourse of a voxel in an eccentricity scan:		The traveling wave of response generated by the ring and wedge stimuli allow you to determine the the most effective eccentricity (or polar angle) for driving a given voxel using a technique known as phase encoding. This use of this technique depends on the ring (or wedge) stimulus sweeping across each location in the visual field once in each cycle of the stimulus. Therefore, voxels that are part of a visual field map should illustrate six peaks in their response over the course of a run containing six cycles. The fact that different eccentricities (or polar angles) are sampled at different times in the cycle allows you to determine the particular degree of eccentricity (or polar angle) that most strongly activates each voxel. For example, imagine this were the timecourse of a voxel in an eccentricity scan:

	[[File:foveal_timecourse.jpg\|600px\|thumb\|center\| Figure from [[Mai]]]]		[[File:foveal_timecourse.jpg\|600px\|thumb\|center\| Figure borrowed from [[Mai]]]]

	If the cycle begins with with rings that occupy space in the center of the visual field, the peaks in the response of voxels with a foveal preference should be earlier in time than peaks in the response of voxels with peripheral preference. Shown below is the phase-shifted timecourse of a voxel with a peripheral preference.		If the cycle begins with with rings that occupy space in the center of the visual field, the peaks in the response of voxels with a foveal preference should be earlier in time than peaks in the response of voxels with peripheral preference. Shown below is the phase-shifted timecourse of a voxel with a peripheral preference.

	[[File:peripheral_timecourse.jpg\|600px\|thumb\|center\| Figure from [[Mai]]]]		[[File:peripheral_timecourse.jpg\|600px\|thumb\|center\| Figure borrowed from [[Mai]]]]

	==== Finding the Phase ====		==== Finding the Phase ====

imported>Kweb: /* Phase Encoding */

2013-06-04T23:27:01Z

Phase Encoding

← Older revision		Revision as of 23:27, 4 June 2013
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	If the cycle begins with with rings that occupy space in the center of the visual field, the peaks in the response of voxels with a foveal preference should be earlier in time than peaks in the response of voxels with peripheral preference. Shown below is the phase-shifted timecourse of a voxel with a peripheral preference.		If the cycle begins with with rings that occupy space in the center of the visual field, the peaks in the response of voxels with a foveal preference should be earlier in time than peaks in the response of voxels with peripheral preference. Shown below is the phase-shifted timecourse of a voxel with a peripheral preference.

	[[File:peripheral_timecourse.jpg\|600px\|center]]		[[File:peripheral_timecourse.jpg\|600px\|thumb\|center\| Figure from [[Mai]]]]

	==== Finding the Phase ====		==== Finding the Phase ====

imported>Kweb: /* Phase Encoding */

2013-06-04T23:26:28Z

Phase Encoding

← Older revision		Revision as of 23:26, 4 June 2013
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	The traveling wave of response generated by the ring and wedge stimuli allow you to determine the the most effective eccentricity (or polar angle) for driving a given voxel using a technique known as phase encoding. This use of this technique depends on the ring (or wedge) stimulus sweeping across each location in the visual field once in each cycle of the stimulus. Therefore, voxels that are part of a visual field map should illustrate six peaks in their response over the course of a run containing six cycles. The fact that different eccentricities (or polar angles) are sampled at different times in the cycle allows you to determine the particular degree of eccentricity (or polar angle) that most strongly activates each voxel. For example, imagine this were the timecourse of a voxel in an eccentricity scan:		The traveling wave of response generated by the ring and wedge stimuli allow you to determine the the most effective eccentricity (or polar angle) for driving a given voxel using a technique known as phase encoding. This use of this technique depends on the ring (or wedge) stimulus sweeping across each location in the visual field once in each cycle of the stimulus. Therefore, voxels that are part of a visual field map should illustrate six peaks in their response over the course of a run containing six cycles. The fact that different eccentricities (or polar angles) are sampled at different times in the cycle allows you to determine the particular degree of eccentricity (or polar angle) that most strongly activates each voxel. For example, imagine this were the timecourse of a voxel in an eccentricity scan:

	[[File:foveal_timecourse.jpg\|600px\|thumb\|center\| Figure from [Mai]]]		[[File:foveal_timecourse.jpg\|600px\|thumb\|center\| Figure from [[Mai]]]]

	If the cycle begins with with rings that occupy space in the center of the visual field, the peaks in the response of voxels with a foveal preference should be earlier in time than peaks in the response of voxels with peripheral preference. Shown below is the phase-shifted timecourse of a voxel with a peripheral preference.		If the cycle begins with with rings that occupy space in the center of the visual field, the peaks in the response of voxels with a foveal preference should be earlier in time than peaks in the response of voxels with peripheral preference. Shown below is the phase-shifted timecourse of a voxel with a peripheral preference.

imported>Kweb: /* Methods for Mapping Visual Cortex */

2013-06-04T23:26:14Z

Methods for Mapping Visual Cortex

← Older revision		Revision as of 23:26, 4 June 2013
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	The traveling wave of response generated by the ring and wedge stimuli allow you to determine the the most effective eccentricity (or polar angle) for driving a given voxel using a technique known as phase encoding. This use of this technique depends on the ring (or wedge) stimulus sweeping across each location in the visual field once in each cycle of the stimulus. Therefore, voxels that are part of a visual field map should illustrate six peaks in their response over the course of a run containing six cycles. The fact that different eccentricities (or polar angles) are sampled at different times in the cycle allows you to determine the particular degree of eccentricity (or polar angle) that most strongly activates each voxel. For example, imagine this were the timecourse of a voxel in an eccentricity scan:		The traveling wave of response generated by the ring and wedge stimuli allow you to determine the the most effective eccentricity (or polar angle) for driving a given voxel using a technique known as phase encoding. This use of this technique depends on the ring (or wedge) stimulus sweeping across each location in the visual field once in each cycle of the stimulus. Therefore, voxels that are part of a visual field map should illustrate six peaks in their response over the course of a run containing six cycles. The fact that different eccentricities (or polar angles) are sampled at different times in the cycle allows you to determine the particular degree of eccentricity (or polar angle) that most strongly activates each voxel. For example, imagine this were the timecourse of a voxel in an eccentricity scan:

	[[File:foveal_timecourse.jpg\|600px\|center\| Figure ~~borrowed~~ from [Mai]]]		[[File:foveal_timecourse.jpg\|600px\|thumb\|center\| Figure from [Mai]]]

	If the cycle begins with with rings that occupy space in the center of the visual field, the peaks in the response of voxels with a foveal preference should be earlier in time than peaks in the response of voxels with peripheral preference. Shown below is the phase-shifted timecourse of a voxel with a peripheral preference.		If the cycle begins with with rings that occupy space in the center of the visual field, the peaks in the response of voxels with a foveal preference should be earlier in time than peaks in the response of voxels with peripheral preference. Shown below is the phase-shifted timecourse of a voxel with a peripheral preference.

imported>Kweb: /* Background */

2013-06-04T23:25:33Z

Background

← Older revision		Revision as of 23:25, 4 June 2013
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	The traveling wave of response generated by the ring and wedge stimuli allow you to determine the the most effective eccentricity (or polar angle) for driving a given voxel using a technique known as phase encoding. This use of this technique depends on the ring (or wedge) stimulus sweeping across each location in the visual field once in each cycle of the stimulus. Therefore, voxels that are part of a visual field map should illustrate six peaks in their response over the course of a run containing six cycles. The fact that different eccentricities (or polar angles) are sampled at different times in the cycle allows you to determine the particular degree of eccentricity (or polar angle) that most strongly activates each voxel. For example, imagine this were the timecourse of a voxel in an eccentricity scan:		The traveling wave of response generated by the ring and wedge stimuli allow you to determine the the most effective eccentricity (or polar angle) for driving a given voxel using a technique known as phase encoding. This use of this technique depends on the ring (or wedge) stimulus sweeping across each location in the visual field once in each cycle of the stimulus. Therefore, voxels that are part of a visual field map should illustrate six peaks in their response over the course of a run containing six cycles. The fact that different eccentricities (or polar angles) are sampled at different times in the cycle allows you to determine the particular degree of eccentricity (or polar angle) that most strongly activates each voxel. For example, imagine this were the timecourse of a voxel in an eccentricity scan:

	[[File:foveal_timecourse.jpg\|600px\|center\| Figure borrowed from [[Mai]]]]		[[File:foveal_timecourse.jpg\|600px\|center\| Figure borrowed from [Mai]]]

	If the cycle begins with with rings that occupy space in the center of the visual field, the peaks in the response of voxels with a foveal preference should be earlier in time than peaks in the response of voxels with peripheral preference. Shown below is the phase-shifted timecourse of a voxel with a peripheral preference.		If the cycle begins with with rings that occupy space in the center of the visual field, the peaks in the response of voxels with a foveal preference should be earlier in time than peaks in the response of voxels with peripheral preference. Shown below is the phase-shifted timecourse of a voxel with a peripheral preference.

imported>Kweb: /* Background */

2013-06-04T23:24:26Z

Background

← Older revision		Revision as of 23:24, 4 June 2013
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	The traveling wave of response generated by the ring and wedge stimuli allow you to determine the the most effective eccentricity (or polar angle) for driving a given voxel using a technique known as phase encoding. This use of this technique depends on the ring (or wedge) stimulus sweeping across each location in the visual field once in each cycle of the stimulus. Therefore, voxels that are part of a visual field map should illustrate six peaks in their response over the course of a run containing six cycles. The fact that different eccentricities (or polar angles) are sampled at different times in the cycle allows you to determine the particular degree of eccentricity (or polar angle) that most strongly activates each voxel. For example, imagine this were the timecourse of a voxel in an eccentricity scan:		The traveling wave of response generated by the ring and wedge stimuli allow you to determine the the most effective eccentricity (or polar angle) for driving a given voxel using a technique known as phase encoding. This use of this technique depends on the ring (or wedge) stimulus sweeping across each location in the visual field once in each cycle of the stimulus. Therefore, voxels that are part of a visual field map should illustrate six peaks in their response over the course of a run containing six cycles. The fact that different eccentricities (or polar angles) are sampled at different times in the cycle allows you to determine the particular degree of eccentricity (or polar angle) that most strongly activates each voxel. For example, imagine this were the timecourse of a voxel in an eccentricity scan:

	[[File:foveal_timecourse.jpg\|600px\|center]]		[[File:foveal_timecourse.jpg\|600px\|center\| Figure borrowed from [[Mai]]]]

	If the cycle begins with with rings that occupy space in the center of the visual field, the peaks in the response of voxels with a foveal preference should be earlier in time than peaks in the response of voxels with peripheral preference. Shown below is the phase-shifted timecourse of a voxel with a peripheral preference.		If the cycle begins with with rings that occupy space in the center of the visual field, the peaks in the response of voxels with a foveal preference should be earlier in time than peaks in the response of voxels with peripheral preference. Shown below is the phase-shifted timecourse of a voxel with a peripheral preference.

imported>Psych204B at 23:21, 4 June 2013

2013-06-04T23:21:04Z

← Older revision		Revision as of 23:21, 4 June 2013
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	<br>		<br>

	~~== Subjects & MR Processing ==~~
	== Defining Occipital Field Maps ==		== Defining Occipital Field Maps ==
	In order to interpret the results and make more accurate comparisons and contrasts between the traveling wave and pRF model results, we defined V1-V4 on each subject's brain using the pRF results from the analysis of the sliding bars stimuli. Boundaries were drawn beginning with V1, which is known to have a contralateral hemifield representation, and then radiating visual field maps were drawn at quarter-field mirror reversals. Area hV4 was drawn according to the anatomy of the posterior transverse colateral sulcus (PTCOS).		In order to interpret the results and make more accurate comparisons and contrasts between the traveling wave and pRF model results, we defined V1-V4 on each subject's brain using the pRF results from the analysis of the sliding bars stimuli. Boundaries were drawn beginning with V1, which is known to have a contralateral hemifield representation, and then radiating visual field maps were drawn at quarter-field mirror reversals. Area hV4 was drawn according to the anatomy of the posterior transverse colateral sulcus (PTCOS).

imported>Kweb: /* Background */

2013-06-04T23:19:50Z

Background

← Older revision		Revision as of 23:19, 4 June 2013
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	= Background =		= Background =
	[[File:retinotopy_schematic.png\|thumb\|right\| Representation of left visual field in right V1 (Wandell et al., 2007).]]		[[File:retinotopy_schematic.png\|thumb\|right\| Representation of left visual field in right V1 (Wandell et al. 2007).]]

	== What is Retinotopy? ==		== What is Retinotopy? ==
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	=== Polar Angle and Eccentricity Bias ===		=== Polar Angle and Eccentricity Bias ===
	[[File:EccPolar.png \|thumb\|right\|250px\| Eccentricity and Polar Angle Maps along the Calcarine (adapted from Wandell et al., 2007)]]		[[File:EccPolar.png \|thumb\|right\|250px\| Eccentricity and Polar Angle Maps along the Calcarine (adapted from Wandell et al. 2007)]]

	Each visual field map in each hemisphere has either an entire hemifield representation of visual space (or a quarter-field representation if separating maps such as V2 and V3 into ventral and dorsal subdivisions). In order to determine which part of the visual field an area is representing, we can use a stimulus that sweeps across the visual field at different polar angles (see figure F, to the right). BOLD activity that correlates with either the upper, horizontal, or lower visual field will be color-coded accordingly, allowing us to identify when there is a mirror-reversal of polar angle mapping. These reversals mark the dividing boundaries between different visual field maps in human cortex. For example, V1 has a hemifield representation, but V2v has a quarter-field representations in which the mapping of polar angle is mirror reversed relative to V1. Similarly, the representation of polar angle in V3v is mirror reversed relative to V2v.<br>		Each visual field map in each hemisphere has either an entire hemifield representation of visual space (or a quarter-field representation if separating maps such as V2 and V3 into ventral and dorsal subdivisions). In order to determine which part of the visual field an area is representing, we can use a stimulus that sweeps across the visual field at different polar angles (see figure F, to the right). BOLD activity that correlates with either the upper, horizontal, or lower visual field will be color-coded accordingly, allowing us to identify when there is a mirror-reversal of polar angle mapping. These reversals mark the dividing boundaries between different visual field maps in human cortex. For example, V1 has a hemifield representation, but V2v has a quarter-field representations in which the mapping of polar angle is mirror reversed relative to V1. Similarly, the representation of polar angle in V3v is mirror reversed relative to V2v.<br>
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	=== Beyond the Occipital Lobe ===		=== Beyond the Occipital Lobe ===
	[[File:maps.png \|thumb\|left\|300px\| Visual field maps extending into the intraparietal suclus (IPS) and ventral temporal cortex (VO)]]		[[File:maps.png \|thumb\|left\|300px\| Visual field maps extending into the intraparietal suclus (IPS) and ventral temporal cortex (VO) (Wandell et al. 2007)]]
	[[File:ips.png \|thumb\|right\|150px\| IPS visual field maps from Swisher et al. 2007]]		[[File:ips.png \|thumb\|right\|150px\| IPS visual field maps from Swisher et al. 2007]]
	[[File:phc.png \|thumb\|right\|150px\| PHC maps from Arcaro et al. 2009]]		[[File:phc.png \|thumb\|right\|150px\| PHC maps from Arcaro et al. 2009]]

← Older revision		Revision as of 23:28, 4 June 2013
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	=== Traveling Wave Analysis ===		=== Traveling Wave Analysis ===
	Engel et al. 1994 developed a method for defining visual field maps with fMRI by using stimuli that elicit a traveling wave of activation across the cortical surface. Since visual cortex is organized with according to polar angle and eccentricity, different stimuli must be used to generate traveling waves of activation that sweep from one end of a map through to the other in a single cycle. In typical retinotopic mapping scans, the stimulus cycle is repeated six times and ~~thi~~		Engel et al. 1994 developed a method for defining visual field maps with fMRI by using stimuli that elicit a traveling wave of activation across the cortical surface. Since visual cortex is organized with according to polar angle and eccentricity, different stimuli must be used to generate traveling waves of activation that sweep from one end of a map through to the other in a single cycle. In typical retinotopic mapping scans, the stimulus cycle is repeated six times and this allows phase encoding to be performed.

	==== Stimuli ====		==== Stimuli ====
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	The traveling wave of response generated by the ring and wedge stimuli allow you to determine the the most effective eccentricity (or polar angle) for driving a given voxel using a technique known as phase encoding. This use of this technique depends on the ring (or wedge) stimulus sweeping across each location in the visual field once in each cycle of the stimulus. Therefore, voxels that are part of a visual field map should illustrate six peaks in their response over the course of a run containing six cycles. The fact that different eccentricities (or polar angles) are sampled at different times in the cycle allows you to determine the particular degree of eccentricity (or polar angle) that most strongly activates each voxel. For example, imagine this were the timecourse of a voxel in an eccentricity scan:		The traveling wave of response generated by the ring and wedge stimuli allow you to determine the the most effective eccentricity (or polar angle) for driving a given voxel using a technique known as phase encoding. This use of this technique depends on the ring (or wedge) stimulus sweeping across each location in the visual field once in each cycle of the stimulus. Therefore, voxels that are part of a visual field map should illustrate six peaks in their response over the course of a run containing six cycles. The fact that different eccentricities (or polar angles) are sampled at different times in the cycle allows you to determine the particular degree of eccentricity (or polar angle) that most strongly activates each voxel. For example, imagine this were the timecourse of a voxel in an eccentricity scan:

	[[File:foveal_timecourse.jpg\|600px\|thumb\|center\| Figure ~~borrowed from~~ [[Mai]]]]		[[File:foveal_timecourse.jpg\|600px\|thumb\|center\| Figure courtesy of [[Mai]]]]

	If the cycle begins with with rings that occupy space in the center of the visual field, the peaks in the response of voxels with a foveal preference should be earlier in time than peaks in the response of voxels with peripheral preference. Shown below is the phase-shifted timecourse of a voxel with a peripheral preference.		If the cycle begins with with rings that occupy space in the center of the visual field, the peaks in the response of voxels with a foveal preference should be earlier in time than peaks in the response of voxels with peripheral preference. Shown below is the phase-shifted timecourse of a voxel with a peripheral preference.

	[[File:peripheral_timecourse.jpg\|600px\|thumb\|center\| Figure ~~borrowed from~~ [[Mai]]]]		[[File:peripheral_timecourse.jpg\|600px\|thumb\|center\| Figure courtesy of [[Mai]]]]

	==== Finding the Phase ====		==== Finding the Phase ====
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	Decomposing each voxel's timecourse into discrete frequency bands using a Fourier transform allows you to estimate the proportion of variance explained by each signal modulation at each frequency. If a voxel is retinotopic, the frequency with the most energy should be equal to the number of cycles in the experiment. Shown below is the energy at each frequency extracted with the Fourier transform:		Decomposing each voxel's timecourse into discrete frequency bands using a Fourier transform allows you to estimate the proportion of variance explained by each signal modulation at each frequency. If a voxel is retinotopic, the frequency with the most energy should be equal to the number of cycles in the experiment. Shown below is the energy at each frequency extracted with the Fourier transform:

	[[File:Fourier.jpg\|center\|400px\|thumb\|center\| Figure ~~from~~ [[Mai]]]]]]		[[File:Fourier.jpg\|center\|400px\|thumb\|center\| Figure courtesy of [[Mai]]]]]]

	As expected, the peak in this voxel's power spectrum is at 6 cycles, which is equal to the number of cycles in the experiment. This suggests that the voxel is retinotopic but is not informative about the particular eccentritiy (or polar angle) that optimally activates it. To determine the time lag that best explains the data, the 6-cycle sine wave is shifted and the phase shift that generates the best fit to the data is used to estimate the eccentricity (or polar angle) preferred by the voxel. If a voxel prefers foveal stimuli, for example, a small time shift should produce the best fit because foveal rings are presented at the beginning of the cycles in the eccentricity mapping experiment. Then, the same procedure is performed at every voxel, and a similar analysis can be applied to polar angle mapping experiments. To generate a map of polar angle and eccentricity biases, the range of phase shifts is color coded and mapped onto each voxel.		As expected, the peak in this voxel's power spectrum is at 6 cycles, which is equal to the number of cycles in the experiment. This suggests that the voxel is retinotopic but is not informative about the particular eccentritiy (or polar angle) that optimally activates it. To determine the time lag that best explains the data, the 6-cycle sine wave is shifted and the phase shift that generates the best fit to the data is used to estimate the eccentricity (or polar angle) preferred by the voxel. If a voxel prefers foveal stimuli, for example, a small time shift should produce the best fit because foveal rings are presented at the beginning of the cycles in the eccentricity mapping experiment. Then, the same procedure is performed at every voxel, and a similar analysis can be applied to polar angle mapping experiments. To generate a map of polar angle and eccentricity biases, the range of phase shifts is color coded and mapped onto each voxel.