2009 Bragi Sveinsson - Revision history

imported>Winawer: Unprotected "2009 Bragi Sveinsson"

2010-03-10T01:47:52Z

Unprotected "2009 Bragi Sveinsson"

← Older revision	Revision as of 01:47, 10 March 2010
(No difference)

imported>Winawer: Protected "2009 Bragi Sveinsson" ([edit=sysop] (indefinite) [move=sysop] (indefinite))

2010-03-10T01:42:59Z

Protected "2009 Bragi Sveinsson" ([edit=sysop] (indefinite) [move=sysop] (indefinite))

← Older revision	Revision as of 01:42, 10 March 2010
(No difference)

imported>Psych 204: /* Background */

2009-12-12T00:29:29Z

Background

← Older revision		Revision as of 00:29, 12 December 2009
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	= Background =		= Background =
	Those familiar with the theoretical background of magnetic field distortions may skip this section. The material was mostly gathered from Functional Magnetic Resonance Imaging by S.A. Huettel, A.W. Song and G. McCarthy and from the manuals included with the SPM ~~fieldmap~~ toolbox.		Those familiar with the theoretical background of magnetic field distortions may skip this section. The material was mostly gathered from Functional Magnetic Resonance Imaging by S.A. Huettel, A.W. Song and G. McCarthy and from the manuals included with the SPM FieldMap toolbox.
	<br>		<br>
	== Causes of field disturbances ==		== Causes of field disturbances ==

imported>Psych 204: /* References - Resources and related work */

2009-12-12T00:28:47Z

References - Resources and related work

← Older revision		Revision as of 00:28, 12 December 2009
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	[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WNP-47HPPVD-D&_user=145269&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_searchStrId=1132492567&_rerunOrigin=scholar.google&_acct=C000012078&_version=1&_urlVersion=0&_userid=145269&md5=74a7165d8a40dd5b7ad699220c92273a Cusack R, Brett M, and Osswald K. 2003. An Evaluation of the Use of Magnetic Field Maps to Undistort Echo-Planar Images. NeuroImage 18: 127–142]</li>		[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WNP-47HPPVD-D&_user=145269&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_searchStrId=1132492567&_rerunOrigin=scholar.google&_acct=C000012078&_version=1&_urlVersion=0&_userid=145269&md5=74a7165d8a40dd5b7ad699220c92273a Cusack R, Brett M, and Osswald K. 2003. An Evaluation of the Use of Magnetic Field Maps to Undistort Echo-Planar Images. NeuroImage 18: 127–142]</li>
	<li>		<li>
	[http://kamares.ucsd.edu/~sereno/courses/276/readings/invdistortion2.pdf Zeng H and Constable ~~R T~~. 2002. Image Distortion Correction in EPI: Comparison of Field Mapping With Point Spread Function Mapping. Magnetic Resonance in Medicine 48: 137–146]</li>		[http://kamares.ucsd.edu/~sereno/courses/276/readings/invdistortion2.pdf Zeng H and Constable RT. 2002. Image Distortion Correction in EPI: Comparison of Field Mapping With Point Spread Function Mapping. Magnetic Resonance in Medicine 48: 137–146]</li>
	<li>		<li>
	[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WNP-46HDMPV-M&_user=145269&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_searchStrId=1132517481&_rerunOrigin=scholar.google&_acct=C000012078&_version=1&_urlVersion=0&_userid=145269&md5=594b8f95a5a78c31072cc2c03bedc52f Cusack R and Papadakis N. 2002. New Robust 3-D Phase Unwrapping Algorithms: Application to Magnetic Field Mapping and Undistorting Echoplanar Images. Neuroimage 16: 754-764]</li>		[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WNP-46HDMPV-M&_user=145269&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_searchStrId=1132517481&_rerunOrigin=scholar.google&_acct=C000012078&_version=1&_urlVersion=0&_userid=145269&md5=594b8f95a5a78c31072cc2c03bedc52f Cusack R and Papadakis N. 2002. New Robust 3-D Phase Unwrapping Algorithms: Application to Magnetic Field Mapping and Undistorting Echoplanar Images. Neuroimage 16: 754-764]</li>
	<li>		<li>
	[http://www.sciencemag.org/cgi/content/abstract/sci;254/5028/43 Stehling ~~M K~~, Turner R and Mansfield P. 1991. Echo-planar imaging: magnetic resonance imaging in a fraction of a second. Science 4: 43-50]</li>		[http://www.sciencemag.org/cgi/content/abstract/sci;254/5028/43 Stehling MK, Turner R and Mansfield P. 1991. Echo-planar imaging: magnetic resonance imaging in a fraction of a second. Science 4: 43-50]</li>
	<li>		<li>
	[http://sirl.stanford.edu/~bob/pdf/MRI_methods/Morgan_EPI_RGPM_unwarping_JMRI04.pdf Morgan ~~P S~~, Bowtell ~~R W~~, McIntyre ~~D J O~~, and Worthington, ~~B S~~. 2004. Correction of Spatial Distortion in EPI Due to Inhomogeneous Static Magnetic Fields Using the Reversed Gradient Method. Journal of Magnetic Resonance Imaging 19: 499–507]</li>		[http://sirl.stanford.edu/~bob/pdf/MRI_methods/Morgan_EPI_RGPM_unwarping_JMRI04.pdf Morgan PS, Bowtell RW, McIntyre DJO, and Worthington, BS. 2004. Correction of Spatial Distortion in EPI Due to Inhomogeneous Static Magnetic Fields Using the Reversed Gradient Method. Journal of Magnetic Resonance Imaging 19: 499–507]</li>
	</ol>		</ol>

imported>Psych 204: /* References - Resources and related work */

2009-12-12T00:27:52Z

References - Resources and related work

← Older revision		Revision as of 00:27, 12 December 2009
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	[http://www.fmrib.ox.ac.uk/analysis/techrep/ Jenkinson M. 2003. Fast, automated, N-dimensional phase-unwrapping algorithm. MRM 49:193-197] </li>		[http://www.fmrib.ox.ac.uk/analysis/techrep/ Jenkinson M. 2003. Fast, automated, N-dimensional phase-unwrapping algorithm. MRM 49:193-197] </li>
	<li>		<li>
	[http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.27.8289&rep=rep1&type=pdf S~~. Balac~~ and G~~. Caloz~~ , Mathematical modeling and numerical simulation of magnetic susceptibility artifacts in magnetic resonance imaging. Comput. Methods Biomech. Biomed. Eng. 3 (2000), pp. 335–349.] </li>		[http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.27.8289&rep=rep1&type=pdf Balac S and Caloz G, Mathematical modeling and numerical simulation of magnetic susceptibility artifacts in magnetic resonance imaging. Comput. Methods Biomech. Biomed. Eng. 3 (2000), pp. 335–349.] </li>
	<li>		<li>
	[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WNP-47HPPVD-D&_user=145269&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_searchStrId=1132492567&_rerunOrigin=scholar.google&_acct=C000012078&_version=1&_urlVersion=0&_userid=145269&md5=74a7165d8a40dd5b7ad699220c92273a R~~. Cusack~~, M~~. Brett~~, and K~~. Osswald~~. 2003. An Evaluation of the Use of Magnetic Field Maps to Undistort Echo-Planar Images. NeuroImage 18: 127–142]</li>		[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WNP-47HPPVD-D&_user=145269&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_searchStrId=1132492567&_rerunOrigin=scholar.google&_acct=C000012078&_version=1&_urlVersion=0&_userid=145269&md5=74a7165d8a40dd5b7ad699220c92273a Cusack R, Brett M, and Osswald K. 2003. An Evaluation of the Use of Magnetic Field Maps to Undistort Echo-Planar Images. NeuroImage 18: 127–142]</li>
	<li>		<li>
	[http://kamares.ucsd.edu/~sereno/courses/276/readings/invdistortion2.pdf H~~. Zeng~~ and R. T~~.Constable~~. 2002. Image Distortion Correction in EPI: Comparison of Field Mapping With Point Spread Function Mapping. Magnetic Resonance in Medicine 48: 137–146]</li>		[http://kamares.ucsd.edu/~sereno/courses/276/readings/invdistortion2.pdf Zeng H and Constable R T. 2002. Image Distortion Correction in EPI: Comparison of Field Mapping With Point Spread Function Mapping. Magnetic Resonance in Medicine 48: 137–146]</li>
	<li>		<li>
	[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WNP-46HDMPV-M&_user=145269&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_searchStrId=1132517481&_rerunOrigin=scholar.google&_acct=C000012078&_version=1&_urlVersion=0&_userid=145269&md5=594b8f95a5a78c31072cc2c03bedc52f R~~. Cusack~~ and N~~. Papadakis~~. 2002. New Robust 3-D Phase Unwrapping Algorithms: Application to Magnetic Field Mapping and Undistorting Echoplanar Images. Neuroimage 16: 754-764]</li>		[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WNP-46HDMPV-M&_user=145269&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_searchStrId=1132517481&_rerunOrigin=scholar.google&_acct=C000012078&_version=1&_urlVersion=0&_userid=145269&md5=594b8f95a5a78c31072cc2c03bedc52f Cusack R and Papadakis N. 2002. New Robust 3-D Phase Unwrapping Algorithms: Application to Magnetic Field Mapping and Undistorting Echoplanar Images. Neuroimage 16: 754-764]</li>
	<li>		<li>
	[http://www.sciencemag.org/cgi/content/abstract/sci;254/5028/43 M.K~~. Stehling~~, R~~. Turner~~ and P~~. Mansfield~~. 1991. Echo-planar imaging: magnetic resonance imaging in a fraction of a second. Science 4: 43-50]</li>		[http://www.sciencemag.org/cgi/content/abstract/sci;254/5028/43 Stehling M K, Turner R and Mansfield P. 1991. Echo-planar imaging: magnetic resonance imaging in a fraction of a second. Science 4: 43-50]</li>
	<li>		<li>
	[http://sirl.stanford.edu/~bob/pdf/MRI_methods/Morgan_EPI_RGPM_unwarping_JMRI04.pdf P.S~~. Morgan~~, R. W~~. Bowtell~~, D.J.O~~. McIntyre~~, and ~~Brian~~ S~~. Worthington~~. 2004. Correction of Spatial Distortion in EPI Due to Inhomogeneous Static Magnetic Fields Using the Reversed Gradient Method. Journal of Magnetic Resonance Imaging 19: 499–507]</li>		[http://sirl.stanford.edu/~bob/pdf/MRI_methods/Morgan_EPI_RGPM_unwarping_JMRI04.pdf Morgan P S, Bowtell R W, McIntyre D J O, and Worthington, B S. 2004. Correction of Spatial Distortion in EPI Due to Inhomogeneous Static Magnetic Fields Using the Reversed Gradient Method. Journal of Magnetic Resonance Imaging 19: 499–507]</li>
	</ol>		</ol>

imported>Psych 204: /* Some technical comments about the code */

2009-12-12T00:18:55Z

Some technical comments about the code

← Older revision		Revision as of 00:18, 12 December 2009
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	<br>		<br>
	The original FieldMap toolbox for SPM had some additional functions that were not included in my application, most importantly the option to create the field map out of the two images. This was omitted mostly because I didn't have data from VISTA lab to test this on, but also for time constraint reasons. Also, in the original toolbox you could choose your method of phase unwrapping as described in the theoretical section of this site. In this project I only used the method of dividing the brain into distinct regions as described in the same section.		The original FieldMap toolbox for SPM had some additional functions that were not included in my application, most importantly the option to create the field map out of the two images. This was omitted mostly because I didn't have data from VISTA lab to test this on, but also for time constraint reasons. Also, in the original toolbox you could choose your method of phase unwrapping as described in the theoretical section of this site. In this project I only used the method of dividing the brain into distinct regions as described in the same section.
			<br>
			Every effort was made to make sure that the software would work on any computer, however I have only tested it on my own computer.

	= Conclusions =		= Conclusions =

imported>Psych 204: /* Some technical comments about the code */

2009-12-12T00:15:23Z

Some technical comments about the code

← Older revision		Revision as of 00:15, 12 December 2009
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	<br>		<br>
	The code can be quite slow to run but that is mostly due to the error estimates that I added. The unwarping algorithms are quite fast. The brain image described above took a much longer time to compute than the phantom images - about 9 minutes compared to about 30 seconds for the phantoms.		The code can be quite slow to run but that is mostly due to the error estimates that I added. The unwarping algorithms are quite fast. The brain image described above took a much longer time to compute than the phantom images - about 9 minutes compared to about 30 seconds for the phantoms.
			<br>
			The original FieldMap toolbox for SPM had some additional functions that were not included in my application, most importantly the option to create the field map out of the two images. This was omitted mostly because I didn't have data from VISTA lab to test this on, but also for time constraint reasons. Also, in the original toolbox you could choose your method of phase unwrapping as described in the theoretical section of this site. In this project I only used the method of dividing the brain into distinct regions as described in the same section.

	= Conclusions =		= Conclusions =

imported>Psych 204: /* How to use the software */

2009-12-11T23:57:11Z

How to use the software

← Older revision		Revision as of 23:57, 11 December 2009
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	The user can choose to apply Jacobian modulation in the unwarping. This increases the intensity in the unwarped image of voxels which are stretched and decreases the intensity of compressed voxels.		The user can choose to apply Jacobian modulation in the unwarping. This increases the intensity in the unwarped image of voxels which are stretched and decreases the intensity of compressed voxels.
	<br>		<br>
	Finally, one can enter the readout time of the EPI measurement. This is used to convert the field map, which is in units of Hz (i.e. it is in the frequency domain) to the spatial domain by simple multiplication. This is defaulted to 32 ms.		Finally, one can enter the readout time of the EPI measurement. This is used to convert the field map, which is in units of Hz (i.e. it is in the frequency domain) into a voxel displacement map (i.e. to the spatial domain) by simple multiplication. This is defaulted to 32 ms.
	<br>		<br>

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	This GUI is an altered version of the mrViewer GUI and allows the user to choose any slice along any of the three main axis. The user can also switch between any of the loaded images and the unwarped image, as well as an image showing the difference between the unwarped image and the structural image, to make the estimation of the performance of the unwarping algorithms easier.		This GUI is an altered version of the mrViewer GUI and allows the user to choose any slice along any of the three main axis. The user can also switch between any of the loaded images and the unwarped image, as well as an image showing the difference between the unwarped image and the structural image, to make the estimation of the performance of the unwarping algorithms easier.

	Once the correction button in the main GUI is clicked, the unwarped image is automatically saved into the same directory as the distorted image, and two graphs appear, showing the difference between the distorted image and the structural image on the one hand, and between the unwarped image and the structural image on the other hand. The user can choose between simple mean square error or the mutual information between the images as the error metric.		Once the correction button in the main GUI is clicked, the unwarped image is automatically saved into the same directory as the distorted image, and two graphs appear, showing the difference between the distorted image and the structural image on the one hand, and between the unwarped image and the structural image on the other hand (the voxel displacement map described above is also saved into the same directory). The user can choose between simple mean square error or the mutual information between the images as the error metric.
	<br>		<br>
	<br>		<br>

imported>Psych 204: /* Results */

2009-12-11T23:54:24Z

Results

← Older revision		Revision as of 23:54, 11 December 2009
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	<br><br>		<br><br>

	=== Some technical comments about the code ===		== Some technical comments about the code ==
	The whole set of functions required to run the mrFieldMap software is about 5.7 MB in size (in unzipped format), of which about 3 MB are SPM functions that were too difficult to untangle from the FieldMap code. The software is provided at the bottom of this page. The test images for trying out the code are about 15 MB and are provided in a separate file.		The whole set of functions required to run the mrFieldMap software is about 5.7 MB in size (in unzipped format), of which about 3 MB are SPM functions that were too difficult to untangle from the FieldMap code. The software is provided at the bottom of this page. The test images for trying out the code are about 15 MB and are provided in a separate file.
	<br>		<br>

imported>Psych 204: /* Results */

2009-12-11T23:53:49Z

Results

← Older revision		Revision as of 23:53, 11 December 2009
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	The error graphs show that the difference between the images spikes at slice 32 which is also what one would expect, since at that slice the frame appears and its lines mostly don't overlap with the structural image.		The error graphs show that the difference between the images spikes at slice 32 which is also what one would expect, since at that slice the frame appears and its lines mostly don't overlap with the structural image.
	<br><br>		<br><br>

			=== Some technical comments about the code ===
			The whole set of functions required to run the mrFieldMap software is about 5.7 MB in size (in unzipped format), of which about 3 MB are SPM functions that were too difficult to untangle from the FieldMap code. The software is provided at the bottom of this page. The test images for trying out the code are about 15 MB and are provided in a separate file.
			<br>
			The code can be quite slow to run but that is mostly due to the error estimates that I added. The unwarping algorithms are quite fast. The brain image described above took a much longer time to compute than the phantom images - about 9 minutes compared to about 30 seconds for the phantoms.

	= Conclusions =		= Conclusions =