Unfolding - Revision history

SRP Wiki: /* Creating Segmentation Files */

2014-10-13T18:39:15Z

Creating Segmentation Files

← Older revision		Revision as of 18:39, 13 October 2014
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	::5. Another window with the image scan of the subject will appear. Begin drawing a rectangular box around the hippocampal region, covering both the left and right sides.		::5. Another window with the image scan of the subject will appear. Begin drawing a rectangular box around the hippocampal region, covering both the left and right sides.
	:::*Note: It is important to draw the rectangle with enough vertical space above and below the region to account for positional differences of the hippocampal region across different slides.		:::*Note: It is important to draw the rectangle with enough vertical space above and below the region to account for positional differences of the hippocampal region across different slides.
	::6. Once the box has been drawn, double click inside the drawn region and Matlab will begin ~~creating~~ the file.		::6. Once the box has been drawn, double click inside the drawn region and Matlab will begin initializing the file.

	===Getting Started: The Initial Segmentation Checklist===		===Getting Started: The Initial Segmentation Checklist===

SRP Wiki: /* Segmentation */

2014-10-13T18:38:11Z

Segmentation

← Older revision		Revision as of 18:38, 13 October 2014
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	==Segmentation==		==Segmentation==
	~~Creating Segmentation files~~
	===Overview===		===Overview===
	The goal of segmentation is to create a strip of gray matter in the hippocampus by locating the boundaries of the hippocampus in the brain. Using FMRI technology, the brain is sliced anteriorly to posteriorly to obtain slices of all parts of the hippocampus, creating a 2D version of the 3D hippocampus that can be mapped and analyzed. After opening [[VirtualBox]], we run a computer program, [[MrGray Segmentation software for Windows]], where we can view and find all the slices of the brain that show a portion of the hippocampus. On these slices,the hippocampal gray matter is surrounded by white matter and cerebral spinal fluid (CSF). We must mark the surrounding white matter and CSF respectively to obtain our strip of gray matter in between. The CSF material is the strip of atrophy on the interior of the gray matter, which begins at the hippocampal fissure, follows down to the collateral sulcus, and finishes after the second sulcus. The white matter is the material on the exterior portion of the gray matter. It is important to note that the shape of the hippocampal head changes from anterior to posterior in the brain. On the anterior slices, the hippocampal head has a long, oval shape. In the posterior slices, the hippocampal head has a round, almond shape. On the anterior slices, the CSF matter comes up to meet the white matter at the hippocampus head and also continues through the second sulcus through the gray matter to close off our strip. In the posterior slices, the CSF still continues through the second sulcus to the gray matter to close off the strip, but the white matter comes down to the CSF at the hippocampal fissure on the hippocampal head.		The goal of segmentation is to create a strip of gray matter in the hippocampus by locating the boundaries of the hippocampus in the brain. Using FMRI technology, the brain is sliced anteriorly to posteriorly to obtain slices of all parts of the hippocampus, creating a 2D version of the 3D hippocampus that can be mapped and analyzed. After opening [[VirtualBox]], we run a computer program, [[MrGray Segmentation software for Windows]], where we can view and find all the slices of the brain that show a portion of the hippocampus. On these slices,the hippocampal gray matter is surrounded by white matter and cerebral spinal fluid (CSF). We must mark the surrounding white matter and CSF respectively to obtain our strip of gray matter in between. The CSF material is the strip of atrophy on the interior of the gray matter, which begins at the hippocampal fissure, follows down to the collateral sulcus, and finishes after the second sulcus. The white matter is the material on the exterior portion of the gray matter. It is important to note that the shape of the hippocampal head changes from anterior to posterior in the brain. On the anterior slices, the hippocampal head has a long, oval shape. In the posterior slices, the hippocampal head has a round, almond shape. On the anterior slices, the CSF matter comes up to meet the white matter at the hippocampus head and also continues through the second sulcus through the gray matter to close off our strip. In the posterior slices, the CSF still continues through the second sulcus to the gray matter to close off the strip, but the white matter comes down to the CSF at the hippocampal fissure on the hippocampal head.

SRP Wiki: /* Segmentation */

2014-10-13T18:38:00Z

Segmentation

@@ Line 12: / Line 12: @@
 Creating Segmentation files
 ===Overview===
-The goal of [[segmentation]] is to create a strip of gray matter in the hippocampus by locating the boundaries of the hippocampus in the brain. Using FMRI technology, the brain is sliced anteriorly to posteriorly to obtain slices of all parts of the hippocampus, creating a 2D version of the 3D hippocampus that can be mapped and analyzed. After opening [[VirtualBox]], we run a computer program, [[MrGray Segmentation software for Windows]], where we can view and find all the slices of the brain that show a portion of the hippocampus. On these slices,the hippocampal gray matter is surrounded by white matter and cerebral spinal fluid (CSF). We must mark the surrounding white matter and CSF respectively to obtain our strip of gray matter in between. The CSF material is the strip of atrophy on the interior of the gray matter, which begins at the hippocampal fissure, follows down to the collateral sulcus, and finishes after the second sulcus. The white matter is the material on the exterior portion of the gray matter. It is important to note that the shape of the hippocampal head changes from anterior to posterior in the brain. On the anterior slices, the hippocampal head has a long, oval shape. In the posterior slices, the hippocampal head has a round, almond shape. On the anterior slices, the CSF matter comes up to meet the white matter at the hippocampus head and also continues through the second sulcus through the gray matter to close off our strip. In the posterior slices, the CSF still continues through the second sulcus to the gray matter to close off the strip, but the white matter comes down to the CSF at the hippocampal fissure on the hippocampal head.
+The goal of segmentation is to create a strip of gray matter in the hippocampus by locating the boundaries of the hippocampus in the brain. Using FMRI technology, the brain is sliced anteriorly to posteriorly to obtain slices of all parts of the hippocampus, creating a 2D version of the 3D hippocampus that can be mapped and analyzed. After opening [[VirtualBox]], we run a computer program, [[MrGray Segmentation software for Windows]], where we can view and find all the slices of the brain that show a portion of the hippocampus. On these slices,the hippocampal gray matter is surrounded by white matter and cerebral spinal fluid (CSF). We must mark the surrounding white matter and CSF respectively to obtain our strip of gray matter in between. The CSF material is the strip of atrophy on the interior of the gray matter, which begins at the hippocampal fissure, follows down to the collateral sulcus, and finishes after the second sulcus. The white matter is the material on the exterior portion of the gray matter. It is important to note that the shape of the hippocampal head changes from anterior to posterior in the brain. On the anterior slices, the hippocampal head has a long, oval shape. In the posterior slices, the hippocampal head has a round, almond shape. On the anterior slices, the CSF matter comes up to meet the white matter at the hippocampus head and also continues through the second sulcus through the gray matter to close off our strip. In the posterior slices, the CSF still continues through the second sulcus to the gray matter to close off the strip, but the white matter comes down to the CSF at the hippocampal fissure on the hippocampal head.
 ===Getting Started: The Initial Segmentation Checklist===

SRP Wiki: /* Segmentation */

2014-09-30T20:10:19Z

Segmentation

← Older revision		Revision as of 20:10, 30 September 2014
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	==Segmentation==		==Segmentation==
	Creating /* Segmentation */ files		Creating Segmentation files
	===Overview===		===Overview===
	The goal of [[segmentation]] is to create a strip of gray matter in the hippocampus by locating the boundaries of the hippocampus in the brain. Using FMRI technology, the brain is sliced anteriorly to posteriorly to obtain slices of all parts of the hippocampus, creating a 2D version of the 3D hippocampus that can be mapped and analyzed. After opening [[VirtualBox]], we run a computer program, [[MrGray Segmentation software for Windows]], where we can view and find all the slices of the brain that show a portion of the hippocampus. On these slices,the hippocampal gray matter is surrounded by white matter and cerebral spinal fluid (CSF). We must mark the surrounding white matter and CSF respectively to obtain our strip of gray matter in between. The CSF material is the strip of atrophy on the interior of the gray matter, which begins at the hippocampal fissure, follows down to the collateral sulcus, and finishes after the second sulcus. The white matter is the material on the exterior portion of the gray matter. It is important to note that the shape of the hippocampal head changes from anterior to posterior in the brain. On the anterior slices, the hippocampal head has a long, oval shape. In the posterior slices, the hippocampal head has a round, almond shape. On the anterior slices, the CSF matter comes up to meet the white matter at the hippocampus head and also continues through the second sulcus through the gray matter to close off our strip. In the posterior slices, the CSF still continues through the second sulcus to the gray matter to close off the strip, but the white matter comes down to the CSF at the hippocampal fissure on the hippocampal head.		The goal of [[segmentation]] is to create a strip of gray matter in the hippocampus by locating the boundaries of the hippocampus in the brain. Using FMRI technology, the brain is sliced anteriorly to posteriorly to obtain slices of all parts of the hippocampus, creating a 2D version of the 3D hippocampus that can be mapped and analyzed. After opening [[VirtualBox]], we run a computer program, [[MrGray Segmentation software for Windows]], where we can view and find all the slices of the brain that show a portion of the hippocampus. On these slices,the hippocampal gray matter is surrounded by white matter and cerebral spinal fluid (CSF). We must mark the surrounding white matter and CSF respectively to obtain our strip of gray matter in between. The CSF material is the strip of atrophy on the interior of the gray matter, which begins at the hippocampal fissure, follows down to the collateral sulcus, and finishes after the second sulcus. The white matter is the material on the exterior portion of the gray matter. It is important to note that the shape of the hippocampal head changes from anterior to posterior in the brain. On the anterior slices, the hippocampal head has a long, oval shape. In the posterior slices, the hippocampal head has a round, almond shape. On the anterior slices, the CSF matter comes up to meet the white matter at the hippocampus head and also continues through the second sulcus through the gray matter to close off our strip. In the posterior slices, the CSF still continues through the second sulcus to the gray matter to close off the strip, but the white matter comes down to the CSF at the hippocampal fissure on the hippocampal head.

SRP Wiki: /* Segmentation */

2014-09-30T20:09:56Z

Segmentation

← Older revision		Revision as of 20:09, 30 September 2014
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	==Segmentation==		==Segmentation==
	Creating Segmentation files		Creating /* Segmentation */ files
	===Overview===		===Overview===
	The goal of [[segmentation]] is to create a strip of gray matter in the hippocampus by locating the boundaries of the hippocampus in the brain. Using FMRI technology, the brain is sliced anteriorly to posteriorly to obtain slices of all parts of the hippocampus, creating a 2D version of the 3D hippocampus that can be mapped and analyzed. After opening [[VirtualBox]], we run a computer program, [[MrGray Segmentation software for Windows]], where we can view and find all the slices of the brain that show a portion of the hippocampus. On these slices,the hippocampal gray matter is surrounded by white matter and cerebral spinal fluid (CSF). We must mark the surrounding white matter and CSF respectively to obtain our strip of gray matter in between. The CSF material is the strip of atrophy on the interior of the gray matter, which begins at the hippocampal fissure, follows down to the collateral sulcus, and finishes after the second sulcus. The white matter is the material on the exterior portion of the gray matter. It is important to note that the shape of the hippocampal head changes from anterior to posterior in the brain. On the anterior slices, the hippocampal head has a long, oval shape. In the posterior slices, the hippocampal head has a round, almond shape. On the anterior slices, the CSF matter comes up to meet the white matter at the hippocampus head and also continues through the second sulcus through the gray matter to close off our strip. In the posterior slices, the CSF still continues through the second sulcus to the gray matter to close off the strip, but the white matter comes down to the CSF at the hippocampal fissure on the hippocampal head.		The goal of [[segmentation]] is to create a strip of gray matter in the hippocampus by locating the boundaries of the hippocampus in the brain. Using FMRI technology, the brain is sliced anteriorly to posteriorly to obtain slices of all parts of the hippocampus, creating a 2D version of the 3D hippocampus that can be mapped and analyzed. After opening [[VirtualBox]], we run a computer program, [[MrGray Segmentation software for Windows]], where we can view and find all the slices of the brain that show a portion of the hippocampus. On these slices,the hippocampal gray matter is surrounded by white matter and cerebral spinal fluid (CSF). We must mark the surrounding white matter and CSF respectively to obtain our strip of gray matter in between. The CSF material is the strip of atrophy on the interior of the gray matter, which begins at the hippocampal fissure, follows down to the collateral sulcus, and finishes after the second sulcus. The white matter is the material on the exterior portion of the gray matter. It is important to note that the shape of the hippocampal head changes from anterior to posterior in the brain. On the anterior slices, the hippocampal head has a long, oval shape. In the posterior slices, the hippocampal head has a round, almond shape. On the anterior slices, the CSF matter comes up to meet the white matter at the hippocampus head and also continues through the second sulcus through the gray matter to close off our strip. In the posterior slices, the CSF still continues through the second sulcus to the gray matter to close off the strip, but the white matter comes down to the CSF at the hippocampal fissure on the hippocampal head.

SRP Wiki: /* Segmentation */

2014-09-30T20:09:26Z

Segmentation

← Older revision		Revision as of 20:09, 30 September 2014
Line 10:		Line 10:

	==Segmentation==		==Segmentation==
			Creating Segmentation files
	===Overview===		===Overview===
	The goal of [[segmentation]] is to create a strip of gray matter in the hippocampus by locating the boundaries of the hippocampus in the brain. Using FMRI technology, the brain is sliced anteriorly to posteriorly to obtain slices of all parts of the hippocampus, creating a 2D version of the 3D hippocampus that can be mapped and analyzed. After opening [[VirtualBox]], we run a computer program, [[MrGray Segmentation software for Windows]], where we can view and find all the slices of the brain that show a portion of the hippocampus. On these slices,the hippocampal gray matter is surrounded by white matter and cerebral spinal fluid (CSF). We must mark the surrounding white matter and CSF respectively to obtain our strip of gray matter in between. The CSF material is the strip of atrophy on the interior of the gray matter, which begins at the hippocampal fissure, follows down to the collateral sulcus, and finishes after the second sulcus. The white matter is the material on the exterior portion of the gray matter. It is important to note that the shape of the hippocampal head changes from anterior to posterior in the brain. On the anterior slices, the hippocampal head has a long, oval shape. In the posterior slices, the hippocampal head has a round, almond shape. On the anterior slices, the CSF matter comes up to meet the white matter at the hippocampus head and also continues through the second sulcus through the gray matter to close off our strip. In the posterior slices, the CSF still continues through the second sulcus to the gray matter to close off the strip, but the white matter comes down to the CSF at the hippocampal fissure on the hippocampal head.		The goal of [[segmentation]] is to create a strip of gray matter in the hippocampus by locating the boundaries of the hippocampus in the brain. Using FMRI technology, the brain is sliced anteriorly to posteriorly to obtain slices of all parts of the hippocampus, creating a 2D version of the 3D hippocampus that can be mapped and analyzed. After opening [[VirtualBox]], we run a computer program, [[MrGray Segmentation software for Windows]], where we can view and find all the slices of the brain that show a portion of the hippocampus. On these slices,the hippocampal gray matter is surrounded by white matter and cerebral spinal fluid (CSF). We must mark the surrounding white matter and CSF respectively to obtain our strip of gray matter in between. The CSF material is the strip of atrophy on the interior of the gray matter, which begins at the hippocampal fissure, follows down to the collateral sulcus, and finishes after the second sulcus. The white matter is the material on the exterior portion of the gray matter. It is important to note that the shape of the hippocampal head changes from anterior to posterior in the brain. On the anterior slices, the hippocampal head has a long, oval shape. In the posterior slices, the hippocampal head has a round, almond shape. On the anterior slices, the CSF matter comes up to meet the white matter at the hippocampus head and also continues through the second sulcus through the gray matter to close off our strip. In the posterior slices, the CSF still continues through the second sulcus to the gray matter to close off the strip, but the white matter comes down to the CSF at the hippocampal fissure on the hippocampal head.
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	:[[File:unfolding-Seg_P1.png]]		:[[File:unfolding-Seg_P1.png]]
	:[[File:unfolding-Seg_P2.png]]		:[[File:unfolding-Seg_P2.png]]


	==Interpolation==		==Interpolation==

SRP Wiki: /* Interpolation */

2014-09-12T17:19:16Z

Interpolation

← Older revision		Revision as of 17:19, 12 September 2014
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	==Interpolation==		==Interpolation==
	Explain [[~~interpolation~~]] here.		Explain [[Interpolation]] here.

	To load an existing project, when you're in MrGray, you'll click on Load project and you can select any .mrp file.		To load an existing project, when you're in MrGray, you'll click on Load project and you can select any .mrp file.
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	# The window that pops up will ask you to select a class file. This will be AD_1XXXX_interpright or interpleft that already exists in the directory. Select the side for which you created and hit enter.		# The window that pops up will ask you to select a class file. This will be AD_1XXXX_interpright or interpleft that already exists in the directory. Select the side for which you created and hit enter.
	# Check to make sure the masks align correctly.		# Check to make sure the masks align correctly.


	==Demarcations==		==Demarcations==

Ccn admin: /* Directory Outline: How to Open FSLView Through Terminal */

2014-01-28T01:55:16Z

Directory Outline: How to Open FSLView Through Terminal

← Older revision		Revision as of 01:55, 28 January 2014
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	:Below is an outline for the directory path. In order to open files for segmentation, interpolation, and demarcation in the unfolding process, you must be able to navigate the Terminal.		:Below is an outline for the directory path. In order to open files for segmentation, interpolation, and demarcation in the unfolding process, you must be able to navigate the Terminal.

	::[[File:unfolding-~~directory_route~~.png]]		::[[File:unfolding-Dir_Route.png]]

	The best way to open FSLview in order to do demarcations is through the FSLview path in ''Terminal''. Below are the following steps to open a file for demarcations.		The best way to open FSLview in order to do demarcations is through the FSLview path in ''Terminal''. Below are the following steps to open a file for demarcations.
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	#cp nii/hhr_struct_6.nii.gz ../analysis/preprocessing/hhr_struct_6.nii.gz		#cp nii/hhr_struct_6.nii.gz ../analysis/preprocessing/hhr_struct_6.nii.gz
	##fslview hhr_struct_6.nii.gz (check if this step is fslview analysis/preprocessing/hhr_struct_6.nii.gz)		##fslview hhr_struct_6.nii.gz (check if this step is fslview analysis/preprocessing/hhr_struct_6.nii.gz)


	==External Links==		==External Links==

Ccn admin: /* Individual Boundaries */

2014-01-28T01:54:39Z

Individual Boundaries

← Older revision		Revision as of 01:54, 28 January 2014
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	:::* Bump shown in red, boundary between Sub and CA1 shown in blue		:::* Bump shown in red, boundary between Sub and CA1 shown in blue
	:::* Sub is medial to the boundary, CA1 is lateral		:::* Sub is medial to the boundary, CA1 is lateral
	::: [[File:unfolding-~~SubCA1_anterior~~.jpg]]		::: [[File:unfolding-SubCA1_Anterior.jpg]]
	::*''Posterior'': boundary more medial; draw boundary where the hippocampus pinches off into a tear-drop shape, or folds into itself		::*''Posterior'': boundary more medial; draw boundary where the hippocampus pinches off into a tear-drop shape, or folds into itself
	:::*Teardrop shown in red, boundary between Sub and CA1 shown in blue		:::*Teardrop shown in red, boundary between Sub and CA1 shown in blue
	:::*Sub is medial to the boundary, CA1 is lateral		:::*Sub is medial to the boundary, CA1 is lateral
	:::[[File:unfolding-~~SubCA1_posterior~~.jpg]]		:::[[File:unfolding-SubCA1_Posterior.jpg]]
	'''Separating CA1 from CA23DG (CA1CA23DG)'''		'''Separating CA1 from CA23DG (CA1CA23DG)'''
	::[[File:unfolding-CA1CA23DG.jpg]]		::[[File:unfolding-CA1CA23DG.jpg]]

Ccn admin at 01:44, 28 January 2014

2014-01-28T01:44:57Z

← Older revision		Revision as of 01:44, 28 January 2014
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	:[[File:unfolding-Seg_P1.png]]		:[[File:unfolding-Seg_P1.png]]
	:[[File:unfolding-Seg_P2.png]]		:[[File:unfolding-Seg_P2.png]]


	==Interpolation==		==Interpolation==
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	# The window that pops up will ask you to select a class file. This will be AD_1XXXX_interpright or interpleft that already exists in the directory. Select the side for which you created and hit enter.		# The window that pops up will ask you to select a class file. This will be AD_1XXXX_interpright or interpleft that already exists in the directory. Select the side for which you created and hit enter.
	# Check to make sure the masks align correctly.		# Check to make sure the masks align correctly.


	==Demarcations==		==Demarcations==
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	#cp nii/hhr_struct_6.nii.gz ../analysis/preprocessing/hhr_struct_6.nii.gz		#cp nii/hhr_struct_6.nii.gz ../analysis/preprocessing/hhr_struct_6.nii.gz
	##fslview hhr_struct_6.nii.gz (check if this step is fslview analysis/preprocessing/hhr_struct_6.nii.gz)		##fslview hhr_struct_6.nii.gz (check if this step is fslview analysis/preprocessing/hhr_struct_6.nii.gz)


	==External Links==		==External Links==