Diffusion MRI - Revision history

Jadrian Miles: /* Neuroscience Collaborations */ clarifying orientation details

2012-08-30T12:52:15Z

Neuroscience Collaborations: clarifying orientation details

← Older revision		Revision as of 12:52, 30 August 2012
Line 12:		Line 12:
	In the "Resolution" and "Voxel Size" columns, dimensions are ordered XxYxZ.		In the "Resolution" and "Voxel Size" columns, dimensions are ordered XxYxZ.

	In the "Orientation" columns, "L" stands for "patient's left". "R" stands for "patient's right". "A" stands for "anterior" (front), "P" for "posterior" (back), "I" for "inferior" (bottom), and "S" for "superior" (top). See the [[w:Anatomical terms of location#Medical (human) directional terms\|wikipedia page on anatomical coordinate systems]] for more information. ~~Ordinarily you will see these pairs~~ in ~~order as~~ "RL", "AP", and "IS"; if they are in the opposite order it indicates a [[Diagnose tensor orientation problems\|direction flip]].		In the "Orientation" columns, "L" stands for "patient's left". "R" stands for "patient's right". "A" stands for "anterior" (front), "P" for "posterior" (back), "I" for "inferior" (bottom), and "S" for "superior" (top). See the [[w:Anatomical terms of location#Medical (human) directional terms\|wikipedia page on anatomical coordinate systems]] for more information. The default orientation in the table below is "RL", "AP", and "IS"; if they are in the opposite order it indicates a [[Diagnose tensor orientation problems\|direction flip]].

	Note that this "default orientation" is non-standard; NIfTI, Talairach, and MNI coordinate systems all specify that X increases L-to-R; Y, P-to-A; and Z, I-to-S. The default orientation is still a right-handed coordinate system (thank goodness), but it's a little wonky and may cause problems with certain software. Check out [http://nifti.nimh.nih.gov/nifti-1/documentation/faq#Q14 the NIfTI FAQ on orientation] and [http://www.grahamwideman.com/gw/brain/orientation/orientterms.htm Graham Wideman's helpful tutorial] for more information. There's the chance that all of the orientation tags in this table have systematic errors, so a wholesale review of them might be worthwhile at some point. For the time being, take them with a grain of salt and double-check if it's important.		Note that this "default orientation" is non-standard; NIfTI, Talairach, and MNI coordinate systems all specify that X increases L-to-R; Y, P-to-A; and Z, I-to-S. The default orientation is still a right-handed coordinate system (thank goodness), but it's a little wonky and may cause problems with certain software. Check out [http://nifti.nimh.nih.gov/nifti-1/documentation/faq#Q14 the NIfTI FAQ on orientation] and [http://www.grahamwideman.com/gw/brain/orientation/orientterms.htm Graham Wideman's helpful tutorial] for more information. There's the chance that all of the orientation tags in this table have systematic errors, so a wholesale review of them might be worthwhile at some point. For the time being, take them with a grain of salt and double-check if it's important.

Jadrian Miles: /* Neuroscience Collaborations */

2012-08-29T22:29:04Z

Neuroscience Collaborations

← Older revision		Revision as of 22:29, 29 August 2012
Line 12:		Line 12:
	In the "Resolution" and "Voxel Size" columns, dimensions are ordered XxYxZ.		In the "Resolution" and "Voxel Size" columns, dimensions are ordered XxYxZ.

	In the "Orientation" columns, "L" stands for ~~"left side of patient from an anterior view", or~~ "patient's ~~right~~". "R" stands for ~~"right side of patient from an anterior view", or~~ "patient's ~~left~~". "A" stands for "anterior" (front), "P" for "posterior" (back), "I" for "inferior" (bottom), and "S" for "superior" (top). See the [[w:Anatomical terms of location#Medical (human) directional terms\|wikipedia page on anatomical coordinate systems]] for more information. Ordinarily you will see these pairs in order as "LR", "AP", and "IS"; if they are in the opposite order it indicates a [[Diagnose tensor orientation problems\|direction flip]].		In the "Orientation" columns, "L" stands for "patient's left". "R" stands for "patient's right". "A" stands for "anterior" (front), "P" for "posterior" (back), "I" for "inferior" (bottom), and "S" for "superior" (top). See the [[w:Anatomical terms of location#Medical (human) directional terms\|wikipedia page on anatomical coordinate systems]] for more information. Ordinarily you will see these pairs in order as "RL", "AP", and "IS"; if they are in the opposite order it indicates a [[Diagnose tensor orientation problems\|direction flip]].

			Note that this "default orientation" is non-standard; NIfTI, Talairach, and MNI coordinate systems all specify that X increases L-to-R; Y, P-to-A; and Z, I-to-S. The default orientation is still a right-handed coordinate system (thank goodness), but it's a little wonky and may cause problems with certain software. Check out [http://nifti.nimh.nih.gov/nifti-1/documentation/faq#Q14 the NIfTI FAQ on orientation] and [http://www.grahamwideman.com/gw/brain/orientation/orientterms.htm Graham Wideman's helpful tutorial] for more information. There's the chance that all of the orientation tags in this table have systematic errors, so a wholesale review of them might be worthwhile at some point. For the time being, take them with a grain of salt and double-check if it's important.

	=== Collaboration Table ===		=== Collaboration Table ===
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	\| 36		\| 36
	\| 2.0x2.0x2.0		\| 2.0x2.0x2.0
	\| L \|\| R \|\| {{no\|P}} \|\| {{no\|A}} \|\| I \|\| S		\| R \|\| L \|\| {{no\|P}} \|\| {{no\|A}} \|\| I \|\| S
	\| L \|\| R \|\| A \|\| P \|\| I \|\| S		\| R \|\| L \|\| A \|\| P \|\| I \|\| S
	\|-		\|-
	\| {{hidden \| fw1 = normal \| ta1 = left \| headercss = font-size: 100%; width: 18ex; \| contentcss = font-size: 90%; width: 60ex;		\| {{hidden \| fw1 = normal \| ta1 = left \| headercss = font-size: 100%; width: 18ex; \| contentcss = font-size: 90%; width: 60ex;
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	\| 64 for d1 scans; 72 for d2 scans		\| 64 for d1 scans; 72 for d2 scans
	\| 2.0x2.0x2.0		\| 2.0x2.0x2.0
	\| L \|\| R \|\| {{no\|P}} \|\| {{no\|A}} \|\| I \|\| S		\| R \|\| L \|\| {{no\|P}} \|\| {{no\|A}} \|\| I \|\| S
	\| L \|\| R \|\| A \|\| P \|\| I \|\| S		\| R \|\| L \|\| A \|\| P \|\| I \|\| S
	\|-		\|-
	\| {{Hl2}} rowspan="2" \| [[Fibers at Risk]]		\| {{Hl2}} rowspan="2" \| [[Fibers at Risk]]
Line 274:		Line 276:
	\| 74		\| 74
	\| 1.76562x1.76562x1.8		\| 1.76562x1.76562x1.8
	\| L \|\| R \|\| A \|\| P \|\| I \|\| S		\| R \|\| L \|\| A \|\| P \|\| I \|\| S
	\| {{no\|R}} \|\| {{no\|L}} \|\| A \|\| P \|\| I \|\| S		\| {{no\|L}} \|\| {{no\|R}} \|\| A \|\| P \|\| I \|\| S
	\|-		\|-
	\| {{Hl2}} \| Kids		\| {{Hl2}} \| Kids
Line 299:		Line 301:
	\| 65		\| 65
	\| 1.765625x1.765625x1.8		\| 1.765625x1.765625x1.8
	\| L \|\| R \|\| A \|\| P \|\| I \|\| S		\| R \|\| L \|\| A \|\| P \|\| I \|\| S
	\| L \|\| R \|\| A \|\| P \|\| I \|\| s		\| R \|\| L \|\| A \|\| P \|\| I \|\| S
	\|-		\|-
	\| {{Hl2}} \| Macaque		\| {{Hl2}} \| Macaque
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	}}		}}
	\| 1.875x1.875x1.9		\| 1.875x1.875x1.9
	\| L \|\| R \|\| A \|\| P \|\| I \|\| S		\| R \|\| L \|\| A \|\| P \|\| I \|\| S
	\| L \|\| R \|\| A \|\| P \|\| I \|\| S		\| R \|\| L \|\| A \|\| P \|\| I \|\| S
	\|-		\|-
	\| {{hidden \| fw1 = normal \| ta1 = left \| headercss = font-size: 100%; width: 18ex; \| contentcss = font-size: 90%; width: 85ex;		\| {{hidden \| fw1 = normal \| ta1 = left \| headercss = font-size: 100%; width: 18ex; \| contentcss = font-size: 90%; width: 85ex;
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	\| 71		\| 71
	\| 2.0x2.0x2.0		\| 2.0x2.0x2.0
	\| L \|\| R \|\| A \|\| P \|\| I \|\| S		\| R \|\| L \|\| A \|\| P \|\| I \|\| S
	\| L \|\| R \|\| {{no\|P}} \|\| {{no\|A}} \|\| I \|\| S		\| R \|\| L \|\| {{no\|P}} \|\| {{no\|A}} \|\| I \|\| S
	\|-		\|-
	\| {{hidden \| fw1 = normal \| ta1 = left \| headercss = font-size: 100%; width: 18ex; \| contentcss = font-size: 90%; width: 60ex;		\| {{hidden \| fw1 = normal \| ta1 = left \| headercss = font-size: 100%; width: 18ex; \| contentcss = font-size: 90%; width: 60ex;
Line 515:		Line 517:
	\| 71		\| 71
	\| 2.0x2.0x2.0		\| 2.0x2.0x2.0
	\| L \|\| R \|\| A \|\| P \|\| I \|\| S		\| R \|\| L \|\| A \|\| P \|\| I \|\| S
	\| L \|\| R \|\| {{no\|P}} \|\| {{no\|A}} \|\| I \|\| S		\| R \|\| L \|\| {{no\|P}} \|\| {{no\|A}} \|\| I \|\| S
	\|-		\|-
	\| {{hidden \| fw1 = normal \| ta1 = left \| headercss = font-size: 100%; width: 18ex; \| contentcss = font-size: 90%; width: 60ex;		\| {{hidden \| fw1 = normal \| ta1 = left \| headercss = font-size: 100%; width: 18ex; \| contentcss = font-size: 90%; width: 60ex;
Line 537:		Line 539:
	\| 71		\| 71
	\| 2.0x2.0x2.0		\| 2.0x2.0x2.0
	\| L \|\| R \|\| A \|\| P \|\| I \|\| S		\| R \|\| L \|\| A \|\| P \|\| I \|\| S
	\| L \|\| R \|\| {{no\|P}} \|\| {{no\|A}} \|\| I \|\| S		\| R \|\| L \|\| {{no\|P}} \|\| {{no\|A}} \|\| I \|\| S
	\|}		\|}

Ryan Cabeen at 16:28, 30 May 2012

2012-05-30T16:28:14Z

← Older revision		Revision as of 16:28, 30 May 2012
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	* [[Diffusion MRI Design Notes]]		* [[Diffusion MRI Design Notes]]
	* [[Brain Networks]]		* [[Brain Networks]]
			* [[Neuroimaging Systems]]

	[[Category:Projects]][[Category:Diffusion MRI]]		[[Category:Projects]][[Category:Diffusion MRI]]

Ryan Cabeen at 16:18, 5 April 2012

2012-04-05T16:18:27Z

← Older revision		Revision as of 16:18, 5 April 2012
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	* [[Work With Histology Data]]		* [[Work With Histology Data]]
	* [[Diffusion MRI Design Notes]]		* [[Diffusion MRI Design Notes]]
			* [[Brain Networks]]

	[[Category:Projects]][[Category:Diffusion MRI]]		[[Category:Projects]][[Category:Diffusion MRI]]

Jadrian Miles: /* Collaboration Table */ added dimensions for SA RP study

2011-11-22T16:33:39Z

Collaboration Table: added dimensions for SA RP study

← Older revision		Revision as of 16:33, 22 November 2011
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	\| [[DICOM#Mosaic\|DICOM Mosaic]]		\| [[DICOM#Mosaic\|DICOM Mosaic]]
	\| 30		\| 30
	\| ~~{{?}}~~		\| 128x128x70
	\| ~~{{?}}~~		\| 33
	\| ~~{{?}}~~		\| 1.71875x1.71875x1.7
	\| colspan="6" {{?}}		\| colspan="6" {{?}}
	\| colspan="6" {{?}}		\| colspan="6" {{?}}

Jadrian Miles: /* Collaboration Table */ updated St. Louis info

2011-05-04T14:53:48Z

Collaboration Table: updated St. Louis info

← Older revision		Revision as of 14:53, 4 May 2011
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	\| {{?}}		\| {{?}}
	\| {{?}}		\| {{?}}
	\| [[Interfile]]		\| [[Analyze]] .img + [[Interfile]] .ifh header
	\| 1		\| 1
	\| 83x110x64		\| 83x110x64
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	\| {{?}}		\| {{?}}
	\| {{?}}		\| {{?}}
	\| [[~~DICOM~~]] .hdr/.img		\| [[Analyze]] .hdr/.img + [[Interfile]] .ifh header (supplementary)
	\| 81		\| 81
	\| 83x110x64		\| 83x110x64
	\| 36		\| 64 for d1 scans; 72 for d2 scans
	\| 2.0x2.0x2.0		\| 2.0x2.0x2.0
	\| L \|\| R \|\| {{no\|P}} \|\| {{no\|A}} \|\| I \|\| S		\| L \|\| R \|\| {{no\|P}} \|\| {{no\|A}} \|\| I \|\| S

Jadrian Miles: /* HOWTOs */

2010-12-11T17:44:59Z

HOWTOs

← Older revision		Revision as of 17:44, 11 December 2010
Line 577:		Line 577:

	== HOWTOs ==		== HOWTOs ==
			* [[Set up your environment for diffusion MRI processing]]
	* [[Run the diffusion processing pipeline at low resolution]]		* [[Run the diffusion processing pipeline at low resolution]]
	* [[Diagnose tensor orientation problems]]		* [[Diagnose tensor orientation problems]]

Jadrian Miles: /* Neuroscience Collaborations */ added new section on protocol study

2010-10-22T19:58:32Z

Neuroscience Collaborations: added new section on protocol study

← Older revision		Revision as of 19:58, 22 October 2010
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	\| L \|\| R \|\| {{no\|P}} \|\| {{no\|A}} \|\| I \|\| S		\| L \|\| R \|\| {{no\|P}} \|\| {{no\|A}} \|\| I \|\| S
	\|}		\|}

			=== Brown Protocol Compatibility Study ===

			The 3T scanner at Brown has changed its configuration several times, necessitating a study to determine whether data from these different configurations are compatible. Please see the page [[/Brown Protocol Compatibility Study]] for details.

	== Software ==		== Software ==

Jadrian Miles: /* See Also */

2010-10-18T13:52:34Z

Jadrian Miles: /* Collaboration Table */ added Edinburgh normals

2010-09-07T15:03:33Z

Collaboration Table: added Edinburgh normals

@@ Line 446: / Line 446: @@
 | colspan="6" {{?}}
 |-
-| {{Hl2}} rowspan="3" | [[Tumors]]
+| {{Hl2}} rowspan="4" | [[Tumors]]
-| rowspan="3" | Edinburgh
+| rowspan="4" | Edinburgh
-| rowspan="3" | Mark Bastin
+| rowspan="4" | Mark Bastin
 | {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
 | header = 2007-11-06
@@ Line 512: / Line 512: @@
 | [[DICOM#Tar|DICOM tarball]]
 | 17
 | 128x128x72
 | 71

← Older revision		Revision as of 13:52, 18 October 2010
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	== See Also ==		== See Also ==
	* [[/Introductory Reading List\|Introductory Reading List]] --- a minimal guide of good references for understanding the background of this project		* [[/Introductory Reading List\|Introductory Reading List]] --- a minimal guide of good references for understanding the background of this project
			* [[Diffusion Processing Pipeline]] --- a series of small programs that turns data we get from collaborators into tensor models, scalar measures, tractograms, etc.
			* [[Brainapp]] --- a GUI program for viewing tractograms and computing scalar statistics on them.
			* [[Diffusion MRI Matlab Scripts]] --- Matlab scripts to read, write, view, and manipulate MRI data (especially in [[MRIimage]] format)
	* [[Diffusion MRI techniques]] --- technical information about the diffusion MRI process		* [[Diffusion MRI techniques]] --- technical information about the diffusion MRI process
	* [[Brain anatomy]]		* [[Brain anatomy]]