In-House Diffusion MRI Software - Revision history

Jadrian Miles at 22:35, 6 July 2009

2009-07-06T22:35:04Z

← Older revision		Revision as of 22:35, 6 July 2009
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	{{stub}}		{{stub}}

	The following is a list of all the unique programs in $G containing the strings "mri" or "tube". Some of it may actually be [[3rd Party Diffusion MRI Software\|3rd-party software]], but eventually this page should detail all the programs we've developed to handle [[diffusion MRI]] data. You may also want to check out the list of [[~~Diffusion~~ MRI Matlab scripts]].		The following is a list of all the unique programs in $G containing the strings "mri" or "tube". Some of it may actually be [[3rd Party Diffusion MRI Software\|3rd-party software]], but eventually this page should detail all the programs we've developed to handle [[diffusion MRI]] data. You may also want to check out the list of [[diffusion MRI Matlab scripts]].

	== Viewers and Other Interactive Programs ==		== Viewers and Other Interactive Programs ==

Jadrian Miles at 22:34, 6 July 2009

2009-07-06T22:34:04Z

← Older revision		Revision as of 22:34, 6 July 2009
Line 1:		Line 1:
	{{stub}}		{{stub}}

	The following is a list of all the unique programs in $G containing the strings "mri" or "tube". Some of it may actually be [[3rd Party Diffusion MRI Software\|3rd-party software]], but eventually this page should detail all the programs we've developed to handle [[diffusion MRI]] data.		The following is a list of all the unique programs in $G containing the strings "mri" or "tube". Some of it may actually be [[3rd Party Diffusion MRI Software\|3rd-party software]], but eventually this page should detail all the programs we've developed to handle [[diffusion MRI]] data. You may also want to check out the list of [[Diffusion MRI Matlab scripts]].

	== Viewers and Other Interactive Programs ==		== Viewers and Other Interactive Programs ==

Jadrian Miles at 21:32, 22 March 2009

2009-03-22T21:32:44Z

← Older revision		Revision as of 21:32, 22 March 2009
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	* <tt>tubeinfo</tt>		* <tt>tubeinfo</tt>
	* <tt>tubelength</tt>		* <tt>tubelength</tt>

			== See Also ==
			* [[3rd Party Diffusion MRI Software]]

	[[Category:Diffusion MRI]][[Category:Software]]		[[Category:Diffusion MRI]][[Category:Software]]

Jadrian Miles at 21:32, 22 March 2009

2009-03-22T21:32:03Z

← Older revision		Revision as of 21:32, 22 March 2009
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	* <tt>mridfit</tt> --- Fit diffusion tensors to a collection of [[MRIimage]] DWIs. See also <tt>run_mridfit.py</tt>.		* <tt>mridfit</tt> --- Fit diffusion tensors to a collection of [[MRIimage]] DWIs. See also <tt>run_mridfit.py</tt>.
	* <tt>mritensormult</tt> --- Apply a linear transformation to all the tensors in an [[MRIimage]] DTI.		* <tt>mritensormult</tt> --- Apply a linear transformation to all the tensors in an [[MRIimage]] DTI.
			* <tt>mritensor_v0</tt> --- Compute a wide variety of scalar measures for each tensor in an [[MRIimage]] DTI.

	== Streamtube Operations ==		== Streamtube Operations ==
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	* <tt>mrireadTensInterleave</tt>		* <tt>mrireadTensInterleave</tt>
	* <tt>mrisubset</tt>		* <tt>mrisubset</tt>
	* <tt>mritensor_v0</tt>
	* <tt>mrixform</tt>		* <tt>mrixform</tt>
	* <tt>startmricro</tt>
	* <tt>test-libmri</tt>		* <tt>test-libmri</tt>
	* <tt>tubeClusterInter</tt>		* <tt>tubeClusterInter</tt>

Jadrian Miles at 14:23, 17 March 2009

2009-03-17T14:23:57Z

← Older revision		Revision as of 14:23, 17 March 2009
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	The following is a list of all the unique programs in $G containing the strings "mri" or "tube". Some of it may actually be [[3rd Party Diffusion MRI Software\|3rd-party software]], but eventually this page should detail all the programs we've developed to handle [[diffusion MRI]] data.		The following is a list of all the unique programs in $G containing the strings "mri" or "tube". Some of it may actually be [[3rd Party Diffusion MRI Software\|3rd-party software]], but eventually this page should detail all the programs we've developed to handle [[diffusion MRI]] data.

			== Viewers and Other Interactive Programs ==
			* <tt>mriatlas</tt> --- Create a PDF "atlas" of one [[MRIimage]] or a collection of them.
			* <tt>mrihdr</tt> --- Print the header of an [[MRIimage]] file.
			* <tt>mrislice</tt> --- Extract a slice from an [[MRIimage]] volume.

			== DWI Operations ==
			* <tt>mricrop</tt> --- Crop (or pad) an [[MRIimage]] DWI to a new size, measured in voxels. See also <tt>diffusionResize.py</tt>.
			* <tt>mrifilt3</tt> --- Apply a linear filter to an [[MRIimage]] DWI. Generally used for resampling. See also <tt>diffusionResize.py</tt>.
			* <tt>mritransp</tt> --- Transpose and/or flip dimensions of an [[MRIimage]] DWI.
			* <tt>nifti2mriimage</tt> --- Convert a [[NIfTI]] DWI to an [[MRIimage]] DWI.

			== DTI Operations ==
			* <tt>mridfit</tt> --- Fit diffusion tensors to a collection of [[MRIimage]] DWIs. See also <tt>run_mridfit.py</tt>.
			* <tt>mritensormult</tt> --- Apply a linear transformation to all the tensors in an [[MRIimage]] DTI.

			== Streamtube Operations ==
			* <tt>[[tubegen]]</tt> --- Generate a streamtube model

			== Deprecated Programs ==
			* <tt>mriflipX</tt> --- Flip the X coordinate in an [[MRIimage]] DTI. Superseded by <tt>mritensormult</tt>.

			== Unknown Programs ==
	* <tt>mri2analyze</tt>		* <tt>mri2analyze</tt>
	* <tt>mri2raw</tt>		* <tt>mri2raw</tt>
	* <tt>mri_to_avw</tt>		* <tt>mri_to_avw</tt>
	* <tt>mriatlas</tt> --- Create a PDF "atlas" of one [[MRIimage]] or a collection of them.
	* <tt>mribrukerparms</tt>		* <tt>mribrukerparms</tt>
	* <tt>mricoordchg</tt>		* <tt>mricoordchg</tt>
	* <tt>mricrop</tt> --- Crop (or pad) an [[MRIimage]] to a new size, measured in voxels. See also <tt>diffusionResize.py</tt>.
	* <tt>mridfit</tt> --- Fit diffusion tensors to a collection of [[MRIimage]] DWIs. See also <tt>run_mridfit.py</tt>.
	* <tt>mriecholabel</tt>		* <tt>mriecholabel</tt>
	* <tt>mriechoref</tt>		* <tt>mriechoref</tt>
	* <tt>mrifilt3</tt> --- Apply a linear filter to an [[MRIimage]]. Generally used for resampling. See also <tt>diffusionResize.py</tt>.
	* <tt>mriflipX</tt> --- Flip the X coordinate in an [[MRIimage]] DTI. Superseded by <tt>mritensormult</tt>.
	* <tt>mriften</tt>		* <tt>mriften</tt>
	* <tt>mrigetecholabel</tt>		* <tt>mrigetecholabel</tt>
	* <tt>mrigetechoref</tt>		* <tt>mrigetechoref</tt>
	* <tt>mrihalf</tt>		* <tt>mrihalf</tt>
	* <tt>mrihdr</tt> --- Read the header of an [[MRIimage]] file.
	* <tt>mrilentil</tt>		* <tt>mrilentil</tt>
	* <tt>mrilentil2</tt>		* <tt>mrilentil2</tt>
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	* <tt>mrireadTens</tt>		* <tt>mrireadTens</tt>
	* <tt>mrireadTensInterleave</tt>		* <tt>mrireadTensInterleave</tt>
	* <tt>mrislice</tt> --- Extract a slice from an [[MRIimage]] volume.
	* <tt>mrisubset</tt>		* <tt>mrisubset</tt>
	* <tt>mritensor_v0</tt>		* <tt>mritensor_v0</tt>
	* <tt>mritensormult</tt> --- Apply a linear transformation to all the tensors in an [[MRIimage]] DTI.
	* <tt>mritransp</tt> --- Transpose and/or flip dimensions of an [[MRIimage]] DWI.
	* <tt>mrixform</tt>		* <tt>mrixform</tt>
	* <tt>nifti2mriimage</tt> --- Convert a [[NIfTI]] DWI to an [[MRIimage]] DWI.
	* <tt>startmricro</tt>		* <tt>startmricro</tt>
	* <tt>test-libmri</tt>		* <tt>test-libmri</tt>
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	* <tt>tubefit</tt>		* <tt>tubefit</tt>
	* <tt>tubefitD</tt>		* <tt>tubefitD</tt>
	* <tt>[[tubegen]]</tt> --- Generate a streamtube model
	* <tt>tubegen.old</tt>		* <tt>tubegen.old</tt>
	* <tt>tubeinfo</tt>		* <tt>tubeinfo</tt>

Jadrian Miles at 14:17, 17 March 2009

2009-03-17T14:17:56Z

← Older revision		Revision as of 14:17, 17 March 2009
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	* <tt>mritensor_v0</tt>		* <tt>mritensor_v0</tt>
	* <tt>mritensormult</tt> --- Apply a linear transformation to all the tensors in an [[MRIimage]] DTI.		* <tt>mritensormult</tt> --- Apply a linear transformation to all the tensors in an [[MRIimage]] DTI.
	* <tt>mritransp</tt>		* <tt>mritransp</tt> --- Transpose and/or flip dimensions of an [[MRIimage]] DWI.
	* <tt>mrixform</tt>		* <tt>mrixform</tt>
	* <tt>nifti2mriimage</tt> --- Convert a [[NIfTI]] DWI to an [[MRIimage]] DWI.		* <tt>nifti2mriimage</tt> --- Convert a [[NIfTI]] DWI to an [[MRIimage]] DWI.

Jadrian Miles at 02:10, 11 February 2009

2009-02-11T02:10:16Z

← Older revision		Revision as of 02:10, 11 February 2009
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	* <tt>tubefit</tt>		* <tt>tubefit</tt>
	* <tt>tubefitD</tt>		* <tt>tubefitD</tt>
	* <tt>tubegen</tt>		* <tt>[[tubegen]]</tt> --- Generate a streamtube model
	* <tt>tubegen.old</tt>		* <tt>tubegen.old</tt>
	* <tt>tubeinfo</tt>		* <tt>tubeinfo</tt>

Jadrian Miles at 22:25, 12 January 2009

2009-01-12T22:25:53Z

← Older revision		Revision as of 22:25, 12 January 2009
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	* <tt>mri2raw</tt>		* <tt>mri2raw</tt>
	* <tt>mri_to_avw</tt>		* <tt>mri_to_avw</tt>
	* <tt>mriatlas</tt> ~~—~~ Create a PDF "atlas" of one [[MRIimage]] or a collection of them.		* <tt>mriatlas</tt> --- Create a PDF "atlas" of one [[MRIimage]] or a collection of them.
	* <tt>mribrukerparms</tt>		* <tt>mribrukerparms</tt>
	* <tt>mricoordchg</tt>		* <tt>mricoordchg</tt>
	* <tt>mricrop</tt> ~~—~~ Crop (or pad) an [[MRIimage]] to a new size, measured in voxels. See also <tt>diffusionResize.py</tt>.		* <tt>mricrop</tt> --- Crop (or pad) an [[MRIimage]] to a new size, measured in voxels. See also <tt>diffusionResize.py</tt>.
	* <tt>mridfit</tt> ~~—~~ Fit diffusion tensors to a collection of [[MRIimage]] DWIs. See also <tt>run_mridfit.py</tt>.		* <tt>mridfit</tt> --- Fit diffusion tensors to a collection of [[MRIimage]] DWIs. See also <tt>run_mridfit.py</tt>.
	* <tt>mriecholabel</tt>		* <tt>mriecholabel</tt>
	* <tt>mriechoref</tt>		* <tt>mriechoref</tt>
	* <tt>mrifilt3</tt> ~~—~~ Apply a linear filter to an [[MRIimage]]. Generally used for resampling. See also <tt>diffusionResize.py</tt>.		* <tt>mrifilt3</tt> --- Apply a linear filter to an [[MRIimage]]. Generally used for resampling. See also <tt>diffusionResize.py</tt>.
	* <tt>mriflipX</tt> ~~—~~ Flip the X coordinate in an [[MRIimage]] DTI. Superseded by <tt>mritensormult</tt>.		* <tt>mriflipX</tt> --- Flip the X coordinate in an [[MRIimage]] DTI. Superseded by <tt>mritensormult</tt>.
	* <tt>mriften</tt>		* <tt>mriften</tt>
	* <tt>mrigetecholabel</tt>		* <tt>mrigetecholabel</tt>
	* <tt>mrigetechoref</tt>		* <tt>mrigetechoref</tt>
	* <tt>mrihalf</tt>		* <tt>mrihalf</tt>
	* <tt>mrihdr</tt> ~~—~~ Read the header of an [[MRIimage]] file.		* <tt>mrihdr</tt> --- Read the header of an [[MRIimage]] file.
	* <tt>mrilentil</tt>		* <tt>mrilentil</tt>
	* <tt>mrilentil2</tt>		* <tt>mrilentil2</tt>
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	* <tt>mrireadTens</tt>		* <tt>mrireadTens</tt>
	* <tt>mrireadTensInterleave</tt>		* <tt>mrireadTensInterleave</tt>
	* <tt>mrislice</tt> ~~—~~ Extract a slice from an [[MRIimage]] volume.		* <tt>mrislice</tt> --- Extract a slice from an [[MRIimage]] volume.
	* <tt>mrisubset</tt>		* <tt>mrisubset</tt>
	* <tt>mritensor_v0</tt>		* <tt>mritensor_v0</tt>
	* <tt>mritensormult</tt> ~~—~~ Apply a linear transformation to all the tensors in an [[MRIimage]] DTI.		* <tt>mritensormult</tt> --- Apply a linear transformation to all the tensors in an [[MRIimage]] DTI.
	* <tt>mritransp</tt>		* <tt>mritransp</tt>
	* <tt>mrixform</tt>		* <tt>mrixform</tt>
	* <tt>nifti2mriimage</tt> ~~—~~ Convert a [[NIfTI]] DWI to an [[MRIimage]] DWI.		* <tt>nifti2mriimage</tt> --- Convert a [[NIfTI]] DWI to an [[MRIimage]] DWI.
	* <tt>startmricro</tt>		* <tt>startmricro</tt>
	* <tt>test-libmri</tt>		* <tt>test-libmri</tt>

Jadrian Miles at 21:19, 7 January 2009

2009-01-07T21:19:57Z

← Older revision		Revision as of 21:19, 7 January 2009
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	* <tt>mribrukerparms</tt>		* <tt>mribrukerparms</tt>
	* <tt>mricoordchg</tt>		* <tt>mricoordchg</tt>
	* <tt>mricro</tt>
	* <tt>mricrop</tt> — Crop (or pad) an [[MRIimage]] to a new size, measured in voxels. See also <tt>diffusionResize.py</tt>.		* <tt>mricrop</tt> — Crop (or pad) an [[MRIimage]] to a new size, measured in voxels. See also <tt>diffusionResize.py</tt>.
	* <tt>mridfit</tt> — Fit diffusion tensors to a collection of [[MRIimage]] DWIs. See also <tt>run_mridfit.py</tt>.		* <tt>mridfit</tt> — Fit diffusion tensors to a collection of [[MRIimage]] DWIs. See also <tt>run_mridfit.py</tt>.
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	* <tt>mritransp</tt>		* <tt>mritransp</tt>
	* <tt>mrixform</tt>		* <tt>mrixform</tt>
	* <tt>nifti2mriimage</tt> — Convert [[NIfTI]] ~~DWIs~~ to [[MRIimage]] ~~DWIs~~.		* <tt>nifti2mriimage</tt> — Convert a [[NIfTI]] DWI to an [[MRIimage]] DWI.
	* <tt>startmricro</tt>		* <tt>startmricro</tt>
	* <tt>test-libmri</tt>		* <tt>test-libmri</tt>

Jadrian Miles at 03:42, 29 December 2008

2008-12-29T03:42:07Z

← Older revision		Revision as of 03:42, 29 December 2008
Line 3:		Line 3:
	The following is a list of all the unique programs in $G containing the strings "mri" or "tube". Some of it may actually be [[3rd Party Diffusion MRI Software\|3rd-party software]], but eventually this page should detail all the programs we've developed to handle [[diffusion MRI]] data.		The following is a list of all the unique programs in $G containing the strings "mri" or "tube". Some of it may actually be [[3rd Party Diffusion MRI Software\|3rd-party software]], but eventually this page should detail all the programs we've developed to handle [[diffusion MRI]] data.

	<~~pre~~>		* <tt>mri2analyze</tt>
	mri2analyze		* <tt>mri2raw</tt>
	mri2raw		* <tt>mri_to_avw</tt>
	mri_to_avw		* <tt>mriatlas</tt> — Create a PDF "atlas" of one [[MRIimage]] or a collection of them.
	mriatlas		* <tt>mribrukerparms</tt>
	mribrukerparms		* <tt>mricoordchg</tt>
	mricoordchg		* <tt>mricro</tt>
	mricro		* <tt>mricrop</tt> — Crop (or pad) an [[MRIimage]] to a new size, measured in voxels. See also <tt>diffusionResize.py</tt>.
	mricrop		* <tt>mridfit</tt> — Fit diffusion tensors to a collection of [[MRIimage]] DWIs. See also <tt>run_mridfit.py</tt>.
	mridfit		* <tt>mriecholabel</tt>
	mriecholabel		* <tt>mriechoref</tt>
	mriechoref		* <tt>mrifilt3</tt> — Apply a linear filter to an [[MRIimage]]. Generally used for resampling. See also <tt>diffusionResize.py</tt>.
	mrifilt3		* <tt>mriflipX</tt> — Flip the X coordinate in an [[MRIimage]] DTI. Superseded by <tt>mritensormult</tt>.
	~~mrifilt3_g~~		* <tt>mriften</tt>
	mriflipX		* <tt>mrigetecholabel</tt>
	mriften		* <tt>mrigetechoref</tt>
	mrigetecholabel		* <tt>mrihalf</tt>
	mrigetechoref		* <tt>mrihdr</tt> — Read the header of an [[MRIimage]] file.
	mrihalf		* <tt>mrilentil</tt>
	mrihdr		* <tt>mrilentil2</tt>
	mrilentil		* <tt>mrimask</tt>
	mrilentil2		* <tt>mrimaxmin</tt>
	mrimask		* <tt>mrimkI0</tt>
	mrimaxmin		* <tt>mrimultifit_9</tt>
	mrimkI0		* <tt>mrireadScaleByte</tt>
	mrimultifit_9		* <tt>mrireadScaleFloat</tt>
	mrireadScaleByte		* <tt>mrireadScaleInt</tt>
	mrireadScaleFloat		* <tt>mrireadScaleShort</tt>
	mrireadScaleInt		* <tt>mrireadTens</tt>
	mrireadScaleShort		* <tt>mrireadTensInterleave</tt>
	mrireadTens		* <tt>mrislice</tt> — Extract a slice from an [[MRIimage]] volume.
	mrireadTensInterleave		* <tt>mrisubset</tt>
	mrislice		* <tt>mritensor_v0</tt>
	mrisubset		* <tt>mritensormult</tt> — Apply a linear transformation to all the tensors in an [[MRIimage]] DTI.
	mritensor_v0		* <tt>mritransp</tt>
	mritensormult		* <tt>mrixform</tt>
	mritransp		* <tt>nifti2mriimage</tt> — Convert [[NIfTI]] DWIs to [[MRIimage]] DWIs.
	mrixform		* <tt>startmricro</tt>
	nifti2mriimage		* <tt>test-libmri</tt>
	startmricro		* <tt>tubeClusterInter</tt>
	test-libmri		* <tt>tubeClusterIntra</tt>
	tubeClusterInter		* <tt>tubeFA</tt>
	tubeClusterIntra		* <tt>tubeNorm</tt>
	tubeFA		* <tt>tubecut</tt>
	tubeNorm		* <tt>tubedist</tt>
	tubecut		* <tt>tubefit</tt>
	tubedist		* <tt>tubefitD</tt>
	tubefit		* <tt>tubegen</tt>
	tubefitD		* <tt>tubegen.old</tt>
	tubegen		* <tt>tubeinfo</tt>
	tubegen.old		* <tt>tubelength</tt>
	tubeinfo
	tubelength
	</~~pre~~>

	[[Category:Diffusion MRI]][[Category:Software]]		[[Category:Diffusion MRI]][[Category:Software]]