In-House Diffusion MRI Software: Difference between revisions

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New page: {{stub}} The following is a list of all the unique programs in $G containing the string "mri". Some of it may actually be 3rd-party software, but eve...
 
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The following is a list of all the unique programs in $G containing the string "mri".  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]].


<pre>
== Viewers and Other Interactive Programs ==
mri2analyze
* <tt>mriatlas</tt> --- Create a PDF "atlas" of one [[MRIimage]] or a collection of them.
mri2raw
* <tt>mrihdr</tt> --- Print the header of an [[MRIimage]] file.
mri_to_avw
* <tt>mrislice</tt> --- Extract a slice from an [[MRIimage]] volume.
mriatlas
 
mribrukerparms
== DWI Operations ==
mricoordchg
* <tt>mricrop</tt> --- Crop (or pad) an [[MRIimage]] DWI to a new size, measured in voxels.  See also <tt>diffusionResize.py</tt>.
mricro
* <tt>mrifilt3</tt> --- Apply a linear filter to an [[MRIimage]] DWI.  Generally used for resampling.  See also <tt>diffusionResize.py</tt>.
mricrop
* <tt>mritransp</tt> --- Transpose and/or flip dimensions of an [[MRIimage]] DWI.
mridfit
* <tt>nifti2mriimage</tt> --- Convert a [[NIfTI]] DWI to an [[MRIimage]] DWI.
mriecholabel
 
mriechoref
== DTI Operations ==
mrifilt3
* <tt>mridfit</tt> --- Fit diffusion tensors to a collection of [[MRIimage]] DWIs.  See also <tt>run_mridfit.py</tt>.
mrifilt3_g
* <tt>mritensormult</tt> --- Apply a linear transformation to all the tensors in an [[MRIimage]] DTI.
mriflipX
* <tt>mritensor_v0</tt> --- Compute a wide variety of scalar measures for each tensor in an [[MRIimage]] DTI.
mriften
 
mrigetecholabel
== Streamtube Operations ==
mrigetechoref
* <tt>[[tubegen]]</tt> --- Generate a streamtube model
mrihalf
 
mrihdr
== Deprecated Programs ==
mrilentil
* <tt>mriflipX</tt> --- Flip the X coordinate in an [[MRIimage]] DTI.  Superseded by <tt>mritensormult</tt>.
mrilentil2
 
mrimask
== Unknown Programs ==
mrimaxmin
* <tt>mri2analyze</tt>
mrimkI0
* <tt>mri2raw</tt>
mrimultifit_9
* <tt>mri_to_avw</tt>
mrireadScaleByte
* <tt>mribrukerparms</tt>
mrireadScaleFloat
* <tt>mricoordchg</tt>
mrireadScaleInt
* <tt>mriecholabel</tt>
mrireadScaleShort
* <tt>mriechoref</tt>
mrireadTens
* <tt>mriften</tt>
mrireadTensInterleave
* <tt>mrigetecholabel</tt>
mrislice
* <tt>mrigetechoref</tt>
mrisubset
* <tt>mrihalf</tt>
mritensor_v0
* <tt>mrilentil</tt>
mritensormult
* <tt>mrilentil2</tt>
mritransp
* <tt>mrimask</tt>
mrixform
* <tt>mrimaxmin</tt>
nifti2mriimage
* <tt>mrimkI0</tt>
startmricro
* <tt>mrimultifit_9</tt>
test-libmri
* <tt>mrireadScaleByte</tt>
</pre>
* <tt>mrireadScaleFloat</tt>
* <tt>mrireadScaleInt</tt>
* <tt>mrireadScaleShort</tt>
* <tt>mrireadTens</tt>
* <tt>mrireadTensInterleave</tt>
* <tt>mrisubset</tt>
* <tt>mrixform</tt>
* <tt>test-libmri</tt>
* <tt>tubeClusterInter</tt>
* <tt>tubeClusterIntra</tt>
* <tt>tubeFA</tt>
* <tt>tubeNorm</tt>
* <tt>tubecut</tt>
* <tt>tubedist</tt>
* <tt>tubefit</tt>
* <tt>tubefitD</tt>
* <tt>tubegen.old</tt>
* <tt>tubeinfo</tt>
* <tt>tubelength</tt>
 
== See Also ==
* [[3rd Party Diffusion MRI Software]]


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

Latest revision as of 22:35, 6 July 2009

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 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

  • mriatlas --- Create a PDF "atlas" of one MRIimage or a collection of them.
  • mrihdr --- Print the header of an MRIimage file.
  • mrislice --- Extract a slice from an MRIimage volume.

DWI Operations

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

DTI Operations

  • mridfit --- Fit diffusion tensors to a collection of MRIimage DWIs. See also run_mridfit.py.
  • mritensormult --- Apply a linear transformation to all the tensors in an MRIimage DTI.
  • mritensor_v0 --- Compute a wide variety of scalar measures for each tensor in an MRIimage DTI.

Streamtube Operations

  • tubegen --- Generate a streamtube model

Deprecated Programs

  • mriflipX --- Flip the X coordinate in an MRIimage DTI. Superseded by mritensormult.

Unknown Programs

  • mri2analyze
  • mri2raw
  • mri_to_avw
  • mribrukerparms
  • mricoordchg
  • mriecholabel
  • mriechoref
  • mriften
  • mrigetecholabel
  • mrigetechoref
  • mrihalf
  • mrilentil
  • mrilentil2
  • mrimask
  • mrimaxmin
  • mrimkI0
  • mrimultifit_9
  • mrireadScaleByte
  • mrireadScaleFloat
  • mrireadScaleInt
  • mrireadScaleShort
  • mrireadTens
  • mrireadTensInterleave
  • mrisubset
  • mrixform
  • test-libmri
  • tubeClusterInter
  • tubeClusterIntra
  • tubeFA
  • tubeNorm
  • tubecut
  • tubedist
  • tubefit
  • tubefitD
  • tubegen.old
  • tubeinfo
  • tubelength

See Also

Retrieved from "http://vrl.cs.brown.edu/wiki/index.php?title=In-House_Diffusion_MRI_Software&oldid=3633"