In-House Diffusion MRI Software: Difference between revisions

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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  Superseded by 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>

Revision as of 14:23, 17 March 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.

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.

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
  • mritensor_v0
  • mrixform
  • startmricro
  • test-libmri
  • tubeClusterInter
  • tubeClusterIntra
  • tubeFA
  • tubeNorm
  • tubecut
  • tubedist
  • tubefit
  • tubefitD
  • tubegen.old
  • tubeinfo
  • tubelength
Retrieved from "http://vrl.cs.brown.edu/wiki/index.php?title=In-House_Diffusion_MRI_Software&oldid=2521"