In-House Diffusion MRI Software

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 Superseded by mritensormult.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

• 3rd Party Diffusion MRI Software