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.

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 Superseded by mritensormult.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