MiND: Metadata in NIfTI for DWI
Overview
The LONI MiND standard provides a unified representation for storing DWI-related metadata within NIfTI files. This page provides information about the MiND File Utilities, a set of software tools for creating, manipulating, and inspecting MiND files. The current release, v0.1, is comprised of the following programs:
- DICOM to MiND (mind-dcm2mind)
- NIfTI Tensor to MiND (mind-niitensor2mind)
- Nrrd DWI to MiND (mind-nrrddwi2mind)
- Nrrd Tensor to MiND (mind-nrrdtensor2mind)
- FSL DWI to MiND (mind-fsldwi2mind)
- FSL Tensor to MiND (mind-fsltensor2mind)
- FSL Eigen to MiND (mind-fsleigen2mind)
- Get MiND Metadata (mind-mind2xml)
- Set MiND Metadata (mind-xml2mind)
- MiND Masker (mind-masker)
- MiND Splitter (mind-splitter)
Getting the MiND File Utilities
- General Public
- The MiND File Utilities are available as a set of modules on the LONI Pipeline
- The MiND File Utilities are available as a set of modules on the LONI Pipeline
- LONI Members
- Access the binaries on Cranium at
/usr/local/loniApps/vpatel/bin
- Access the binaries on Cranium at
Documentation
A. DICOM to MiND
The mind-dcm2mind program converts a DICOM directory into the MiND format
for diffusion-weighted data sets.
mind-dcm2mind.sh dicom-directory output-list
dicom-directory path to the DICOM directory containing the diffusion-
weighted data
output-list output file containing a list of converted MiND files
B. NIfTI Tensor to MiND
The mind-niitensor2mind program converts a second order diffusion tensor
volume from NIfTI matrix format to the NIfTI/MiND standard.
mind-niitensor2mind.sh nifti-matrix output-mind
nifti-matrix second order diffusion tensor volume in NIfTI matrix
format
output-mind output NIfTI volume containing diffusion tensors in MiND
format
C. Nrrd DWI to MiND
The mind-nrrddwi2mind program converts a diffusion-weighted data set from
nrrd format to the NIfTI/MiND standard.
mind-nrrddwi2mind.sh nrrd-dwi output-mind
nrrd-dwi nrrd file containing an attached diffusion-weighted data
set
output-mind output NIfTI volume containing diffusion-weighted data set
in MiND format
D. Nrrd Tensor to MiND
The mind-nrrdtensor2mind program converts a second order diffusion tensor
volume from nrrd format to the NIfTI/MiND standard.
mind-nrrdtensor2mind.sh nrrd-tensor output-mind
nrrd-tensor nrrd file containing an attached second order diffusion
tensor data set
output-mind output NIfTI volume containing diffusion tensors in MiND
format
E. FSL DWI to MiND
The mind-fsldwi2mind program converts a diffusion-weighted data set from
FSL format to the NIfTI/MiND standard.
mind-fsldwi2mind.sh fsl-dwi fsl-bval fsl-bvec output-mind
fsl-dwi FSL's 4-D NIfTI diffusion-weighted image volume
fsl-bval FSL's plain text file containing a list of b-values
fsl-bvec FSL's plain text file containing a list of diffusion-
weighting gradient vectors
output-mind output NIfTI volume containing diffusion-weighted data set
in MiND format
F. FSL Tensor to MiND
The mind-fsltensor2mind program converts a diffusion tensor volume from
FSL format to the NIfTI/MiND standard.
mind-fsltensor2mind.sh fsl-tensor output-mind
fsl-tensor FSL's 4-D NIfTI diffusion tensor volume
output-mind output NIfTI volume containing diffusion tensors in MiND
format
G. FSL Eigen to MiND
The mind-fsleigen2mind program converts an FSL eigendecomposition to a
NIfTI/MiND diffusion tensor volume.
mind-fsleigen2mind.sh fsl-L1 fsl-L2 fsl-L3 fsl-V1 fsl-V2 fsl-V3
output-mind
fsl-L1 FSL's primary eigenvalue volume
fsl-L2 FSL's secondary eigenvalue volume
fsl-L3 FSL's tertiary eigenvalue volume
fsl-V1 FSL's primary eigenvector volume
fsl-V2 FSL's secondary eigenvector volume
fsl-V3 FSL's tertiary eigenvector volume
output-mind output NIfTI volume containing diffusion tensors in MiND
format
H. Get MiND Metadata
The mind-mind2xml program extracts NIfTI/MiND extended header information
as an XML document that conforms to the MiND XML Schema Definition
[http://www.vishalpatel.net/research/mind/mind-1.0.xsd].
mind-mind2xml.sh mind-file output-xml
mind-file any NIfTI/MiND file
output-xml the MiND metadata as XML
I. Set MiND Metadata
The mind-xml2mind program inserts NIfTI/MiND extended header information
from an XML document that conforms to the MiND XML Schema Definition
[http://www.vishalpatel.net/research/mind/mind-1.0.xsd]. The recipient
NIfTI volume will be converted into a MiND file if necessary; any existing
MiND header information will be overwritten.
mind-xml2mind.sh nifti-file xml-metadata output-mind
nifti-file any NIfTI/MiND file
xml-metadata the MiND metadata to be inserted as XML
output-mind the NIfTI/MiND file with metadata inserted
J. MiND Masker
The mind-masker program applies a mask to a NIfTI/MiND file.
mind-masker.sh [-n] mind-file mask-file output-mind
-n, --nan replace masked voxels with NaN instead of zero
mind-file any NIfTI/MiND file
mask-file a NIfTI volume with nonzero voxels marking the brain region
output-mind masked NIfTI/MiND volume
K. MiND Splitter
The mind-splitter program splits a NIfTI/MiND file into individual 3-D
NIfTI volumes along the vector (5th) dimension.
mind-splitter.sh mind-file output-list
mind-file any NIfTI/MiND file
output-list output file containing a list of the split NIfTI volumes
Attribution
If you use the MiND File Utilities in your work, please cite the following publication: