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: