BDP: Output

BDP writes out many different files during the processing. Output files are saved in the directory containing the bfc file, unless --output-subdir flag is used to defined output sub-directory. The table below describes different output files. Most image volumes are saved in NIfTI-1 format with “RAS” convention, i.e. the most rapidly increasing voxel index increases along Right side of subject, followed by Anterior side and then by Superior side of the subject. Please see supported file-formats for more details about file-formats.

Important note: The output filenames, as explained below, are chosen such that they are self-descriptive. However, if a file with the same name already exists then BDP will overwrite the file without any warnings. Accidental overwriting of output files can be avoided by using flag --output-subdir which changes the default output directory.

In the following, fileprefix is the bias-field corrected file’s prefix (e.g. “testsubj” for the file “testsubj.bfc.nii.gz”), dMRI refers to the diffusion MRI, and sMRI refers to the structural MRI.

dMRI Distortion Correction and Co-Registration
Filename Description
fileprefix.BDPSummary.txt A txt file summarizing all the processing with references. It also saves the command used for future reference.
fileprefix.dwi.RAS.nii.gz Diffusion weighted images in NIfTI format
fileprefix.dwi.RAS.bmat B-matrices in plaintext format, in voxel (image) space
fileprefix.dwi.RAS.bvec B-vectors in plaintext format, in voxel (image) space
fileprefix.dwi.bval B-values in plaintext format
fileprefix.dwi.RAS.mask.nii.gz Mask for b=0 image used for co-registration. Not generated when --dwi-mask is used.
fileprefix.dwi.RAS.correct.nii.gz Diffusion weighted images corrected for distortion
fileprefix.dwi.RAS.correct.distortion.map.nii.gz Distortion map (saved in units of voxels in diffusion image coordinates)
fileprefix.bfc.D_coord.rigid_registration_result.mat Rigid registration parameters (4×4 affine matrix)
fileprefix.bfc.D_coord.nii.gz BFC image in Diffusion coordinates
fileprefix.dwi.RAS.correct.0_diffusion.T1_coord.nii.gz b=0 image in T1 coordinates
fileprefix.dwi.RAS.correct.mask.fieldmap_overlay..png PNG images showing overlay of fieldmap and b=0 image. Generated only when --fieldmap-correction is used. See Fieldmap flag for more details.
Diffusion Tensor Estimation
Filename Description
fileprefix.dwi.RAS.correct.FA.T1_coord.nii.gz Fractional anisotropy (FA) image in sMRI space
fileprefix.dwi.RAS.correct.FA.color.T1_coord.nii.gz Color fractional anisotropy image in sMRI space
fileprefix.dwi.RAS.correct.MD.T1_coord.nii.gz Mean diffusivity (MD) image in sMRI space
fileprefix.dwi.RAS.correct.mADC.T1_coord.nii.gz Mean apparent diffusivity coefficient image in sMRI space (Model free)
fileprefix.dwi.RAS.correct.axial.T1_coord.nii.gz Axial diffusivity image in sMRI space
fileprefix.dwi.RAS.correct.radial.T1_coord.nii.gz Radial diffusivity image in sMRI space
fileprefix.dwi.RAS.correct.L2.T1_coord.nii.gz Second eigenvalue image in sMRI space
fileprefix.dwi.RAS.correct.L3.T1_coord.nii.gz Third eigenvalue image in sMRI space
fileprefix.dwi.RAS.correct.T1_coord.eig.nii.gz BrainSuite eigen file of eigenvalues and eigenvectors
fileprefix.tensor.T1_coord.bst This BST file can be opened in BrainSuite to easily load all the data required for tractography and connectivity analysis using diffusion tensors.
Orientation distribution function (ODF) estimation
Filename Description
fileprefix.dwi.RAS.correct.FRT_GFA.nii.gz Generalized fractional anisotropy for ODFs estimated by Funk-Radon Transform (FRT) in sMRI space.
fileprefix.dwi.RAS.correct.SH.FRT.<001…045>.T1_coord.nii.gz Spherical harmonic coefficients of ODFs estimated by Funk-Radon Transform (FRT) in sMRI space. These files are located in the FRT folder.
fileprefix.dwi.RAS.correct.SH.FRT.T1_coord.odf Plaintext list of FRT files for loading into BrainSuite for ODF visualization and analysis. This file is located in the FRT folder.
fileprefix.dwi.RAS.correct.SH.FRACT.<001…045>.T1_coord.nii.gz Spherical harmonic coefficients of ODFs estimated by Funk-Radon and Cosine Transform (FRACT) in sMRI space. These files are located in the FRACT folder.
fileprefix.dwi.RAS.correct.SH.FRACT.T1_coord.odf Plaintext list of FRACT files for loading into BrainSuite for ODF visualization and analysis. This folder is located in the FRACT folder.
fileprefix.dwi.RAS.correct.SH.3DSHORE.<001…045>.T1_coord.nii.gz Spherical harmonic coefficients of ODFs estimated by Simple Harmonic Oscillator based Reconstruction and Estimation (3D-SHORE) method in sMRI space. These files are located in the 3DSHORE folder.
fileprefix.dwi.RAS.correct.SH.3DSHORE.T1_coord.odf Plaintext list of 3DSHORE files for loading into BrainSuite for ODF visualization and analysis. This folder is located in the 3DSHORE folder.
fileprefix.FRACT.T1_coord.bst This BST file can be opened in BrainSuite to easily load all the data required for tractography and connectivity analysis using ODFs estimated by FRACT.
fileprefix.FRT.T1_coord.bst This BST file can be opened in BrainSuite to easily load all the data required for tractography and connectivity analysis using ODFs estimated by FRT.
ROI-wise Statistics
Filename Description
fileprefix.dwi.RAS.correct.FA.T1_coord.stat.csv ROI-wise statistics of Fractional anisotropy (FA) image in sMRI space
fileprefix.dwi.RAS.correct.MD.T1_coord.stat.csv ROI-wise statistics of Mean diffusivity (MD) image in sMRI space
fileprefix.dwi.RAS.correct.axial.T1_coord.stat.csv ROI-wise statistics of Axial diffusivity image in sMRI space
fileprefix.dwi.RAS.correct.radial.T1_coord.stat.csv ROI-wise statistics of Radial diffusivity image in sMRI space
fileprefix.dwi.RAS.correct.L2.T1_coord.stat.csv ROI-wise statistics of Second eigenvalue image in sMRI space
fileprefix.dwi.RAS.correct.L3.T1_coord.stat.csv ROI-wise statistics of Third eigenvalue image in sMRI space
fileprefix.BDP_ROI_MAP.xml XML file describing the map between ROI-id used in above statistics files and the voxel intensities found in the custom mask/label files. Generated only when --custom-diffusion-label or --custom-t1-label is used.

NOTE

Please note that list of files described above may not be exhaustive and depending on the input flags used more files may be written by BDP. If flag --output-diffusion-coordinate is used, a directory with name “diffusion_coord_outputs” will be created and all outputs in diffusion coordinates (tensor, odf and statistics files etc.) will be saved in the directory. Files with T1_coord in their filename implies that the data in the file has been transferred to T1-coordinate from diffusion-coordinate. Similarly, files with D_coord in their filename implies that the data in the file has been transferred to diffusion-coordinate from T1-coordinate. Please check description of all the available flags on BDP flags page to understand all output files.


The tensor and ODF files can be used for tractography as described here.