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.
--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.