[Export] Menu
Use [Export] to save per-voxel diffusion metrics, fiber orientations, ODFs, attached slices, and template-aligned MNI volumes from the open FIB session, or to apply in-memory bias-field correction. Its entries build dynamically from the loaded FIB file and refresh automatically as volumes are added or removed under [Slices].
Menu items
Items appear in up to three separator-divided groups depending on the loaded FIB file:
| Menu item | Behavior |
|---|---|
metric... |
Saves the selected 3D metric or slice on the FIB voxel grid (mm spacing) as NIfTI (.nii.gz, .nii) or raw MATLAB .mat (default <fib_stem>_<metric>.nii.gz). External slices with different grid dimensions are resampled onto the FIB grid using their active registration. |
Exports all resolved per-voxel unit fiber orientation vectors on the FIB grid as a 4D NIfTI volume (.nii.gz or .nii, default <fib_stem>_fiber.nii.gz), ordered by fiber population and (x, y, z) components. |
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Exports per-voxel half-sphere orientation distribution functions on the FIB grid as a 4D NIfTI volume (.nii.gz or .nii, default <fib_stem>_odfs.nii.gz). Shown only when ODF data was saved in the FIB file during reconstruction. |
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metric in mni... |
Warps the scalar map from a native-space FIB into MNI template space and saves a 3D NIfTI volume (.nii.gz or .nii); omitted for QSDR/template FIBs and directional / data. Rename <fib_stem>_<metric>.nii.gz (for example, .mni.nii.gz) and avoid .mat, which saves unwarped data. |
Estimates and removes smooth intensity bias across in-memory iso, fiber anisotropy (qa/fa), and restricted diffusion maps immediately without a dialog (shown only when iso is present). Changes stay in memory until saved via [File][Save FIB As…], leave DTI maps unchanged, and repeat if clicked again. |
Dynamic metric entries
Available metric rows depend on the reconstruction method, saved scalar maps, template alignment, and attached slices:
| Menu item | Behavior |
|---|---|
| Exports quantitative anisotropy as a 3D scalar map, serving as the primary fiber anisotropy volume in multi-fiber GQI and QSDR reconstructions. | |
| Exports primary fractional anisotropy as a 3D scalar map in single-fiber DTI and 2D histology FIB reconstructions. | |
Exports the isotropy-normalized quantitative anisotropy ratio as a 3D scalar map, automatically computed for multi-fiber FIB files that include an iso volume. |
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| Exports the isotropic diffusion component from GQI or QSDR reconstruction as a 3D scalar map; its presence also enables . | |
Exports diffusion tensor fractional anisotropy (0–1) as a 3D scalar map when tensor metrics were saved alongside multi-fiber reconstruction. |
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Exports diffusion tensor mean diffusivity ((λ₁ + λ₂ + λ₃) / 3, in 10⁻³ mm²/s) as a 3D scalar map when saved during reconstruction. |
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Exports axial diffusivity (principal tensor eigenvalue λ₁, in 10⁻³ mm²/s) as a 3D scalar map when saved during reconstruction. |
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Exports radial diffusivity (mean perpendicular diffusivity (λ₂ + λ₃) / 2, in 10⁻³ mm²/s) as a 3D scalar map when saved during reconstruction. |
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Exports the second diffusion tensor eigenvalue diffusivity (λ₂, in 10⁻³ mm²/s) as a 3D scalar map when saved during reconstruction. |
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Exports the third diffusion tensor eigenvalue diffusivity (λ₃, in 10⁻³ mm²/s) as a 3D scalar map when saved during reconstruction. |
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| Exports generalized fractional anisotropy computed from the orientation distribution function as a 3D scalar map when saved during reconstruction. | |
| Exports the restricted diffusion imaging map as a 3D scalar volume when saved during GQI or QSDR reconstruction. | |
Exports the non-restricted diffusion imaging map at sampling length 0.2 (along with any additional nrdi*L... sampling-length maps saved during reconstruction). |
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| Exports fiber helix angle (in degrees) as a 3D scalar map when saved during tensor reconstruction. | |
Exports individual symmetric diffusion tensor components (mm²/s) as 3D maps when tensor output was enabled during reconstruction. |
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| Exports raw histology image intensity as a scalar volume when saved in histology FIB reconstructions. | |
Exports the 3D relative tissue volume (Jacobian determinant) map normalized around 1.0 relative to the template. Included directly in QSDR FIBs and available on native-space FIBs once template normalization has been computed. |
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Exports the stored directional color map on the FIB voxel grid as a 24-bit RGB 3D NIfTI volume (.nii.gz or .nii; .mat output is not supported). |
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| Exports built-in anatomical or white-matter template volumes attached to template-aligned FIB sessions onto the FIB diffusion grid. | |
slice_name... |
Exports auto-loaded companion BIDS images, embedded modalities, or external slices added under [Slices] onto the FIB diffusion grid. Use [Slices][Save Slices as…] to save an inserted slice on its own native voxel grid instead. |
Coordinate, registration, and bias-field cautions
Wait for background slice registration to finish before exporting external volumes added under [Slices], and export custom slices to FIB space first (or save them on their native grid via [Slices][Save Slices as…]) rather than warping unaligned custom grids directly with metric in mni.... Give MNI exports a .mni.nii.gz suffix so they do not overwrite native maps and are recognized automatically in Differential Tractography.
Related exports in other menus
Other Fiber Tracking exports live in their respective menus: modified .fz files and workspaces in File, tract bundles, density maps, and connectivity tables in Tracts, ROIs and voxel tables in Regions and Regions Misc, and native-grid slices or DICOMs in Slices. Stereotactic .dv.csv trajectories are saved from Devices, screenshots, videos, and 3D .obj/.glb meshes from Screen, and multi-subject batch exports in Export Data.