brainreg will create a number of output files. Many of these are for use with other software (e.g., brainreg-segment and cellfinder), but they may be useful for your own software.
N.B. This is not an exhaustive list, as brainreg has many options which may create additional files.
boundaries.tiff- A 3D tiff image of the atlas boundaries, transformed to the space of the raw data.
brainreg_DATE_TIME.log- A log file detailing the registration process. Useful for debugging and raising issues.
brainreg.json- A record of all the input parameters, used by other software, e.g. brainreg-segment.
deformation_field_0.tiff- A 3D tiff describing the deformation from raw data space to atlas space, in the first dimension (based on the supplied orientation and voxel sizes).
deformation_field_1.tiff- Deformation in the second dimension.
deformation_field_2.tiff- Deformation in the third dimension.
downsampled.tiff- The raw data, reoriented to the atlas orientation, and downsampled to the atlas resolution.
downsampled_standard_IMAGE_NAME.tiff- The raw data, transformed to the atlas (standard) space.
registered_atlas.tiff- The atlas annotations image, warped to the raw data space. N.B. This is the reoriented, downsampled space of
registered_hemispheres.tiff- Same as
downsampled_atlas.tiffbut for the image coding the hemispheres.
volumes.csvA CSV file outlining the volumes of each brain area, based on the atlas registration.
Some other files may also be created:
downsampled_IMAGE_NAME.tiff- Similar to
downsampled.tiffbut additional image channels, processed when using the
niftyregThis directory contains the intermediate files used by the niftyreg registration. Created when using the
registered_atlas.tiff, but without the reorientation to the atlas orientation. Created when using the