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Output files#

brainreg will create a number of output files. Many of these are for use with other software (e.g., brainglobe-segmentation 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. brainglobe-segmentation.

  • 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 downsampled.tiff.

  • registered_hemispheres.tiff - Same as downsampled_atlas.tiff but for the image coding the hemispheres.

  • volumes.csv A 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.tiff but additional image channels, processed when using the -d flag.

  • niftyreg This directory contains the intermediate files used by the niftyreg registration. Created when using the --debug flag.

  • registered_atlas_original_orientation.tiffSame as registered_atlas.tiff, but without the reorientation to the atlas orientation. Created when using the --save-original-orientation flag.