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transform-standard-space.md

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Transforming cells to standard space

To transform cell positions from the coordinate space of the raw data to that of another coordinate framework (usually the atlas).

cellfinder_cell_standard --cells /path/to/classified_cells.xml --transformation /path/to/control_point_file.nii --ref /path/to/reference_image.nii -o /path/to/output/directory -x 2 -y 2 -z 5

Arguments

Mandatory

  • --cells Path of the xml file containing cells to be transformed.
  • --transformation Path to the control point file (from niftyreg or cellfinder registration)
  • --ref Reference nii image, in the same space as the downsampled raw data
  • -o or --output-dir Output directory

{% hint style="warning" %} You must also specify the pixel sizes, see Specifying pixel size {% endhint %}

The following options can also be used:

  • --transform-all Transform all cell positions (including artifacts).
  • --registration-config To supply your own, custom registration configuration file.

Performance/debugging

  • -V or --verbose Increase verbosity of statements printed to console (all debug information is saved to file regardless of this flag)
  • --n-free-cpus The number of CPU cores on the machine to leave unused by the program to spare resources.

All other options (and their defaults) can be round by running:

cellfinder_cell_standard -h

``