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GM_WM_Normalize brick

Normalises only the grey or/and white matter from a set of images

The GM_WM_Normalize brick is equivalent to the Normalize12 brick from the mia_processes library, with an additional filter (in_filter parameter) for grey and/or white matter, applied to the apply_to_files input parameter [1]. A list of native space probability maps (apply_to_files parameter) and an inverse deformation field (deformation_file parameter) may have been, for example, obtained after a previous segmentation. The jobtype input parameter is therefore fixed to write.

The in_filter parameter can take the following values:

  • GM (grey matter images will be selected before to be normalised).

  • WM (white matter images will be selected before to be normalised).

  • GM & WM (grey and white matter images will be selected before to be normalised).

  • GM + WM (grey and white matter images will be selected and then added together before to be normalised).

For the deformation_file, apply_to_files, write_bounding_box, write_voxel_sizes, write_interp input parameters and normalized_files output parameter, please see the Normalize12 brick of the mia_processes library.