cmind.utils.nifti_utils

NIFTI Handling Utilities A series of utilities for working with NIFTI files

cmind_save_nii_mod_header

Functions

cmind_save_nii_mod_header(old_nii, data, ...) save data to out_name.nii.gz, reusing the nifti header from old_nii with
round_affine_to_axial(nii_filename) Resets the affine to axial (preserving sign)
cmind.utils.nifti_utils.cmind_save_nii_mod_header(old_nii, data, out_name, nii_type=None, cal_range=None)[source]
save data to out_name.nii.gz, reusing the nifti header from old_nii with
appropriate modifications to image dimensions
Parameters:

old_nii : Nifti1Image

Nifti-1 image as read in by nibabel

data : ndarray

array of image data to write to out_name

out_name : str

filename for the output image. File type will be determined by the extension given here (e.g. myfile.nii.gz would write a gzipped Nifti-1 image)

nii_type : str, optional

data type for the output image. if unspecified, will be whatever was in old_nii

cal_range : list or tuple

two-element list of the intensities to store in the cal_min and cal_max fields of the nifti file

Notes

Write out an image file containing the data in data with header information copied from old_nii. If old_nii is 3D, but data is 4D, the image dimensions will be updated accordingly. Whether the output is NIFTI or NIFTI-GZ will be determined by the extension of out_name

cmind.utils.nifti_utils.round_affine_to_axial(nii_filename)[source]

Resets the affine to axial (preserving sign)