xcp_d.utils.write_save module

Utilities to read and write nifiti and cifti data.

xcp_d.utils.write_save.get_cifti_intents()[source]

Return a dictionary of CIFTI extensions and associated intents.

Copied from https://www.nitrc.org/projects/cifti/ PDF.

xcp_d.utils.write_save.read_gii(surf_gii)[source]

Use nibabel to read surface file.

xcp_d.utils.write_save.read_ndata(datafile, maskfile=None)[source]

Read nifti or cifti file.

Parameters:

  • datafile (str) – nifti or cifti file

  • maskfile (str) – Path to a binary mask. Unused for CIFTI data.

Outputs:

data ((TxS) numpy.ndarray) – Vertices or voxels by timepoints.

xcp_d.utils.write_save.write_gii(datat, template, filename, hemi)[source]

Use nibabel to write surface file.

Parameters:

  • datatt (numpy.ndarray) – vector

  • template (str) – real file loaded with nibabel to get header and filemap

  • filename (str) – name of the output

Return type:

filename

xcp_d.utils.write_save.write_ndata(data_matrix, template, filename, mask=None, TR=1)[source]

Save numpy array to a nifti or cifti file.

Parameters:

  • data matrix ((SxT) numpy.ndarray) – The array to save to a file.

  • template (str) – Path to a template image, from which header and affine information will be used.

  • filename (str) – Name of the output file to be written.

  • mask (str or None, optional) – The path to a binary mask file. The mask is only used for nifti files- masking is not supported in ciftis. Default is None.

  • TR (float) – Repetition time of the BOLD run, in seconds.

Returns:

filename – The name of the generated output file. Same as the “filename” input.

Return type:

str