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ciftiTools (version 0.1.6.0)

info_cifti: Get CIFTI metadata

Description

Get CIFTI metadata from the NIFTI header and XML using the Connectome Workbench command -nifti-information. The information is formatted as the meta component in a "xifti" object (see template_xifti), and includes:

  1. medial wall masks for the left and right cortex

  2. the subcortical labels (ordered spatially)

  3. the subcortical mask

  4. other NIFTI intent-specific metadata

Usage

info_cifti(cifti_fname, wb_path = NULL)
infoCIfTI(cifti_fname, wb_path = NULL)
infocii(cifti_fname, wb_path = NULL)

Arguments

cifti_fname

File path of CIFTI-format data (ending in ".d*.nii").

wb_path

(Optional) Path to Connectome Workbench folder or executable. If not provided, should be set with ciftiTools.setOption("wb_path", "path/to/workbench").

Value

The metadata component of a "xifti" for the input CIFTI file

Label Levels

xifti$meta$subcort$labels is a factor with the following levels:

  1. Cortex-L

  2. Cortex-R

  3. Accumbens-L

  4. Accumbens-R

  5. Amygdala-L

  6. Amygdala-R

  7. Brain Stem

  8. Caudate-L

  9. Caudate-R

  10. Cerebellum-L

  11. Cerebellum-R

  12. Diencephalon-L

  13. Diencephalon-R

  14. Hippocampus-L

  15. Hippocampus-R

  16. Pallidum-L

  17. Pallidum-R

  18. Putamen-L

  19. Putamen-R

  20. Thalamus-L

  21. Thalamus-R

These correspond to the same structures as given by ft_read_cifti in the cifti-matlab MATLAB toolbox.

Connectome Workbench Requirement

This function uses a system wrapper for the 'wb_command' executable. The user must first download and install the Connectome Workbench, available from https://www.humanconnectome.org/software/get-connectome-workbench . The wb_path argument is the full file path to the Connectome Workbench folder. (The full file path to the 'wb_cmd' executable also works.)

Details

Additional metadata depends on the type of CIFTI file:

  1. "dtseries"

    1. time_start Start time

    2. time_step The TR

    3. time_unit Unit of time

  2. "dscalar"

    1. names Name of each data column

  3. "dlabels"

    1. names( Names of each data column.)

    2. labels( List of \(L x 5\) data.frames. Row names are the label names. Column names are Key, Red, Green, Blue, and Alpha. List entry names are the names of each data column.)