Make "xifti" subcortical components

Coerce subcortical data into valid entries for xifti$data$subcort and xifti$meta$subcort. The data arguments can be matrices/arrays or NIFTI file paths. If the mask is not provided, it will be inferred from the labels.

make_subcort(vol, labs, mask = NULL, validate_mask = FALSE)

represents the data values of the subcortex. It is either a NIFTI file path, 3D/4D data array (\(i x j x k x T\)), or a vectorized data matrix (\(V_S\) voxels x \(T\) measurements). If it's vectorized, the voxels should be in spatial order.


represents the brainstructure labels of each voxel: see substructure_table. It is either a NIFTI file path, a 3D data array (\(i x j x k\)) of numeric brainstructure indices, or a \(V_S\) length vector in spatial order with brainstructure names as factors or integer indices. The indices should be 3-21 (2 and 3 correspond to left and right cortex, respectively) or 1-19 (cortex labels omitted), with 0 representing out-of-mask voxels.


is a NIFTI file path or logical 3D data array (\(i x j x k\)) where TRUE values indicate subcortical voxels (in-mask). If it is not provided, the mask will be inferred from voxels with labels 0 or NA in subcortLabs. If subcortLabs are vectorized and subcortMask is not provided, the mask cannot be inferred so an error will occur.


If mask is provided, set this to TRUE to check that the mask only removes voxels with NA and 0 values in vol and labs. Default: FALSE (saves time).


To read in the labels as the primary data, use the labels NIFTI for both vol and labs.


A list with components "data", "labels", "mask", and "trans_mat". The first two will be vectorized and ordered spatially.

The volume can be recovered using: vol <- unmask_vol(data, mask, fill=NA) labs <- unmask_vol(labels, mask, fill=0)

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.

  • make_subcort
Documentation reproduced from package ciftiTools, version, License: GPL-3

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