"xifti" from dataAssembles cortical data, subcortical data, and/or surface geometry to form a
"xifti". The inputs must be data objects (vectors, matrices or
arrays, depending on the argument).
as.xifti(
cortexL = NULL,
cortexL_mwall = NULL,
cortexR = NULL,
cortexR_mwall = NULL,
mwall_values = c(NA, NaN),
subcortVol = NULL,
subcortLabs = NULL,
subcortMask = NULL,
surfL = NULL,
surfR = NULL,
col_names = NULL,
HCP_32k_auto_mwall = TRUE,
validate = TRUE
)as_xifti(
cortexL = NULL,
cortexL_mwall = NULL,
cortexR = NULL,
cortexR_mwall = NULL,
mwall_values = c(NA, NaN),
subcortVol = NULL,
subcortLabs = NULL,
subcortMask = NULL,
surfL = NULL,
surfR = NULL
)
as.cifti(
cortexL = NULL,
cortexL_mwall = NULL,
cortexR = NULL,
cortexR_mwall = NULL,
mwall_values = c(NA, NaN),
subcortVol = NULL,
subcortLabs = NULL,
subcortMask = NULL,
surfL = NULL,
surfR = NULL
)
as_cifti(
cortexL = NULL,
cortexL_mwall = NULL,
cortexR = NULL,
cortexR_mwall = NULL,
mwall_values = c(NA, NaN),
subcortVol = NULL,
subcortLabs = NULL,
subcortMask = NULL,
surfL = NULL,
surfR = NULL
)
A "xifti"
Left cortex data and ROI. Each must be a data matrix or vector.
If cortexL_mwall is not provided, cortexL should have data for
all vertices on the left cortical surface (\(V_L \times T\) data matrix). There
will not be a mask for the medial wall. Not providing the medial wall mask
is appropriate for ".dlabels.nii" files where the medial wall may have its
own label and therefore should not be treated as missing data.
If cortexL_mwall is provided, cortexL should either have data
for all vertices on the left cortical surface (\(V_L \times T\) data matrix, with
filler values e.g. 0 or NaN for medial wall vertices), or have data
only for non-medial wall vertices (\((V_L - mwall_L) \times T\) data matrix).
The medial wall mask will be the 0 values in cortexL_mwall.
The medial wall mask should be provided whenever the medial wall should be
treated as missing data.
Since the unmasked cortices must have the same number of vertices,
V_L should match V_R.
Right cortex data and ROI. Each must be a data matrix or vector.
If cortexR_mwall is not provided, cortexR should have data for
all vertices on the right cortical surface (\(V_R \times T\) data mre
will not be a mask for the medial wall. Not providing the medial wall mask
is appropriate for ".dlabels.nii" files where the medial wall may have its
own label and therefore should not be treated as missing data.
If cortexR_mwall is provided, cortexR should either have data
for all vertices on the right cortical surface (\(V_R \times T\) data matrix, with
filler values e.g. 0 or NaN for medial wall vertices), or have data
only for non-medial wall vertices (\((V_R - mwall_R) \times T\) data matrix).
The medial wall mask will be the 0 values in cortexR_mwall.
The medial wall mask should be provided whenever the medial wall should be
treated as missing data.
Since the unmasked cortices must have the same number of vertices,
V_L should match V_R.
If cortex[L/R]_mwall was not provided, or if it
was invalid (i.e. bad length or all TRUE), the medial wall mask will
be inferred from rows in cortex[L/R] that are constantly one of these
values. Default: c(NA, NaN). If NULL, do not attempt to infer
the medial wall from the data values. NULL should be used if NA
or NaN are legitimate values that non-medial wall vertices might
take on.
subcortVol represents the
data values of the subcortex. It is either a 3D/4D numeric array
(\(i \times j \times k \times T\)), or a vectorized matrix (\(V_S\) voxels by \(T\)
measurements). If it's vectorized, the voxels should be in spatial order
(\(i\) index increasing fastest, then \(j\), then \(k\)).
subcortLabs represents the brainstructure labels of each voxel: see
substructure_table. It is either a 3D data array
(\(i \times j \times k\)) of integer brainstructure indices, or a \(V_S\) length
vector in spatial order with brainstructure names as factors or integer
indices. The indices should be 3-22 (1 and 2 correspond to left and right
cortex, respectively) or 1-19 (cortex labels omitted), with 0 representing
out-of-mask voxels.
subcortMask is logical 3D data array (\(i \times j \times k\)) where TRUE
values indicate subcortical voxels (in-mask). If it is not provided, the
mask will be inferred from voxels with labels 0, NA, or
NaN in subcortLabs. If subcortLabs are vectorized and
subcortMask is not provided, the mask cannot be inferred so an error
will occur.
(Optional) Surface geometries for the left or right cortex.
Can be a surface GIFTI file path or "surf" object; see
make_surf for a full description of valid inputs.
Names of each measurement/column in the data.
If left and/or right cortex data is provided, and
the number of vertices matches that of the HCP 32k mesh (29696 on left, and
29716 on right), should the medial wall masks be added to the "xifti"
if not provided? Default: TRUE.
Validate that the result is a "xifti"? Default:
TRUE. If FALSE, the result may not be properly formatted
if the inputs were invalid.
Each data or surface component is optional. Metadata components
(cortex[L/R]_mwall, subcortLabs, and subcortMask) will
be ignored if its corresponding data component is not provided. If no data or
surface components are provided, then the template_xifti will
be returned.
If cortical data are provided without a corresponding medial wall mask, or
if the provided mask is invalid or empty, then the medial wall will be
inferred from data rows that are constantly a value in mwall_values.
But if mwall_values is NULL, no attempt to infer the medial
wall will be made and the medial wall metadata entry will be NULL.
The total number of grayordinates will be \(G = (V_L - mwall_L) + (V_R - mwall_R) + V_S\): \(V_L - mwall_L\) left vertices, \(V_R - mwall_R\) right vertices and \(V_S\) subcortical voxels. \(T\), the total number of measurements (columns of data), must be the same for each brainstructure.
Other reading:
info_cifti(),
load_parc(),
load_surf(),
read_cifti(),
read_surf(),
read_xifti2()