
FSLRvextract
FSLRvextract.Rd
Extracts vertex-wise surface-based measures for each subject from HCP, fMRIprep or XCP-D preprocessed directories, and stores it as a single .RDS file.
Usage
FSLRvextract(
sdirpath = "./",
filename,
dscalar,
subj_ID = TRUE,
silent = FALSE,
VWR_check = TRUE
)
Arguments
- sdirpath
A string object containing the path to the HCP or fMRIprep preprocessed directory. Default is the current working directory ("./").
- filename
A string object containing the desired name of the output RDS file. Default is 'fslr32k.rds' in the R temporary directory (tempdir()).
- dscalar
A string object containing the filename suffix of the dscalar file. These dscalar files are named differently depending on the preprocessing pipeline used. Examples of filename suffixes are shown below
.thickness_MSMAll.32k_fs_LR.dscalar.nii
(HCP MSMAll pipeline).sulc_MSMAll.32k_fs_LR.dscalar.nii
(HCP MSMAll pipeline).thickness.32k_fs_LR.dscalar.nii
(HCP legacy pipeline).sulc.32k_fs_LR.dscalar.nii
(HCP legacy pipeline)_space-fsLR_den-91k_thickness.dscalar.nii
(fMRIprep; using the--cifti-output 91k
flag)_space-fsLR_den-91k_curv.dscalar.nii
(fMRIprep; using the--cifti-output 91k
flag)_space-fsLR_den-91k_sulc.dscalar.nii
(fMRIprep; using the--cifti-output 91k
flag)
- subj_ID
A logical object to determine whether to return a list object containing both subject ID and data matrix.
- silent
A logical object to determine whether messages will be silenced. Set to 'FALSE' by default
- VWR_check
A boolean object specifying whether to check and validate system requirements. Default is TRUE.
Value
A .RDSfile with a list containing 1. the list of subject IDs (first element) and 2. a surface data matrix object (second element), or only a data matrix object. The matrix has N subjects x M vertices dimensions and can be readily used by VertexWiseR statistical analysis functions. Each row corresponds to a subject (in the order they are listed in the folder) and contains the left to right hemispheres' vertex-wise values.