get_NIFTI_ROI_masks: Get NIFTI ROI masks
In neuroconductor/fMRIscrub: Scrubbing and Other Data Cleaning Routines for fMRI

Get NIFTI ROI masks

1	get_NIFTI_ROI_masks(nii_labels, ROI_noise = c("wm_cort", "csf"))

nii_labels

I by J by K NIFTI object or array (or file path to the NIFTI) which contains the corresponding labels to each voxel in nii. Values should be according to this table: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorLUT . In the HCP, the corresponding file is "ROIs/Atlas_wmparc.2.nii.gz".

ROI_noise

A list of numeric vectors. Each entry should represent labels in nii_labels belonging to a single noise ROI, named by that entry's name. Or, this can be a character vector of at least one of the following: "wm_cort" (cortical white matter), "wm_cblm" (cerebellar white matter), "csf" (cerebrospinal fluid). In the latter case, these labels will be used:

"wm_cort": c(3000:4035, 5001, 5002)
"wm_cblm": c(7, 46)
"csf": c(4, 5, 14, 15, 24, 31, 43, 44, 63, 250, 251, 252, 253, 254, 255))

These default ROIs are based on this forum post: https://www.mail-archive.com/hcp-users@humanconnectome.org/msg00931.html

Default: c("wm_cort", "csf")

The ROIs

neuroconductor/fMRIscrub documentation built on Dec. 22, 2021, 1:10 a.m.