fill_atlas_with_stats: Populates parcel-wise statistics from an atlas or set of...

In UNCDEPENdLab/fmri.pipeline: Analysis of fMRI Data on HPC clusters

Populates parcel-wise statistics from an atlas or set of clusters back into NIfTIs in the original space

Description

Populates parcel-wise statistics from an atlas or set of clusters back into NIfTIs in the original space

Usage

fill_atlas_with_stats(
  atlas_nifti,
  stat_dt,
  stat_cols = c("t", "p"),
  stat_labels = NULL,
  atlas_col = "atlas_value",
  split_on = NULL,
  stack_along = NULL,
  img_prefix = "atlasfill",
  out_dir = getwd(),
  overwrite = FALSE,
  afni_dir = "~/abin"
)

Arguments

atlas_nifti	The filename of the NIfTI image containing atlas values to match against stat_dt
stat_dt	a data.table object containing the statistics to write to parcels in the atlas
stat_cols	The column names in stat_dt that should be written to parcels in the NIfTI. By default, each column will be written as a separate sub-brik (i.e., along the 4th dimension of the NIfTI), but this can be modified by the stack_along argument.
stat_labels	A character vector of the same length as stat_cols giving the names for each statistic that will be used in the output NIfTI files. By default the labels are simply the stat_cols.
atlas_col	The column name in stat_dt containing the integer values that correspond to parcel numbers in atlas_nifti. This is used to map the statistics back into the atlas_nifti space.
split_on	An optional character vector that yields an output image for each unique combination of splits. For example, if stat_dt contains multiple GLM contrasts in "contrast" and multiple subjects in "subject", then split_on = c("contrast", "subject") would yield a separate NIfTI with the statistics for each contrast and subject. This allows the fill operation to be repeated over an arbitrarily stacked dataset.
stack_along	By default, this is NULL, in which case each output NIfTI will have a sub-briks for each statistic in stat_cols. Alternatively, stack_along can be a character vector of other columns in stat_dt. In this case,
img_prefix	A string prefixing the filenames for all NIfTIs
out_dir	The directory in which to place the stat NIfTIs. If not present, it will be created
overwrite	Whether to allow existing files to be overwritten. Default: FALSE
afni_dir	The location of your AFNI installation, which is used to cobble together NIfTIs

UNCDEPENdLab/fmri.pipeline documentation built on April 3, 2025, 3:21 p.m.