format_data

Format data for pscrub and CompCor

internal

Supports fMRI (functional magnetic resonance imaging)
analysis tasks including reading in 'CIFTI', 'GIFTI' and
'NIFTI' data, temporal filtering, nuisance regression, and
aCompCor (anatomical Components Correction) (Muschelli et al.
(2014) <doi:10.1016/j.neuroimage.2014.03.028>).

Amanda Mejia

fMRItools

Routines for Common fMRI Processing Tasks

Damon Pham

Mark Fiecas

format_data function

<dl><dt>X</dt>
<dd>description</dd>
<dt>ROI_data, ROI_noise</dt>
<dd>description</dd>
<dt>noise_nPC</dt>
<dd>The number of principal components to compute for each noise
ROI. Alternatively, values between 0 and 1, in which case they will
represent the minimum proportion of variance explained by the PCs used for
each noise ROI. The smallest number of PCs will be used to achieve this
proportion of variance explained.
Should be a list or numeric vector with the same length as <code>ROI_noise</code>.
It will be matched to each ROI based on the name of each entry, or if the
names are missing, the order of entries. If it is an unnamed vector, its
elements will be recycled. Default: <code>5</code> (compute the top 5 PCs for
each noise ROI).</dd>
<dt>noise_erosion</dt>
<dd>The number of voxel layers to erode the noise ROIs by.
Should be a list or numeric vector with the same length as <code>ROI_noise</code>.
It will be matched to each ROI based on the name of each entry, or if the
names are missing, the order of entries. If it is an unnamed vector, its
elements will be recycled. Default: <code>NULL</code>, which will use a value of
0 (do not erode the noise ROIs).</dd></dl>

Arguments

Format data for pscrub and CompCor — format_data

<dl>

<dt>X</dt>
<dd>description</dd>


<dt>ROI_data, ROI_noise</dt>
<dd>description</dd>


<dt>noise_nPC</dt>
<dd>The number of principal components to compute for each noise
ROI. Alternatively, values between 0 and 1, in which case they will
represent the minimum proportion of variance explained by the PCs used for
each noise ROI. The smallest number of PCs will be used to achieve this
proportion of variance explained.
Should be a list or numeric vector with the same length as <code>ROI_noise</code>.
It will be matched to each ROI based on the name of each entry, or if the
names are missing, the order of entries. If it is an unnamed vector, its
elements will be recycled. Default: <code>5</code> (compute the top 5 PCs for
each noise ROI).</dd>


<dt>noise_erosion</dt>
<dd>The number of voxel layers to erode the noise ROIs by.
Should be a list or numeric vector with the same length as <code>ROI_noise</code>.
It will be matched to each ROI based on the name of each entry, or if the
names are missing, the order of entries. If it is an unnamed vector, its
elements will be recycled. Default: <code>NULL</code>, which will use a value of
0 (do not erode the noise ROIs).</dd>

</dl>

format_data: Format data for pscrub and CompCor

Description

Usage

Value

Arguments