get_NIFTI_ROI_masks

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

get_NIFTI_ROI_masks function

<dl><dt>nii_labels</dt>
<dd>\(I\) by \(J\) by \(K\)
NIFTI object or array (or file path to the NIFTI) which
contains the corresponding labels to each voxel in <code>nii</code>. 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".</dd>
<dt>ROI_noise</dt>
<dd>A list of numeric vectors. Each entry should represent labels
in <code>nii_labels</code> 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:
<code>"wm_cort"</code> (cortical white matter), <code>"wm_cblm"</code> (cerebellar white
matter), <code>"csf"</code> (cerebrospinal fluid). In the latter case, these labels
will be used:
<dl>
<dt><code>"wm_cort"</code></dt>
<dd><code>c(3000:4035, 5001, 5002)</code></dd></dl></dd><dt><code>"wm_cblm"</code></dt>
<dd><code>c(7, 46)</code></dd><dt><code>"csf"</code></dt>
<dd><code>c(4, 5, 14, 15, 24, 31, 43, 44, 63, 250, 251, 252, 253, 254, 255))</code></dd>
</dl>These default ROIs are based on this forum post:
https://www.mail-archive.com/hcp-users@humanconnectome.org/msg00931.html
Default: <code>c("wm_cort", "csf")</code>

Arguments

Get NIFTI ROI masks — get_NIFTI_ROI_masks

<dl>

<dt>nii_labels</dt>
<dd>\(I\) by \(J\) by \(K\)
NIFTI object or array (or file path to the NIFTI) which
contains the corresponding labels to each voxel in <code>nii</code>. 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".</dd>


<dt>ROI_noise</dt>
<dd>A list of numeric vectors. Each entry should represent labels
in <code>nii_labels</code> 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:
<code>"wm_cort"</code> (cortical white matter), <code>"wm_cblm"</code> (cerebellar white
matter), <code>"csf"</code> (cerebrospinal fluid). In the latter case, these labels
will be used:
<dl>
<dt><code>"wm_cort"</code></dt>
<dd><code>c(3000:4035, 5001, 5002)</code></dd>

<dt><code>"wm_cblm"</code></dt>
<dd><code>c(7, 46)</code></dd>

<dt><code>"csf"</code></dt>
<dd><code>c(4, 5, 14, 15, 24, 31, 43, 44, 63, 250, 251, 252, 253, 254, 255))</code></dd>


</dl>

These default ROIs are based on this forum post:
https://www.mail-archive.com/hcp-users@humanconnectome.org/msg00931.html
Default: <code>c("wm_cort", "csf")</code></dd>

</dl>

get_NIFTI_ROI_masks: Get NIFTI ROI masks

Description

Usage

Value

Arguments