cmd_run_3dAllineate

This is a legacy script and possibly contain errors. Please use
<code>cmd_run_ants_coreg</code> for faster and stable implementation
instead.

Defines storage standard for Read, process, and analyze
intracranial electroencephalography and deep-brain stimulation in 'RAVE',
a reproducible framework for analysis and visualization of iEEG
by Magnotti, Wang, and Beauchamp, (2020,
<doi:10.1016/j.neuroimage.2020.117341>).
Supports brain imaging data structure (BIDS)
<https://bids.neuroimaging.io> and native file structure to
ingest signals from 'Matlab' data files, hierarchical data format 5 (HDF5),
European data format (EDF), BrainVision core data format (BVCDF), or
BlackRock Microsystem (NEV/NSx); process images in
Neuroimaging informatics technology initiative (NIfTI) and
'FreeSurfer' formats, providing brain imaging normalization to template
brain, facilitating 'threeBrain' package for comprehensive electrode
localization via 'YAEL' (your advanced electrode localizer) by Wang,
Magnotti, Zhang, and Beauchamp
(2023, <doi:10.1523/ENEURO.0328-23.2023>).

Zhengjia Wang

ravecore

Core File Structures and Workflows for 'RAVE'

Xiang Zhang

John Magnotti

Michael Beauchamp

Trustees of the University of Pennsylvania 

cmd_run_3dAllineate function

<dl><dt>subject</dt>
<dd>subject ID</dd>
<dt>ct_path, mri_path</dt>
<dd>absolute paths to 'CT' and 'MR' image files</dd>
<dt>overwrite</dt>
<dd>whether to overwrite existing files</dd>
<dt>command_path</dt>
<dd>path to 'AFNI' home</dd>
<dt>dry_run</dt>
<dd>dry-run flag</dd>
<dt>verbose</dt>
<dd>whether to print out script</dd></dl>

Arguments

Align images using 'AFNI' — cmd_run_3dAllineate

<dl>

<dt>subject</dt>
<dd>subject ID</dd>


<dt>ct_path, mri_path</dt>
<dd>absolute paths to 'CT' and 'MR' image files</dd>


<dt>overwrite</dt>
<dd>whether to overwrite existing files</dd>


<dt>command_path</dt>
<dd>path to 'AFNI' home</dd>


<dt>dry_run</dt>
<dd>dry-run flag</dd>


<dt>verbose</dt>
<dd>whether to print out script</dd>

</dl>

cmd_run_3dAllineate: Align images using 'AFNI'

Description

Usage

Arguments