write.nifti2

Write header and data to a file in NIFTI v2 format.

Provides functions to read and write neuroimaging data in various file formats, with a focus on 'FreeSurfer' formats. This includes, but is not limited to, the following file formats: 1) MGH/MGZ/NIFTI format files, which can contain multi-dimensional images or other data. Typically they contain time-series of three-dimensional brain scans acquired by magnetic resonance imaging (MRI). They can also contain vertex-wise measures of surface morphometry data. The MGH format is named after the Massachusetts General Hospital, and the MGZ format is a compressed version of the same format. 2) 'FreeSurfer' morphometry data files in binary 'curv' format. These contain vertex-wise surface measures, i.e., one scalar value for each vertex of a brain surface mesh. These are typically values like the cortical thickness or brain surface area at each vertex. 3) Annotation file format. This contains a brain surface parcellation derived from a cortical atlas. 4) Surface file format. Contains a brain surface mesh, given by a list of vertices and a list of faces.

Tim Schc3<a4>fer

freesurferformats

Read and Write 'FreeSurfer' Neuroimaging File Formats

Tim Schäfer

Van Essen Lab 

Montreal Neurological Institute (MNI) 

write.nifti2 function

<dl><dt>filepath</dt>
<dd>the file to write. The extension should be '.nii' or '.nii.gz'.</dd>
<dt>niidata</dt>
<dd>array of numeric or integer data, with up to 7 dimensions. Will be written to the file with the datatype and bitpix specified in the 'niiheader' argument.</dd>
<dt>niiheader</dt>
<dd>an optional NIFTI v2 header that is suitable for the passed 'niidata'. If not given, one will be generated with <code>ni2header.for.data</code>.</dd>
<dt>extensions</dt>
<dd>optional list of NIFTI v2 header extensions to write between the header and the data, each
created with <code>nifti2.extension</code>. If left at <code>NULL</code> and the 'niiheader' has a field named
'extensions', that field is used, so that a header read with <code>read.nifti2.header</code> can be written
back to a new file without losing its extensions. The 'vox_offset' field of the header is adapted if it is
too small to fit the extensions, and the data is written directly after them.</dd></dl>

Arguments

Write header and data to a file in NIFTI v2 format. — write.nifti2

<dl>

<dt>filepath</dt>
<dd>the file to write. The extension should be '.nii' or '.nii.gz'.</dd>


<dt>niidata</dt>
<dd>array of numeric or integer data, with up to 7 dimensions. Will be written to the file with the datatype and bitpix specified in the 'niiheader' argument.</dd>


<dt>niiheader</dt>
<dd>an optional NIFTI v2 header that is suitable for the passed 'niidata'. If not given, one will be generated with <code>ni2header.for.data</code>.</dd>


<dt>extensions</dt>
<dd>optional list of NIFTI v2 header extensions to write between the header and the data, each
created with <code>nifti2.extension</code>. If left at <code>NULL</code> and the 'niiheader' has a field named
'extensions', that field is used, so that a header read with <code>read.nifti2.header</code> can be written
back to a new file without losing its extensions. The 'vox_offset' field of the header is adapted if it is
too small to fit the extensions, and the data is written directly after them.</dd>

</dl>

write.nifti2: Write header and data to a file in NIFTI v2 format.

Description

Usage

Arguments

See Also