cifti.stop.if.cifti

The generic readers of this package dispatch on the file name, and a CIFTI
file is a NIFTI file as far as the name is concerned: <code>read.fs.morph()</code> used to
interpret a <code>.dscalar.nii</code> as a NIFTI morphometry file and silently returned the raw
matrix as a per-vertex vector (for the official Conte69 <code>.dtseries</code>, a 121,902 element
vector of a 60,951 x 2 matrix, i.e. plausible looking numbers in an order that means
nothing), and <code>read.fs.volume()</code> failed with the unrelated 'This is not a one-file
NIFTI format' message of <code>oro.nifti</code>. This function detects the CIFTI files and stops
with an error that names the reader to use instead, see <code>read.cifti</code>.
The check only costs a header read, and only for files whose name ends with <code>.nii</code> or
<code>.nii.gz</code>, since a CIFTI file always has such a name.

internal

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) 

cifti.stop.if.cifti function

<dl><dt>filepath</dt>
<dd>character string, the path to a CIFTI-2 file (usually one of
<code>.dscalar.nii</code>, <code>.dtseries.nii</code>, <code>.dlabel.nii</code>, <code>.dconn.nii</code>, <code>.pscalar.nii</code>,
<code>.ptseries.nii</code>, <code>.pconn.nii</code>, <code>.dpconn.nii</code> or <code>.pdconn.nii</code>). Note that
this is not a NIFTI file, despite the <code>.nii</code> part. Gzipped CIFTI files are
not supported, because the CIFTI-2 format forbids compression.</dd></dl>

Arguments

Refuse to read a CIFTI file as a volume or morphometry file. — cifti.stop.if.cifti

<dl>

<dt>filepath</dt>
<dd>character string, the path to a CIFTI-2 file (usually one of
<code>.dscalar.nii</code>, <code>.dtseries.nii</code>, <code>.dlabel.nii</code>, <code>.dconn.nii</code>, <code>.pscalar.nii</code>,
<code>.ptseries.nii</code>, <code>.pconn.nii</code>, <code>.dpconn.nii</code> or <code>.pdconn.nii</code>). Note that
this is not a NIFTI file, despite the <code>.nii</code> part. Gzipped CIFTI files are
not supported, because the CIFTI-2 format forbids compression.</dd>

</dl>

cifti.stop.if.cifti: Refuse to read a CIFTI file as a volume or morphometry file.

Description

Usage

Value

Arguments