validate.dti.gradients

Checks that a set of b-vectors and b-values is consistent,
replaces missing values by <code>b=0</code> volumes, and reports suspicious entries.
This is the validation used by
<code>read.dti.gradients</code>, but it can also be
called directly on gradients from any other source.

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) 

validate.dti.gradients function

<dl><dt>bvec</dt>
<dd>character string (path to a b-vectors file), or a numeric matrix
with one row per volume (or one column per volume) and 3 columns.</dd>
<dt>bval</dt>
<dd>character string (path to a b-values file), or a numeric vector
with one value per volume. Can be <code>NULL</code> if <code>bvec</code> identifies both files.</dd>
<dt>n_volumes</dt>
<dd>scalar numeric or integer, the number of volumes in the DWI
image that the gradients belong to, used to check that the table matches
the image. Typically <code>dim(volume$data)[4]</code>. Set to <code>NULL</code> (the default) to
skip this check.</dd></dl>

Arguments

Validate and normalize a diffusion MRI gradient table. — validate.dti.gradients

<dl>

<dt>bvec</dt>
<dd>character string (path to a b-vectors file), or a numeric matrix
with one row per volume (or one column per volume) and 3 columns.</dd>


<dt>bval</dt>
<dd>character string (path to a b-values file), or a numeric vector
with one value per volume. Can be <code>NULL</code> if <code>bvec</code> identifies both files.</dd>


<dt>n_volumes</dt>
<dd>scalar numeric or integer, the number of volumes in the DWI
image that the gradients belong to, used to check that the table matches
the image. Typically <code>dim(volume$data)[4]</code>. Set to <code>NULL</code> (the default) to
skip this check.</dd>

</dl>

validate.dti.gradients: Validate and normalize a diffusion MRI gradient table.

Description

Usage

Value

Arguments