fsl.scaled.voxel.matrix

FSL does not use the world coordinates of the image header. Its tools work in a space in which
the voxel axes have unit length (the voxel sizes are divided out) and in which the first voxel axis points to
the left, i.e. the transformation has a negative determinant, which is why FSL calls its images
'radiological'. For a volume whose header already uses that convention, the FSL space equals the header space;
otherwise the first axis is flipped, and the origin of that axis is moved to the other end of the volume.
This function implements the mapping that both MRtrix3 (in <code>transformconvert ... flirt_import</code>) and
FreeSurfer (in <code>lta_convert --infsl</code>) apply, and it was verified against both of them on real data: the
resulting transformation matrix is identical to the one of these tools up to numerical precision, while the
plain composition of the header voxel-to-RAS matrices is not (it differs by more than 100 mm on real data).

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) 

fsl.scaled.voxel.matrix function

<dl><dt>geometry</dt>
<dd>named list, the volume geometry as returned by <code>volume.geometry</code>.</dd></dl>

Arguments

Compute the matrix that maps FSL voxel coordinates of a volume to FSL world coordinates. — fsl.scaled.voxel.matrix

<dl>

<dt>geometry</dt>
<dd>named list, the volume geometry as returned by <code>volume.geometry</code>.</dd>

</dl>

fsl.scaled.voxel.matrix: Compute the matrix that maps FSL voxel coordinates of a volume to FSL world coordinates.

Description

Usage

Value

Arguments