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Convert FLIRT transform to world (RAS) coordinates

Source: R/as_ieegio_transform.R
transform_flirt2ras.Rd

Converts an FSL FLIRT matrix from FSL scaled-voxel coordinates to world (RAS) coordinates. Allows partial conversion by specifying only source, only reference, or both images.

Usage

transform_flirt2ras(transform, source = NULL, reference = NULL)

Arguments

transform

an ieegio_transforms object with FSL orientation (typically from io_read_flirt_transform), or a 4x4 matrix

source

source (moving) image used in FLIRT registration. Can be:

  • A file path to a NIfTI image

  • An ieegio_volume object

  • NULL to skip source-side conversion

reference

reference (fixed) image used in FLIRT registration. Can be:

  • A file path to a NIfTI image

  • An ieegio_volume object

  • NULL to skip reference-side conversion

Value

An ieegio_transforms object with updated orientations:

  • Both images provided: RAS -> RAS transform

  • Source only: RAS -> FSL transform (source side converted)

  • Reference only: FSL -> RAS transform (reference side converted)

  • Neither: FSL -> FSL transform (unchanged)

Details

FSL FLIRT matrices operate in a scaled-voxel coordinate system that depends on the image geometry. The conversion to world coordinates uses:

world_transform = ref_vox2ras %*% ref_fsl2vox %*% flirt %*% src_vox2fsl %*% src_ras2vox

Where:

  • src_ras2vox: Inverse of source image's voxel-to-RAS matrix

  • src_vox2fsl: Source voxel-to-FSL coordinate transform

  • flirt: The original FLIRT matrix

  • ref_fsl2vox: Inverse of reference voxel-to-FSL transform

  • ref_vox2ras: Reference image's voxel-to-RAS matrix

The FSL coordinate system uses scaled voxels with possible X-axis flip depending on the image's sform determinant sign.

See also

io_read_flirt_transform for reading FLIRT matrices transform_orientation for general orientation transforms

Examples

if (FALSE) { # \dontrun{
# Read FLIRT matrix
xfm <- io_read_flirt_transform("source_to_reference.mat")

# Full conversion to RAS coordinates
xfm_ras <- transform_flirt2ras(xfm,
                               source = "source.nii.gz",
                               reference = "reference.nii.gz")

# Partial conversion (reference side only)
xfm_partial <- transform_flirt2ras(xfm, reference = "reference.nii.gz")

# Using ieegio_volume objects
src_vol <- read_volume("source.nii.gz", header_only = TRUE)
ref_vol <- read_volume("reference.nii.gz", header_only = TRUE)
xfm_ras <- transform_flirt2ras(xfm, source = src_vol, reference = ref_vol)
} # }