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Read FSL FLIRT transformation matrix

Source: R/as_ieegio_transform.R
io_read_flirt_transform.Rd

Reads a 4x4 affine transformation matrix from an FSL FLIRT output file. FLIRT matrices operate in FSL scaled-voxel coordinate system and require source and reference images to convert to world (RAS) coordinates.

Usage

io_read_flirt_transform(file, space_from, space_to)

Arguments

file

character string specifying the path to the FLIRT matrix file. This is a plain text file containing a 4x4 affine matrix.

space_from

character string or ieegio_space object identifying the source (moving) space. If missing, will be inferred from the filename using BIDS-style from-<space> entity.

space_to

character string or ieegio_space object identifying the target (reference) space. If missing, will be inferred from the filename using BIDS-style to-<space> entity.

Value

An ieegio_transforms object with:

data

List containing the 4x4 FLIRT matrix

type

"affine"

interpretation

"active" (FLIRT matrices are point transforms)

space_from

Source space (with "FSL" orientation)

space_to

Target space (with "FSL" orientation)

dimension

3

Details

FLIRT matrices operate in FSL scaled-voxel coordinate system, which is:

  • Voxel indices multiplied by voxel sizes (pixdim)

  • X-axis inverted if the image has positive sform determinant (neurological convention)

The returned transform has "FSL" orientation for both source and target spaces. To convert to world (RAS) coordinates, use transform_flirt2ras with the source and/or reference images.

FLIRT matrices are active transforms: they map point coordinates from the source (moving) image space to the reference (fixed) image space.

BIDS Support

The function can automatically infer space names from BIDS-compliant file names:

  • from-<source>: Source space identifier

  • to-<target>: Target space identifier

See also

transform_flirt2ras for converting to world coordinates io_read_ants_transform for reading ANTs format transforms as_ieegio_transform for converting objects to transforms

Examples

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

# Convert to RAS coordinates (requires source and reference images)
xfm_ras <- transform_flirt2ras(xfm, source = "source.nii.gz",
                                reference = "reference.nii.gz")

# Explicitly specify spaces
xfm <- io_read_flirt_transform(
  "transform.mat",
  space_from = "T1w",
  space_to = "MNI152"
)
} # }