calc_distortions.pl

calculate geometric distortion fields from phantom measurements

calc_distortions.pl <phantom.mnc> <model_base> <output.xfm> [options]

DESCRIPTION

calc_distortions.pl calculates a geometric distortion field from tag files derived from phantom MRI scans. It compares measured tag point positions in the phantom scan against known model tag positions to produce a deformation field (.xfm) that characterises scanner geometric distortions.

Note: This tool is considered obsolete. For current distortion correction workflows, see phantomfit.pl.

OPTIONS

--verbose: Print progress information during processing.
--clobber: Overwrite existing output files.
--coeff <file>: Read distortion correction coefficients from the specified file.
--spacing <n>: Set the tag point spacing in millimetres. Default: 2.
--tags <file>: Use the specified file as the measured tag point file instead of auto-detecting from the phantom scan.
--model_tags <file>: Use the specified file as the model (ideal) tag point file.
--skip_grid: Skip the generation of the grid deformation field.
--align_xfm <xfm>: Apply the specified alignment transformation before computing distortions.

EXAMPLES

Compute a distortion field from a phantom scan:

calc_distortions.pl phantom.mnc model_base distortion.xfm

Compute distortions with custom tag files and 3 mm spacing:

calc_distortions.pl --spacing 3 --tags measured.tag --model_tags ideal.tag \
    phantom.mnc model_base distortion.xfm

AUTHOR

Vladimir S. Fonov. McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University.

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