lta_convert
convert_convert [options]
This program converts different transformation formats. Some formats may require you to pass an image if the geometry information is missing form the transform file format.
Argument | Explanation |
---|---|
--inlta <in.lta> | input transform of LTA type |
--infsl <in.fslmat> | input transform of FSL type |
--inmni <in.xfm> | input transform of MNI / XFM type |
--inreg <inreg.dat> | input transform of TK REG type (deprecated format) |
--inniftyreg <inniftyreg.dat> | input transform of Nifty Reg type (inverse RAS2RAS) |
--initk <initk.txt> | input ITK transform (inverse LPS2LPS). Convert ANTS .mat binary to ITK format with ConvertTransformFile (in ANTS). |
Argument | Explanation |
---|---|
--outlta <out.lta> | output linear transform (LTA Freesurfer format) |
--outfsl <out.mat> | output transform in FSL format |
--outmni <out.xfm> | output transform in mni/xfm format |
--outreg <reg.dat> | output transform in reg dat format |
--outitk <outitk.txt> | output transform in ITK txt format (inverse LPS2LPS) |
Argument | Explanation |
---|---|
--invert | inverts transform |
--ltavox2vox | (with --ltaout) output type VOX2VOX (default RAS2RAS) |
Argument | Explanation |
---|---|
--src | specify src image geometry (mov volume for TKREG/register.dat) |
--trg | specify trg image geometry |
--trgconform | conform trg image geometry (COR standard). Will be done before inversion, if specified. |
--subject | Specify subject name (overrides if input has subject name defined). |
Convert FSL transform to LTA (FreeSurfer):
lta_convert --infsl fsl.mat --outlta my.lta --src src.nii --trg trg.nii
converts FSL matrix to FreeSurfer LTA, adding missing src and target geometry info (the images used when fsl.mat was created).
Convert ANTS/ITK transform to LTA (FreeSurfer):
First convert the ANTS binary mat file to ITK text file format and then to lta (adding src and trg geometry info, from images that were used to create the transform in ANTS):
$ANTSPATH/ConvertTransformFile 3 3D_antsAffine.mat 3D_antsAffine.txt
lta_convert --initk 3D_antsAffine.txt --outlta 3D_antsAffine.lta --src src.nii --trg trg.nii
Invert transform:
lta_convert --inlta in.lta --outlta out-inverse.lta --invert
Reads in.lta, inverts it and saves it as out-inverse.lta
Conform target geometry:
lta_convert --inlta in.lta --outlta out-conform.lta --trgconform
Reads in.lta, conforms trg geometry and saves it as out-conform.lta
Create transform from header geometries only:
lta_convert --inlta identity.nofile --src src.nii --trg trg.nii --outlta out.lta
Creates LTA from SRC and TRG header geometies, e.g. to convert SPM results to LTA (SPM stores its transforms in the header). Similarly you can create a lta for conform reslicing when specifying --trgconform instead of --trg trg.nii.
Report bugs to <freesurfer@nmr.mgh.harvard.edu>
mri_concatenate_lta (to concatenate or invert LTA transforms).
or mri_convert -at or -ait to apply transforms to an image.