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| ||Flag ||Description || | ||'''Flag''' ||'''Description''' || |
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| ||--inspm <y_rinput.nii> ||input SPM warp (use with --insrcgeom), data format is either abs-ras (default) or abs-crs. use --inwarpformat <> to specify the data format. || | ||--inspm <y_rinput.nii> ||input SPM warp (use with --insrcgeom). Use --inwarpformat <> to specify the data format, which is either abs-ras (default) or abs-crs. || |
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| ||--invox <in.mgz> ||input file with displacements in source-voxel space || | ||--invox <in.mgz> ||input displacement field in source-voxel space || |
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| ||Flag ||Description || | ||'''Flag''' ||'''Description''' || |
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| ||--outvox <out.mgz> ||output file with displacements in source-voxel space || | ||--outvox <out.mgz> ||output displacement field in source-voxel space || |
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| ||Flag ||Description || ||-g, --insrcgeom <geom.mgz> ||specify volume geometry of the input to the warp space, i.e., srcgeom shares an RAS space with the warp volume. Usually this is identical to the geom of the warp volume itself (if the warp input is in a format that has such info). This also allows the input to the warp to have a different geometry than the warp itself, though this is probably better handled with -lta1. || ||-d, --downsample ||downsample output M3Z to spacing of 2. || ||-lta2 LTA (or -lta2-inv) ||create composite morph for warping a source image -> LTA1 -> GCAM -> LTA2 -> atlas/destination image || ||--inwarpformat <format> ||specify warp data format: abs-crs, disp-crs, abs-ras, or disp-ras (default is abs-crs). (Only --inspm <> uses this option.) || ||--outwarpformat <format> ||specify warp data format: abs-crs, disp-crs, abs-ras, or disp-ras (default is abs-crs) || ||--vg-thresh <vgthresh> ||specify threshold for testing diffs in volume geom || |
||'''Flag''' ||'''Description''' || ||-g, --insrcgeom <geom.mgz> ||specify volume geometry of the input to the warp space, i.e., srcgeom shares an RAS space with the warp volume. Usually this is identical to the geom of the warp volume itself (if the warp input is in a format that has such info). This also allows the input to the warp to have a different geometry than the warp itself, though this is probably better handled with -lta1. || ||-d, --downsample ||downsample output M3Z to spacing of 2. || ||-lta2 LTA (or -lta2-inv) ||create composite morph for warping a source image -> LTA1 -> GCAM -> LTA2 -> atlas/destination image || ||--inwarpformat <format> ||specify warp data format: abs-crs, disp-crs, abs-ras, or disp-ras (default is abs-crs). This option only works with '--inspm <>'. || ||--outwarpformat <format> ||specify warp data format: abs-crs, disp-crs, abs-ras, or disp-ras (default is abs-crs) || ||--vg-thresh <vgthresh> ||specify threshold for testing diffs in volume geom || |
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| = See Also = [[lta_convert]] (convert between different linear transform formats) |
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| = See Also = [[mri_convert]] [[lta_convert]] |
[[mri_concatenate_lta]] (concatenate or invert LTA transforms) [[mri_concatenate_gcam]] (concatenate or invert warp fields) [[mri_convert]] -at or -ait (apply transforms to an image) |
Index
Contents
Name
mri_warp_convert
Description
Converts non-linear deformation warp fields between different file formats. Some formats may require you to pass an image if the geometry information is missing from the transform file.
Synopsis
mri_warp_convert <input-type> <output-type> [options]
Arguments
Required Flagged Arguments
Exactly one input is required
Flag |
Description |
--inm3z <in.m3z> |
input Freesurfer 3D morph in M3Z format |
--inmgzwarp <inwarp.mgz> |
input Freesurfer 3D morph in mgz format |
--infsl <in.nii.gz> |
input FSL warp (recommend to use with --insrcgeom) |
--inspm <y_rinput.nii> |
input SPM warp (use with --insrcgeom). Use --inwarpformat <> to specify the data format, which is either abs-ras (default) or abs-crs. |
--inlps, --initk <in.nii.gz> |
input LPS-to-LPS displacement field (e.g. ITK, ANTs) |
--inras <in.nii.gz> |
input RAS-to-RAS displacement field (e.g. NiftyReg) |
--invox <in.mgz> |
input displacement field in source-voxel space |
Exactly one output is required
Flag |
Description |
--outm3z <out.m3z> |
output Freesurfer 3D morph in M3Z format |
--outmgzwarp <outwarp.mgz> |
output Freesurfer 3D morph in mgz format |
--outfsl <out.nii.gz> |
output warp in FSL format |
--outlps, --outitk <out.nii.gz> |
output LPS-to-LPS displacement field (e.g. ITK, ANTs) |
--outras <out.nii.gz> |
output RAS-to-RAS displacement field (e.g. NiftyReg) |
--outvox <out.mgz> |
output displacement field in source-voxel space |
Optional Flagged Arguments
Flag |
Description |
-g, --insrcgeom <geom.mgz> |
specify volume geometry of the input to the warp space, i.e., srcgeom shares an RAS space with the warp volume. Usually this is identical to the geom of the warp volume itself (if the warp input is in a format that has such info). This also allows the input to the warp to have a different geometry than the warp itself, though this is probably better handled with -lta1. |
-d, --downsample |
downsample output M3Z to spacing of 2. |
-lta2 LTA (or -lta2-inv) |
create composite morph for warping a source image -> LTA1 -> GCAM -> LTA2 -> atlas/destination image |
--inwarpformat <format> |
specify warp data format: abs-crs, disp-crs, abs-ras, or disp-ras (default is abs-crs). This option only works with '--inspm <>'. |
--outwarpformat <format> |
specify warp data format: abs-crs, disp-crs, abs-ras, or disp-ras (default is abs-crs) |
--vg-thresh <vgthresh> |
specify threshold for testing diffs in volume geom |
Examples
Example 1
Convert FSL warp to M3Z (FreeSurfer):
mri_warp_convert --infsl fsl.nii.gz --outm3z out.m3z --insrcgeom src.nii.gz
Example 2
Convert ITK warp (e.g. ANTs) to M3Z (FreeSurfer):
mri_warp_convert --initk itk.nii.gz --outm3z out.m3z --insrcgeom src.nii.gz
Example 3
Convert ANTS antsRegistrationSyN.sh or antsRegistrationSyNQuick.shboutput to M3Z (FreeSurfer):
antsRegistrationSyNQuick.sh -d 3 -m mov.mgz -f targ.mgz -o reg.
ConvertTransformFile 3 ants.reg0GenericAffine.mat ants.reg0GenericAffine.txt --hm --ras
lta_convert --src mov.mgz --trg targ.mgz --inniftyreg ants.reg0GenericAffine.txt --outlta ants.reg0GenericAffine.lta
mri_warp_convert --lta1-inv ants.reg0GenericAffine.lta --initk ants.reg1Warp.nii.gz --outm3z out.m3z --insrcgeom targ.mgz
* Note that the insrcgeom is the target, not the mov; this is needed to work with --lta1-inv.
Example 4
Convert M3Z (FreeSurfer) to ITK warp (e.g. ANTs):
mri_warp_convert --inm3z in.m3z --outitk out.nii.gz
Example 5
Convert M3Z (FreeSurfer) to mgz warp (FreeSurfer) in absolute CRS:
mri_warp_convert --inm3z in.m3z --outmgzwarp outwarp.mgz --outwarpformat abs-crs
See Also
lta_convert (convert between different linear transform formats)
mri_concatenate_lta (concatenate or invert LTA transforms)
mri_concatenate_gcam (concatenate or invert warp fields)
mri_convert -at or -ait (apply transforms to an image)
Reporting Bugs
Report bugs to < analysis-bugs@nmr.mgh.harvard.edu >