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| The Freesurfer 3D morph MGZ files (MGZ_INTENT_WARPMAP) can be converted to Nifti with intent code NIFTI_INTENT_DISPVECT. NIFTI_INTENT_DISPVECT has shape [5, c, r, s, 1, 3], and the displacement field vector is in RAS space. Freesurfer reads the 5th dimensions as extra frames in MRI struct. | The Freesurfer 3D morph MGZ files (MGZ_INTENT_WARPMAP) can be converted to Nifti with intent code NIFTI_INTENT_DISPVECT. |
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
Notes on Freesurfer 3D Morph MGZ Format
The Freesurfer 3D morph MGZ files follow Freesurfer MGZ format with intent MGZ_INTENT_WARPMAP and specific TAG attributes.
TAG Attributes
TAG |
Comment |
TAG_GCAMORPH_GEOM |
gcamorph image (source) geom gcamorph atlas (target) geom |
TAG_GCAMORPH_GEOM_PLUSSHEAR |
gcamorph image (source) geom with shears gcamorph atlas (target) geom with shears |
TAG_GCAMORPH_META |
1. WARPFIELD_DTFMT_ABS_CRS, WARPFIELD_DTFMT_DISP_CRS, WARPFIELD_DTFMT_ABS_RAS, or WARPFIELD_DTFMT_DISP_RAS 2. spacing (int) 3. exp_k (double) |
TAG_GCAMORPH_LABELS |
gcamorph label data |
TAG_GCAMORPH_AFFINE |
gcamorph m_affine matrix |
Data Array
The data array (width x height x depth x nframes) is indexed by atlas CRS:
- frame 0 - image voxel ABS coordinate C, image voxel DISP coordinate C, RAS ABS coordinate X, or RAS DISP coordinate X
- frame 1 - image voxel ABS coordinate R, image voxel DISP coordinate R, RAS ABS coordinate Y, or RAS DISP coordinate Y
- frame 2 - image voxel ABS coordinate S, image voxel DISP coordinate S, RAS ABS coordinate Z, or RAS DISP coordinate Z
Data Formats
WARPFIELD_DTFMT_ABS_CRS |
CRS coordinates in image space |
WARPFIELD_DTFMT_DISP_CRS |
displacement CRS, delta = image_CRS - atlas_CRS |
WARPFIELD_DTFMT_ABS_RAS |
RAS coordinates in image space |
WARPFIELD_DTFMT_DISP_RAS |
displacement RAS, delta = image_RAS - atlas_RAS |
MGZ to Nifti Conversion
The Freesurfer 3D morph MGZ files (MGZ_INTENT_WARPMAP) can be converted to Nifti with intent code NIFTI_INTENT_DISPVECT.
NIFTI_INTENT_DISPVECT has shape [5, c, r, s, 1, 3], and the displacement field vector is in RAS space. Freesurfer reads the 5th dimensions as extra frames in MRI struct.
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 >