Usage: 3dWarp [options] dataset
Warp (spatially transform) one 3D dataset.
* Here, the 'warp' is a 3x4 matrix = affine transform of space which
the user supplies.
* Such a transformation can be computed by 3dWarpDrive or 3dAllineate,
by matching one dataset to another.
* However, 3dAllineate can also transform a dataset given a matrix,
so the usefulness of these older 3dWarp programs is now limited.
*****
***** For nonlinear spatial warping, see program 3dQwarp. *****
*****
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Transform Defining Options: [exactly one of these must be used]
--------------------------
-matvec_in2out mmm = Read a 3x4 affine transform matrix+vector
from file 'mmm':
x_out = Matrix x_in + Vector
-matvec_out2in mmm = Read a 3x4 affine transform matrix+vector
from file 'mmm':
x_in = Matrix x_out + Vector
** N.B.: The coordinate vectors described above are
defined in DICOM ('RAI') coordinate order.
(Also see the '-fsl_matvec option, below.)
** N.B.: Using the special name 'IDENTITY' for 'mmm'
means to use the identity matrix.
** N.B.: You can put the matrix on the command line
directly by using an argument of the form
'MATRIX(a11,a12,a13,a14,a21,a22,a23,a24,a31,a32,a33,a34)'
in place of 'mmm', where the aij values are the
matrix entries (aij = i-th row, j-th column),
separated by commas.
* You will need the 'forward single quotes' around
the argument.
-tta2mni = Transform a dataset in Talairach-Tournoux Atlas
coordinates to MNI-152 coordinates.
-mni2tta = Transform a dataset in MNI-152 coordinates to
Talairach-Tournoux Atlas coordinates.
-matparent mset = Read in the matrix from WARPDRIVE_MATVEC_*
attributes in the header of dataset 'mset',
which must have been created by program
3dWarpDrive. In this way, you can apply
a transformation matrix computed from
in 3dWarpDrive to another dataset.
** N.B.: The above option is analogous to the -rotparent
option in program 3drotate. Use of -matparent
should be limited to datasets whose spatial
coordinate system corresponds to that which
was used for input to 3dWarpDrive (i.e., the
input to 3dWarp should overlay properly with
the input to 3dWarpDrive that generated the
-matparent dataset).
-card2oblique obl_dset
or
-oblique_parent obl_dset = Read in the oblique transformation matrix
from an oblique dataset and make cardinal dataset oblique to match.
-deoblique or
-oblique2card = Transform an oblique dataset to a cardinal dataset
Both these oblique transformation options require a new grid for the
output as specified with the -newgrid or -gridset options
or a new grid will be assigned based on the minimum voxel spacing
** N.B.: EPI time series data should be time shifted with 3dTshift before rotating the volumes to a cardinal direction
-disp_obl_xform_only = (new opt) just display the obliquity transform
matrix that would be applied to make the output
dset; very useful for moving between oblique
coords, such as with '-oblique_parent ..' or
'-deoblique'. The result can be dumped into a
text file, e.g.:
> textfile.aff12.1D
No dataset is created or changed.
Sample usages:
3dWarpDrive -affine_general -base d1+orig -prefix d2WW -twopass -input d2+orig
3dWarp -matparent d2WW+orig -prefix epi2WW epi2+orig
3dWarp -card2oblique oblique_epi+orig -prefix oblique_anat card_anat+orig
3dWarp -oblique2card -prefix card_epi_tshift -newgrid 3.5 epi_tshift+orig
3dWarp -card2oblique oblique_epi.nii -disp_obl_transf_only epi_tshift+orig\
> mat_obl_transform.aff12.1D
Example of warping +tlrc results back to +orig space of some subject
(get xform matrix, apply it, tell dataset it is not in orig space):
cat_matvec subj1_anat+tlrc::WARP_DATA > tlrc_xform.1D
3dWarp -matvec_out2in tlrc_xform.1D -prefix group_warped+tlrc \
-gridset subj1_epi+orig -cubic group_data+tlrc
3drefit -view orig group_warped+tlrc
-----------------------
Other Transform Options:
-----------------------
-linear }
-cubic } = Chooses spatial interpolation method.
-NN } = [default = linear]
-quintic }
-wsinc5 }
-fsl_matvec = Indicates that the matrix file 'mmm' uses FSL
ordered coordinates ('LPI'). For use with
matrix files from FSL and SPM.
-newgrid ddd = Tells program to compute new dataset on a
new 3D grid, with spacing of 'ddd' mmm.
* If this option is given, then the new
3D region of space covered by the grid
is computed by warping the 8 corners of
the input dataset, then laying down a
regular grid with spacing 'ddd'.
* If this option is NOT given, then the
new dataset is computed on the old
dataset's grid.
-gridset ggg = Tells program to compute new dataset on the
same grid as dataset 'ggg'.
-zpad N = Tells program to pad input dataset with 'N'
planes of zeros on all sides before doing
transformation.
---------------------
Miscellaneous Options:
---------------------
-verb = Print out some information along the way.
-prefix ppp = Sets the prefix of the output dataset.
++ Compile date = Oct 31 2024 {AFNI_24.3.06:linux_ubuntu_24_64}
