Inputs:
[Mandatory]
analyze_file: (an existing file name)
[Optional]
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the interface fails to
run
matlab_cmd: (a string)
matlab command to use
mfile: (a boolean, nipype default value: True)
Run m-code using m-file
paths: (a directory name)
Paths to add to matlabpath
use_mcr: (a boolean)
Run m-code using SPM MCR
Outputs:
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the interface fails to
run
matlab_cmd: (a string)
matlab command to use
mfile: (a boolean, nipype default value: True)
Run m-code using m-file
nifti_file: (an existing file name)
paths: (a directory name)
Paths to add to matlabpath
use_mcr: (a boolean)
Run m-code using SPM MCR
Uses spm to apply inverse deformation stored in a .mat file or a deformation field to a given file
>>> import nipype.interfaces.spm.utils as spmu
>>> inv = spmu.ApplyInverseDeformation()
>>> inv.inputs.in_files = 'functional.nii'
>>> inv.inputs.deformation = 'struct_to_func.mat'
>>> inv.inputs.target = 'structural.nii'
>>> inv.run()
Inputs:
[Mandatory]
in_files: (an existing file name)
Files on which deformation is applied
[Optional]
bounding_box: (a list of from 6 to 6 items which are a float)
6-element list (opt)
deformation: (an existing file name)
SN SPM deformation file
mutually_exclusive: deformation_field
deformation_field: (an existing file name)
SN SPM deformation file
mutually_exclusive: deformation
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the interface fails to
run
interpolation: (an integer >= 0)
degree of b-spline used for interpolation
matlab_cmd: (a string)
matlab command to use
mfile: (a boolean, nipype default value: True)
Run m-code using m-file
paths: (a directory name)
Paths to add to matlabpath
target: (an existing file name)
File defining target space
use_mcr: (a boolean)
Run m-code using SPM MCR
voxel_sizes: (a list of from 3 to 3 items which are a float)
3-element list (opt)
Outputs:
out_files: (an existing file name)
Transformed files
Uses spm to apply transform stored in a .mat file to given file
>>> import nipype.interfaces.spm.utils as spmu
>>> applymat = spmu.ApplyTransform(matlab_cmd='matlab-spm8')
>>> applymat.inputs.in_file = 'functional.nii'
>>> applymat.inputs.mat = 'func_to_struct.mat'
>>> applymat.run()
Warning
CHANGES YOUR INPUT FILE (applies transform by updating the header) except when used with nipype caching or workflow.
Inputs:
[Mandatory]
in_file: (an existing file name)
file to apply transform to, (only updates header)
mat: (an existing file name)
file holding transform to apply
[Optional]
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the interface fails to
run
matlab_cmd: (a string)
matlab command to use
mfile: (a boolean, nipype default value: True)
Run m-code using m-file
paths: (a directory name)
Paths to add to matlabpath
use_mcr: (a boolean)
Run m-code using SPM MCR
Outputs:
out_file: (an existing file name)
File with updated header
Uses SPM (spm_coreg) to calculate the transform mapping moving to target. Saves Transform in mat (matlab binary file) Also saves inverse transform
>>> import nipype.interfaces.spm.utils as spmu
>>> coreg = spmu.CalcCoregAffine(matlab_cmd='matlab-spm8')
>>> coreg.inputs.target = 'structural.nii'
>>> coreg.inputs.moving = 'functional.nii'
>>> coreg.inputs.mat = 'func_to_struct.mat'
>>> coreg.run()
Note
Inputs:
[Mandatory]
moving: (an existing file name)
volume transform can be applied to register with target
target: (an existing file name)
target for generating affine transform
[Optional]
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the interface fails to
run
invmat: (a file name)
Filename used to store inverse affine matrix
mat: (a file name)
Filename used to store affine matrix
matlab_cmd: (a string)
matlab command to use
mfile: (a boolean, nipype default value: True)
Run m-code using m-file
paths: (a directory name)
Paths to add to matlabpath
use_mcr: (a boolean)
Run m-code using SPM MCR
Outputs:
invmat: (a file name)
Matlab file holding inverse transform
mat: (an existing file name)
Matlab file holding transform
uses spm_reslice to resample in_file into space of space_defining
Inputs:
[Mandatory]
in_file: (an existing file name)
file to apply transform to, (only updates header)
space_defining: (an existing file name)
Volume defining space to slice in_file into
[Optional]
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the interface fails to
run
interp: (0 <= an integer <= 7, nipype default value: 0)
degree of b-spline used for interpolation0 is nearest neighbor (default)
matlab_cmd: (a string)
matlab command to use
mfile: (a boolean, nipype default value: True)
Run m-code using m-file
out_file: (a file name)
Optional file to save resliced volume
paths: (a directory name)
Paths to add to matlabpath
use_mcr: (a boolean)
Run m-code using SPM MCR
Outputs:
out_file: (an existing file name)
resliced volume