interfaces.spm.utils¶
Analyze2nii¶
Inputs:
[Mandatory]
analyze_file: (a pathlike object or string representing an existing
file)
[Optional]
matlab_cmd: (a unicode string)
matlab command to use
paths: (a list of items which are a pathlike object or string
representing a directory)
Paths to add to matlabpath
mfile: (a boolean, nipype default value: True)
Run m-code using m-file
use_mcr: (a boolean)
Run m-code using SPM MCR
use_v8struct: (a boolean, nipype default value: True)
Generate SPM8 and higher compatible jobs
Outputs:
nifti_file: (a pathlike object or string representing an existing
file)
matlab_cmd: (a unicode string)
matlab command to use
paths: (a list of items which are a pathlike object or string
representing a directory)
Paths to add to matlabpath
mfile: (a boolean, nipype default value: True)
Run m-code using m-file
use_mcr: (a boolean)
Run m-code using SPM MCR
use_v8struct: (a boolean, nipype default value: True)
Generate SPM8 and higher compatible jobs
References:¶
None
ApplyInverseDeformation¶
Uses spm to apply inverse deformation stored in a .mat file or a deformation field to a given file
Examples¶
>>> 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() # doctest: +SKIP
Inputs:
[Mandatory]
in_files: (a list of items which are a pathlike object or string
representing an existing file)
Files on which deformation is applied
[Optional]
target: (a pathlike object or string representing an existing file)
File defining target space
deformation: (a pathlike object or string representing an existing
file)
SN SPM deformation file
mutually_exclusive: deformation_field
deformation_field: (a pathlike object or string representing an
existing file)
SN SPM deformation file
mutually_exclusive: deformation
interpolation: (0 <= a long integer <= 7)
degree of b-spline used for interpolation
bounding_box: (a list of from 6 to 6 items which are a float)
6-element list (opt)
voxel_sizes: (a list of from 3 to 3 items which are a float)
3-element list (opt)
matlab_cmd: (a unicode string)
matlab command to use
paths: (a list of items which are a pathlike object or string
representing a directory)
Paths to add to matlabpath
mfile: (a boolean, nipype default value: True)
Run m-code using m-file
use_mcr: (a boolean)
Run m-code using SPM MCR
use_v8struct: (a boolean, nipype default value: True)
Generate SPM8 and higher compatible jobs
Outputs:
out_files: (a list of items which are a pathlike object or string
representing an existing file)
Transformed files
References:¶
None
ApplyTransform¶
Uses SPM to apply transform stored in a .mat file to given file
Examples¶
>>> import nipype.interfaces.spm.utils as spmu
>>> applymat = spmu.ApplyTransform()
>>> applymat.inputs.in_file = 'functional.nii'
>>> applymat.inputs.mat = 'func_to_struct.mat'
>>> applymat.run() # doctest: +SKIP
Inputs:
[Mandatory]
in_file: (a pathlike object or string representing an existing file)
file to apply transform to, (only updates header)
mat: (a pathlike object or string representing an existing file)
file holding transform to apply
[Optional]
out_file: (a pathlike object or string representing a file)
output file name for transformed data
matlab_cmd: (a unicode string)
matlab command to use
paths: (a list of items which are a pathlike object or string
representing a directory)
Paths to add to matlabpath
mfile: (a boolean, nipype default value: True)
Run m-code using m-file
use_mcr: (a boolean)
Run m-code using SPM MCR
use_v8struct: (a boolean, nipype default value: True)
Generate SPM8 and higher compatible jobs
Outputs:
out_file: (a pathlike object or string representing an existing file)
Transformed image file
References:¶
None
CalcCoregAffine¶
Uses SPM (spm_coreg) to calculate the transform mapping moving to target. Saves Transform in mat (matlab binary file) Also saves inverse transform
Examples¶
>>> 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() # doctest: +SKIP
Note
- the output file mat is saves as a matlab binary file
- calculating the transforms does NOT change either input image it does not move the moving image, only calculates the transform that can be used to move it
Inputs:
[Mandatory]
target: (a pathlike object or string representing an existing file)
target for generating affine transform
moving: (a pathlike object or string representing an existing file)
volume transform can be applied to register with target
[Optional]
mat: (a pathlike object or string representing a file)
Filename used to store affine matrix
invmat: (a pathlike object or string representing a file)
Filename used to store inverse affine matrix
matlab_cmd: (a unicode string)
matlab command to use
paths: (a list of items which are a pathlike object or string
representing a directory)
Paths to add to matlabpath
mfile: (a boolean, nipype default value: True)
Run m-code using m-file
use_mcr: (a boolean)
Run m-code using SPM MCR
use_v8struct: (a boolean, nipype default value: True)
Generate SPM8 and higher compatible jobs
Outputs:
mat: (a pathlike object or string representing an existing file)
Matlab file holding transform
invmat: (a pathlike object or string representing a file)
Matlab file holding inverse transform
References:¶
None
DicomImport¶
Uses spm to convert DICOM files to nii or img+hdr.
Examples¶
>>> import nipype.interfaces.spm.utils as spmu
>>> di = spmu.DicomImport()
>>> di.inputs.in_files = ['functional_1.dcm', 'functional_2.dcm']
>>> di.run() # doctest: +SKIP
Inputs:
[Mandatory]
in_files: (a list of items which are a pathlike object or string
representing an existing file)
dicom files to be converted
[Optional]
output_dir_struct: ('flat' or 'series' or 'patname' or 'patid_date'
or 'patid' or 'date_time', nipype default value: flat)
directory structure for the output.
output_dir: (a unicode string, nipype default value:
./converted_dicom)
output directory.
format: ('nii' or 'img', nipype default value: nii)
output format.
icedims: (a boolean, nipype default value: False)
If image sorting fails, one can try using the additional SIEMENS
ICEDims information to create unique filenames. Use this only if
there would be multiple volumes with exactly the same file names.
matlab_cmd: (a unicode string)
matlab command to use
paths: (a list of items which are a pathlike object or string
representing a directory)
Paths to add to matlabpath
mfile: (a boolean, nipype default value: True)
Run m-code using m-file
use_mcr: (a boolean)
Run m-code using SPM MCR
use_v8struct: (a boolean, nipype default value: True)
Generate SPM8 and higher compatible jobs
Outputs:
out_files: (a list of items which are a pathlike object or string
representing an existing file)
converted files
References:¶
None
Reslice¶
uses spm_reslice to resample in_file into space of space_defining
Inputs:
[Mandatory]
in_file: (a pathlike object or string representing an existing file)
file to apply transform to, (only updates header)
space_defining: (a pathlike object or string representing an existing
file)
Volume defining space to slice in_file into
[Optional]
interp: (0 <= a long integer <= 7, nipype default value: 0)
degree of b-spline used for interpolation0 is nearest neighbor
(default)
out_file: (a pathlike object or string representing a file)
Optional file to save resliced volume
matlab_cmd: (a unicode string)
matlab command to use
paths: (a list of items which are a pathlike object or string
representing a directory)
Paths to add to matlabpath
mfile: (a boolean, nipype default value: True)
Run m-code using m-file
use_mcr: (a boolean)
Run m-code using SPM MCR
use_v8struct: (a boolean, nipype default value: True)
Generate SPM8 and higher compatible jobs
Outputs:
out_file: (a pathlike object or string representing an existing file)
resliced volume
References:¶
None
ResliceToReference¶
Uses spm to reslice a volume to a target image space or to a provided voxel size and bounding box
Examples¶
>>> import nipype.interfaces.spm.utils as spmu
>>> r2ref = spmu.ResliceToReference()
>>> r2ref.inputs.in_files = 'functional.nii'
>>> r2ref.inputs.target = 'structural.nii'
>>> r2ref.run() # doctest: +SKIP
Inputs:
[Mandatory]
in_files: (a list of items which are a pathlike object or string
representing an existing file)
Files on which deformation is applied
[Optional]
target: (a pathlike object or string representing an existing file)
File defining target space
interpolation: (0 <= a long integer <= 7)
degree of b-spline used for interpolation
bounding_box: (a list of from 6 to 6 items which are a float)
6-element list (opt)
voxel_sizes: (a list of from 3 to 3 items which are a float)
3-element list (opt)
matlab_cmd: (a unicode string)
matlab command to use
paths: (a list of items which are a pathlike object or string
representing a directory)
Paths to add to matlabpath
mfile: (a boolean, nipype default value: True)
Run m-code using m-file
use_mcr: (a boolean)
Run m-code using SPM MCR
use_v8struct: (a boolean, nipype default value: True)
Generate SPM8 and higher compatible jobs
Outputs:
out_files: (a list of items which are a pathlike object or string
representing an existing file)
Transformed files
References:¶
None