nipype.interfaces.spm.utils module¶
Analyze2nii¶
Bases: SPMCommand
analyze_file : a pathlike object or string representing an existing file
- matlab_cmda unicode string
Matlab command to use.
- mfilea boolean
Run m-code using m-file. (Nipype default value:
True
)- pathsa list of items which are a pathlike object or string representing a directory
Paths to add to matlabpath.
- use_mcra boolean
Run m-code using SPM MCR.
- use_v8structa boolean
Generate SPM8 and higher compatible jobs. (Nipype default value:
True
)
- matlab_cmda unicode string
Matlab command to use.
- mfilea boolean
Run m-code using m-file. (Nipype default value:
True
)nifti_file : a pathlike object or string representing an existing file paths : a list of items which are a pathlike object or string representing a directory
Paths to add to matlabpath.
- use_mcra boolean
Run m-code using SPM MCR.
- use_v8structa boolean
Generate SPM8 and higher compatible jobs. (Nipype default value:
True
)
ApplyInverseDeformation¶
Bases: SPMCommand
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()
- in_filesa list of items which are a pathlike object or string representing an existing file
Files on which deformation is applied.
- bounding_boxa list of from 6 to 6 items which are a float
6-element list (opt).
- deformationa pathlike object or string representing an existing file
SN SPM deformation file. Mutually exclusive with inputs:
deformation_field
.- deformation_fielda pathlike object or string representing an existing file
SN SPM deformation file. Mutually exclusive with inputs:
deformation
.- interpolation0 <= a long integer <= 7
Degree of b-spline used for interpolation.
- matlab_cmda unicode string
Matlab command to use.
- mfilea boolean
Run m-code using m-file. (Nipype default value:
True
)- pathsa list of items which are a pathlike object or string representing a directory
Paths to add to matlabpath.
- targeta pathlike object or string representing an existing file
File defining target space.
- use_mcra boolean
Run m-code using SPM MCR.
- use_v8structa boolean
Generate SPM8 and higher compatible jobs. (Nipype default value:
True
)- voxel_sizesa list of from 3 to 3 items which are a float
3-element list (opt).
- out_filesa list of items which are a pathlike object or string representing an existing file
Transformed files.
ApplyTransform¶
Bases: SPMCommand
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()
- in_filea pathlike object or string representing an existing file
File to apply transform to, (only updates header).
- mata pathlike object or string representing an existing file
File holding transform to apply.
- matlab_cmda unicode string
Matlab command to use.
- mfilea boolean
Run m-code using m-file. (Nipype default value:
True
)- out_filea pathlike object or string representing a file
Output file name for transformed data.
- pathsa list of items which are a pathlike object or string representing a directory
Paths to add to matlabpath.
- use_mcra boolean
Run m-code using SPM MCR.
- use_v8structa boolean
Generate SPM8 and higher compatible jobs. (Nipype default value:
True
)
- out_filea pathlike object or string representing an existing file
Transformed image file.
CalcCoregAffine¶
Bases: SPMCommand
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()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
- movinga pathlike object or string representing an existing file
Volume transform can be applied to register with target.
- targeta pathlike object or string representing an existing file
Target for generating affine transform.
- invmata pathlike object or string representing a file
Filename used to store inverse affine matrix.
- mata pathlike object or string representing a file
Filename used to store affine matrix.
- matlab_cmda unicode string
Matlab command to use.
- mfilea boolean
Run m-code using m-file. (Nipype default value:
True
)- pathsa list of items which are a pathlike object or string representing a directory
Paths to add to matlabpath.
- use_mcra boolean
Run m-code using SPM MCR.
- use_v8structa boolean
Generate SPM8 and higher compatible jobs. (Nipype default value:
True
)
- invmata pathlike object or string representing a file
Matlab file holding inverse transform.
- mata pathlike object or string representing an existing file
Matlab file holding transform.
DicomImport¶
Bases: SPMCommand
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()
- in_filesa list of items which are a pathlike object or string representing an existing file
Dicom files to be converted.
- format‘nii’ or ‘img’
Output format. (Nipype default value:
nii
)- icedimsa boolean
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. (Nipype default value:
False
)- matlab_cmda unicode string
Matlab command to use.
- mfilea boolean
Run m-code using m-file. (Nipype default value:
True
)- output_dira unicode string
Output directory. (Nipype default value:
./converted_dicom
)- output_dir_struct‘flat’ or ‘series’ or ‘patname’ or ‘patid_date’ or ‘patid’ or ‘date_time’
Directory structure for the output. (Nipype default value:
flat
)- pathsa list of items which are a pathlike object or string representing a directory
Paths to add to matlabpath.
- use_mcra boolean
Run m-code using SPM MCR.
- use_v8structa boolean
Generate SPM8 and higher compatible jobs. (Nipype default value:
True
)
- out_filesa list of items which are a pathlike object or string representing an existing file
Converted files.
Reslice¶
Bases: SPMCommand
uses spm_reslice to resample in_file into space of space_defining
- in_filea pathlike object or string representing an existing file
File to apply transform to, (only updates header).
- space_defininga pathlike object or string representing an existing file
Volume defining space to slice in_file into.
- interp0 <= a long integer <= 7
Degree of b-spline used for interpolation0 is nearest neighbor (default). (Nipype default value:
0
)- matlab_cmda unicode string
Matlab command to use.
- mfilea boolean
Run m-code using m-file. (Nipype default value:
True
)- out_filea pathlike object or string representing a file
Optional file to save resliced volume.
- pathsa list of items which are a pathlike object or string representing a directory
Paths to add to matlabpath.
- use_mcra boolean
Run m-code using SPM MCR.
- use_v8structa boolean
Generate SPM8 and higher compatible jobs. (Nipype default value:
True
)
- out_filea pathlike object or string representing an existing file
Resliced volume.
ResliceToReference¶
Bases: SPMCommand
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()
- in_filesa list of items which are a pathlike object or string representing an existing file
Files on which deformation is applied.
- bounding_boxa list of from 6 to 6 items which are a float
6-element list (opt).
- interpolation0 <= a long integer <= 7
Degree of b-spline used for interpolation.
- matlab_cmda unicode string
Matlab command to use.
- mfilea boolean
Run m-code using m-file. (Nipype default value:
True
)- pathsa list of items which are a pathlike object or string representing a directory
Paths to add to matlabpath.
- targeta pathlike object or string representing an existing file
File defining target space.
- use_mcra boolean
Run m-code using SPM MCR.
- use_v8structa boolean
Generate SPM8 and higher compatible jobs. (Nipype default value:
True
)- voxel_sizesa list of from 3 to 3 items which are a float
3-element list (opt).
- out_filesa list of items which are a pathlike object or string representing an existing file
Transformed files.