cmtklib.interfaces.fsl module

The FSL module provides Nipype interfaces for FSL functions missing in Nipype or modified.

ApplymultipleWarp

Bases: nipype.interfaces.base.core.BaseInterface

Apply a deformation field estimated by FSL fnirt to a list of images.

Example
>>> from cmtklib.interfaces import fsl
>>> apply_warp = fsl.ApplymultipleWarp()
>>> apply_warp.inputs.in_files = ['/path/to/sub-01_atlas-L2018_desc-scale1_dseg.nii.gz',
>>>                               '/path/to/sub-01_atlas-L2018_desc-scale2_dseg.nii.gz',
>>>                               '/path/to/sub-01_atlas-L2018_desc-scale3_dseg.nii.gz',
>>>                               '/path/to/sub-01_atlas-L2018_desc-scale4_dseg.nii.gz',
>>>                               '/path/to/sub-01_atlas-L2018_desc-scale5_dseg.nii.gz']
>>> apply_warp.inputs.field_file = '/path/to/fnirt_deformation.nii.gz'
>>> apply_warp.inputs.ref_file = '/path/to/sub-01_meanBOLD.nii.gz'
>>> apply_warp.run()  
field_filea pathlike object or string representing an existing file
Deformation field.

ref_filea pathlike object or string representing an existing file
Reference image used for target space.

in_filesa list of items which are a pathlike object or string representing an existing file
Files to be registered.

interp‘nn’ or ‘trilinear’ or ‘sinc’ or ‘spline’
Interpolation method. Maps to a command-line argument: --interp=%s (position: -2).

out_filesa list of items which are a pathlike object or string representing a file
Warped files.

ApplymultipleXfm

Link to code

Bases: nipype.interfaces.base.core.BaseInterface

Apply an XFM transform estimated by FSL flirt to a list of images.

Example
>>> from cmtklib.interfaces import fsl
>>> apply_xfm = fsl.ApplymultipleXfm
>>> apply_xfm.inputs.in_files = ['/path/to/sub-01_atlas-L2018_desc-scale1_dseg.nii.gz',
>>>                              '/path/to/sub-01_atlas-L2018_desc-scale2_dseg.nii.gz',
>>>                              '/path/to/sub-01_atlas-L2018_desc-scale3_dseg.nii.gz',
>>>                              '/path/to/sub-01_atlas-L2018_desc-scale4_dseg.nii.gz',
>>>                              '/path/to/sub-01_atlas-L2018_desc-scale5_dseg.nii.gz']
>>> apply_xfm.inputs.xfm_file = '/path/to/flirt_transform.xfm'
>>> apply_xfm.inputs.reference = '/path/to/sub-01_meanBOLD.nii.gz'
>>> apply_xfm.run()  
referencea pathlike object or string representing an existing file
Reference image used for target space.

xfm_filea pathlike object or string representing an existing file
Transform file.

in_filesa list of items which are a pathlike object or string representing an existing file
Files to be registered.

interp‘nearestneighbour’ or ‘spline’
Interpolation used.

out_filesa list of items which are a pathlike object or string representing a file
Transformed files.

BinaryThreshold

Link to code

Bases: nipype.interfaces.fsl.base.FSLCommand

Wrapped executable: fslmaths.

Use fslmaths to apply a threshold to an image in a variety of ways.

Examples
>>> from cmtklib.interfaces.fsl import BinaryThreshold
>>> thresh = BinaryThreshold()
>>> thresh.inputs.in_file = '/path/to/probseg.nii.gz'
>>> thresh.inputs.thresh = 0.5
>>> thresh.inputs.out_file = '/path/to/output_binseg.nii.gz'
>>> thresh.run()  
in_filea pathlike object or string representing an existing file
Image to operate on. Maps to a command-line argument: %s (position: 2).

out_filea pathlike object or string representing a file
Image to write. Maps to a command-line argument: %s (position: 5).

thresha float
Threshold value. Maps to a command-line argument: -thr %s (position: 3).

argsa string
Additional parameters to the command. Maps to a command-line argument: %s.

binarizea boolean
Maps to a command-line argument: -bin (position: 4).

environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})

output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’
FSL output type.

out_filea pathlike object or string representing an existing file
Image written after calculations.

CreateAcqpFile

Link to code

Bases: nipype.interfaces.base.core.BaseInterface

Create an acquisition Acqp file for FSL eddy.

Note

This value can be extracted from dMRI data acquired on Siemens scanner

Examples
>>> from cmtklib.interfaces.fsl import CreateAcqpFile
>>> create_acqp = CreateAcqpFile()
>>> create_acqp.inputs.total_readout  = 0.28
>>> create_acqp.run()  
total_readout : a float

acqp : a pathlike object or string representing an existing file

CreateIndexFile

Link to code

Bases: nipype.interfaces.base.core.BaseInterface

Create an index file for FSL eddy from a mrtrix diffusion gradient table.

Examples
>>> from cmtklib.interfaces.fsl import CreateIndexFile
>>> create_index = CreateIndexFile()
>>> create_index.inputs.in_grad_mrtrix  = 'grad.txt'
>>> create_index.run()  
in_grad_mrtrixa pathlike object or string representing an existing file
Input DWI gradient table in MRTrix format.

index : a pathlike object or string representing an existing file

Eddy

Link to code

Bases: nipype.interfaces.fsl.base.FSLCommand

Wrapped executable: eddy.

Performs eddy current distorsion correction using FSL eddy.

Example
>>> from cmtklib.interfaces import fsl
>>> eddyc = fsl.Eddy(in_file='diffusion.nii',
>>>                  bvecs='diffusion.bvecs',
>>>                  bvals='diffusion.bvals',
>>>                  out_file="diffusion_eddyc.nii")
>>> eddyc.run()  
acqpa pathlike object or string representing an existing file
File containing acquisition parameters. Maps to a command-line argument: --acqp=%s (position: 3).

bvalsa pathlike object or string representing an existing file
File containing the b-values for all volumes in –imain. Maps to a command-line argument: --bvals=%s (position: 5).

bvecsa pathlike object or string representing an existing file
File containing the b-vectors for all volumes in –imain. Maps to a command-line argument: --bvecs=%s (position: 4).

in_filea pathlike object or string representing an existing file
File containing all the images to estimate distortions for. Maps to a command-line argument: --imain=%s (position: 0).

indexa pathlike object or string representing an existing file
File containing indices for all volumes in –imain into –acqp and –topup. Maps to a command-line argument: --index=%s (position: 2).

maska pathlike object or string representing an existing file
Mask to indicate brain. Maps to a command-line argument: --mask=%s (position: 1).

argsa string
Additional parameters to the command. Maps to a command-line argument: %s.

environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})

out_filea pathlike object or string representing a file
Basename for output. Maps to a command-line argument: --out=%s (position: 6).

output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’
FSL output type.

verbosea boolean
Display debugging messages. Maps to a command-line argument: --verbose (position: 7).

bvecs_rotateda pathlike object or string representing an existing file
Path/name of rotated DWI gradient bvecs file.

eddy_correcteda pathlike object or string representing an existing file
Path/name of 4D eddy corrected DWI file.

EddyOpenMP

Link to code

Bases: nipype.interfaces.fsl.base.FSLCommand

Wrapped executable: eddy_openmp.

Performs eddy current distorsion correction using FSL eddy_openmp.

Example
>>> from cmtklib.interfaces import fsl
>>> eddyc = fsl.EddyOpenMP(in_file='diffusion.nii',
>>>                        bvecs='diffusion.bvecs',
>>>                        bvals='diffusion.bvals',
>>>                        out_file="diffusion_eddyc.nii")
>>> eddyc.run()  
acqpa pathlike object or string representing an existing file
File containing acquisition parameters. Maps to a command-line argument: --acqp=%s (position: 3).

bvalsa pathlike object or string representing an existing file
File containing the b-values for all volumes in –imain. Maps to a command-line argument: --bvals=%s (position: 5).

bvecsa pathlike object or string representing an existing file
File containing the b-vectors for all volumes in –imain. Maps to a command-line argument: --bvecs=%s (position: 4).

in_filea pathlike object or string representing an existing file
File containing all the images to estimate distortions for. Maps to a command-line argument: --imain=%s (position: 0).

indexa pathlike object or string representing an existing file
File containing indices for all volumes in –imain into –acqp and –topup. Maps to a command-line argument: --index=%s (position: 2).

maska pathlike object or string representing an existing file
Mask to indicate brain. Maps to a command-line argument: --mask=%s (position: 1).

argsa string
Additional parameters to the command. Maps to a command-line argument: %s.

environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})

out_filea pathlike object or string representing a file
Basename for output. Maps to a command-line argument: --out=%s (position: 6).

output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’
FSL output type.

verbosea boolean
Display debugging messages. Maps to a command-line argument: --verbose (position: 7).

bvecs_rotateda pathlike object or string representing an existing file
Path/name of rotated DWI gradient bvecs file.

eddy_correcteda pathlike object or string representing an existing file
Path/name of 4D eddy corrected DWI file.

FSLCreateHD

Link to code

Bases: nipype.interfaces.base.core.CommandLine

Wrapped executable: fslcreatehd.

Calls the fslcreatehd command to create an image for space / dimension reference.

Examples
>>> from cmtklib.interfaces.fsl import FSLCreateHD
>>> fsl_create = FSLCreateHD()
>>> fsl_create.inputs.im_size = [256, 256, 256, 1]
>>> fsl_create.inputs.vox_size = [1, 1, 1]
>>> fsl_create.inputs.tr = 0
>>> fsl_create.inputs.origin = [0, 0, 0]
>>> fsl_create.inputs.datatype = '16' # 16: float
>>> fsl_create.inputs.out_filename = '/path/to/generated_image.nii.gz'
>>> fsl_create.run()  
datatype‘2’ or ‘4’ or ‘8’ or ‘16’ or ‘32’ or ‘64’
Datatype values: 2=char, 4=short, 8=int, 16=float, 64=double. Maps to a command-line argument: %s (position: 5).

im_sizea list of from 4 to 4 items which are an integer
Image size : xsize , ysize, zsize, tsize . Maps to a command-line argument: %s (position: 1).

origina list of from 3 to 3 items which are an integer
Origin coordinates : xorig, yorig, zorig. Maps to a command-line argument: %s (position: 4).

out_filenamea pathlike object or string representing a file

the output temp reference image created.

Maps to a command-line argument: %s (position: 6).

tran integer
<tr>. Maps to a command-line argument: %s (position: 3).

vox_sizea list of from 3 to 3 items which are an integer
Voxel size : xvoxsize, yvoxsize, zvoxsize. Maps to a command-line argument: %s (position: 2).

argsa string
Additional parameters to the command. Maps to a command-line argument: %s.

environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})

out_filea pathlike object or string representing an existing file
Path/name of the output reference image created.

MathsCommand

Link to code

Bases: nipype.interfaces.fsl.base.FSLCommand

Wrapped executable: fslmaths.

Calls the fslmaths command in a variety of ways.

Examples
>>> from cmtklib.interfaces.fsl import MathsCommand
>>> fsl_maths = MathsCommand()
>>> fsl_maths.inputs.in_file = '/path/to/image_with_nans.nii.gz'
>>> fsl_maths.inputs.nan2zeros = True
>>> fsl_maths.inputs.out_file = '/path/to/image_with_no_nans.nii.gz'
>>> fsl_maths.run()  
in_filea pathlike object or string representing an existing file
Image to operate on. Maps to a command-line argument: %s (position: 2).

argsa string
Additional parameters to the command. Maps to a command-line argument: %s.

environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})

internal_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’
Datatype to use for calculations (default is float). Maps to a command-line argument: -dt %s (position: 1).

nan2zerosa boolean
Change NaNs to zeros before doing anything. Maps to a command-line argument: -nan (position: 3).

out_filea pathlike object or string representing a file
Image to write. Maps to a command-line argument: %s (position: -2).

output_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’
Datatype to use for output (default uses input type). Maps to a command-line argument: -odt %s (position: -1).

output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’
FSL output type.

out_filea pathlike object or string representing an existing file
Image written after calculations.

Orient

Link to code

Bases: nipype.interfaces.fsl.base.FSLCommand

Wrapped executable: fslorient.

Use fslorient to get/set orientation information from an image’s header.

Advanced tool that reports or sets the orientation information in a file. Note that only in NIfTI files can the orientation be changed - Analyze files are always treated as “radiological” (meaning that they could be simply rotated into the same alignment as the MNI152 standard images - equivalent to the appropriate sform or qform in a NIfTI file having a negative determinant).

Examples
>>> from cmtklib.interfaces.fsl import Orient
>>> fsl_orient = Orient()
>>> fsl_orient.inputs.in_file = 'input_image.nii.gz'
>>> fsl_orient.inputs.force_radiological = True
>>> fsl_orient.inputs.out_file = 'output_image.nii.gz'
>>> fsl_orient.run()  
in_filea pathlike object or string representing an existing file
Input image. Maps to a command-line argument: %s (position: 2).

argsa string
Additional parameters to the command. Maps to a command-line argument: %s.

copy_qform2sforma boolean
Sets the sform equal to the qform - code and matrix. Maps to a command-line argument: -copyqform2sform (position: 1). Mutually exclusive with inputs: get_orient, get_sform, get_qform, set_sform, set_qform, get_sformcode, get_qformcode, set_sformcode, set_qformcode, copy_sform2qform, copy_qform2sform, delete_orient, force_radiological, force_neurological, swap_orient.

copy_sform2qforma boolean
Sets the qform equal to the sform - code and matrix. Maps to a command-line argument: -copysform2qform (position: 1). Mutually exclusive with inputs: get_orient, get_sform, get_qform, set_sform, set_qform, get_sformcode, get_qformcode, set_sformcode, set_qformcode, copy_sform2qform, copy_qform2sform, delete_orient, force_radiological, force_neurological, swap_orient.

delete_orienta boolean
Removes orient info from header. Maps to a command-line argument: -deleteorient (position: 1). Mutually exclusive with inputs: get_orient, get_sform, get_qform, set_sform, set_qform, get_sformcode, get_qformcode, set_sformcode, set_qformcode, copy_sform2qform, copy_qform2sform, delete_orient, force_radiological, force_neurological, swap_orient.

environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})

force_neurologicala boolean
Makes FSL neurological header - not Analyze. Maps to a command-line argument: -forceneurological (position: 1). Mutually exclusive with inputs: get_orient, get_sform, get_qform, set_sform, set_qform, get_sformcode, get_qformcode, set_sformcode, set_qformcode, copy_sform2qform, copy_qform2sform, delete_orient, force_radiological, force_neurological, swap_orient.

force_radiologicala boolean
Makes FSL radiological header. Maps to a command-line argument: -forceradiological (position: 1). Mutually exclusive with inputs: get_orient, get_sform, get_qform, set_sform, set_qform, get_sformcode, get_qformcode, set_sformcode, set_qformcode, copy_sform2qform, copy_qform2sform, delete_orient, force_radiological, force_neurological, swap_orient.

get_orienta boolean
Gets FSL left-right orientation. Maps to a command-line argument: -getorient (position: 1). Mutually exclusive with inputs: get_orient, get_sform, get_qform, set_sform, set_qform, get_sformcode, get_qformcode, set_sformcode, set_qformcode, copy_sform2qform, copy_qform2sform, delete_orient, force_radiological, force_neurological, swap_orient.

get_qforma boolean
Gets the 16 elements of the qform matrix. Maps to a command-line argument: -getqform (position: 1). Mutually exclusive with inputs: get_orient, get_sform, get_qform, set_sform, set_qform, get_sformcode, get_qformcode, set_sformcode, set_qformcode, copy_sform2qform, copy_qform2sform, delete_orient, force_radiological, force_neurological, swap_orient.

get_qformcodea boolean
Gets the qform integer code. Maps to a command-line argument: -getqformcode (position: 1). Mutually exclusive with inputs: get_orient, get_sform, get_qform, set_sform, set_qform, get_sformcode, get_qformcode, set_sformcode, set_qformcode, copy_sform2qform, copy_qform2sform, delete_orient, force_radiological, force_neurological, swap_orient.

get_sforma boolean
Gets the 16 elements of the sform matrix. Maps to a command-line argument: -getsform (position: 1). Mutually exclusive with inputs: get_orient, get_sform, get_qform, set_sform, set_qform, get_sformcode, get_qformcode, set_sformcode, set_qformcode, copy_sform2qform, copy_qform2sform, delete_orient, force_radiological, force_neurological, swap_orient.

get_sformcodea boolean
Gets the sform integer code. Maps to a command-line argument: -getsformcode (position: 1). Mutually exclusive with inputs: get_orient, get_sform, get_qform, set_sform, set_qform, get_sformcode, get_qformcode, set_sformcode, set_qformcode, copy_sform2qform, copy_qform2sform, delete_orient, force_radiological, force_neurological, swap_orient.

output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’
FSL output type.

set_qforma list of from 16 to 16 items which are a float
<m11 m12 … m44> sets the 16 elements of the qform matrix. Maps to a command-line argument: -setqform %f (position: 1). Mutually exclusive with inputs: get_orient, get_sform, get_qform, set_sform, set_qform, get_sformcode, get_qformcode, set_sformcode, set_qformcode, copy_sform2qform, copy_qform2sform, delete_orient, force_radiological, force_neurological, swap_orient.

set_qformcodean integer
<code> sets qform integer code. Maps to a command-line argument: -setqormcode %d (position: 1). Mutually exclusive with inputs: get_orient, get_sform, get_qform, set_sform, set_qform, get_sformcode, get_qformcode, set_sformcode, set_qformcode, copy_sform2qform, copy_qform2sform, delete_orient, force_radiological, force_neurological, swap_orient.

set_sforma list of from 16 to 16 items which are a float
<m11 m12 … m44> sets the 16 elements of the sform matrix. Maps to a command-line argument: -setsform %f (position: 1). Mutually exclusive with inputs: get_orient, get_sform, get_qform, set_sform, set_qform, get_sformcode, get_qformcode, set_sformcode, set_qformcode, copy_sform2qform, copy_qform2sform, delete_orient, force_radiological, force_neurological, swap_orient.

set_sformcodean integer
<code> sets sform integer code. Maps to a command-line argument: -setformcode %d (position: 1). Mutually exclusive with inputs: get_orient, get_sform, get_qform, set_sform, set_qform, get_sformcode, get_qformcode, set_sformcode, set_qformcode, copy_sform2qform, copy_qform2sform, delete_orient, force_radiological, force_neurological, swap_orient.

swap_orienta boolean
Swaps FSL radiological and FSL neurological. Maps to a command-line argument: -swaporient (position: 1). Mutually exclusive with inputs: get_orient, get_sform, get_qform, set_sform, set_qform, get_sformcode, get_qformcode, set_sformcode, set_qformcode, copy_sform2qform, copy_qform2sform, delete_orient, force_radiological, force_neurological, swap_orient.

orienta string
FSL left-right orientation.

out_filea pathlike object or string representing an existing file
Image with modified orientation.

qforma list of from 16 to 16 items which are a float
The 16 elements of the qform matrix.

qformcodean integer
Qform integer code.

sforma list of from 16 to 16 items which are a float
The 16 elements of the sform matrix.

sformcodean integer
Sform integer code.

Orient.aggregate_outputs(runtime=None, needed_outputs=None)[source]

Collate expected outputs and apply output traits validation.