nipype.interfaces.mrtrix.preprocess module

DWI2Tensor

Link to code

Bases: CommandLine

Wrapped executable: dwi2tensor.

Converts diffusion-weighted images to tensor images.

Example

>>> import nipype.interfaces.mrtrix as mrt
>>> dwi2tensor = mrt.DWI2Tensor()
>>> dwi2tensor.inputs.in_file = 'dwi.mif'
>>> dwi2tensor.inputs.encoding_file = 'encoding.txt'
>>> dwi2tensor.cmdline
'dwi2tensor -grad encoding.txt dwi.mif dwi_tensor.mif'
>>> dwi2tensor.run()                                   
in_filea list of items which are a pathlike object or string representing an existing file

Diffusion-weighted images. Maps to a command-line argument: %s (position: -2).

argsa unicode string

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

debuga boolean

Display debugging messages. Maps to a command-line argument: -debug (position: 1).

encoding_filea pathlike object or string representing a file

Encoding file supplied as a 4xN text file with each line is in the format [ X Y Z b ], where [ X Y Z ] describe the direction of the applied gradient, and b gives the b-value in units (1000 s/mm^2). See FSL2MRTrix(). Maps to a command-line argument: -grad %s (position: 2).

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: {})

ignore_slice_by_volumea list of from 2 to 2 items which are an integer (int or long)

Requires two values (i.e. [34 1] for [Slice Volume] Ignores the image slices specified when computing the tensor. Slice here means the z coordinate of the slice to be ignored. Maps to a command-line argument: -ignoreslices %s (position: 2).

ignore_volumesa list of at least 1 items which are an integer (int or long)

Requires two values (i.e. [2 5 6] for [Volumes] Ignores the image volumes specified when computing the tensor. Maps to a command-line argument: -ignorevolumes %s (position: 2).

out_filenamea pathlike object or string representing a file

Output tensor filename. Maps to a command-line argument: %s (position: -1).

quieta boolean

Do not display information messages or progress status. Maps to a command-line argument: -quiet (position: 1).

tensora pathlike object or string representing an existing file

Path/name of output diffusion tensor image.

Erode

Link to code

Bases: CommandLine

Wrapped executable: erode.

Erode (or dilates) a mask (i.e. binary) image

Example

>>> import nipype.interfaces.mrtrix as mrt
>>> erode = mrt.Erode()
>>> erode.inputs.in_file = 'mask.mif'
>>> erode.run()                                     
in_filea pathlike object or string representing an existing file

Input mask image to be eroded. Maps to a command-line argument: %s (position: -2).

argsa unicode string

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

debuga boolean

Display debugging messages. Maps to a command-line argument: -debug (position: 1).

dilatea boolean

Perform dilation rather than erosion. Maps to a command-line argument: -dilate (position: 1).

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: {})

number_of_passesan integer (int or long)

The number of passes (default: 1). Maps to a command-line argument: -npass %s.

out_filenamea pathlike object or string representing a file

Output image filename. Maps to a command-line argument: %s (position: -1).

quieta boolean

Do not display information messages or progress status. Maps to a command-line argument: -quiet (position: 1).

out_filea pathlike object or string representing an existing file

The output image.

GenerateWhiteMatterMask

Link to code

Bases: CommandLine

Wrapped executable: gen_WM_mask.

Generates a white matter probability mask from the DW images.

Example

>>> import nipype.interfaces.mrtrix as mrt
>>> genWM = mrt.GenerateWhiteMatterMask()
>>> genWM.inputs.in_file = 'dwi.mif'
>>> genWM.inputs.encoding_file = 'encoding.txt'
>>> genWM.run()                                     
binary_maska pathlike object or string representing an existing file

Binary brain mask. Maps to a command-line argument: %s (position: -2).

encoding_filea pathlike object or string representing an existing file

Gradient encoding, supplied as a 4xN text file with each line is in the format [ X Y Z b ], where [ X Y Z ] describe the direction of the applied gradient, and b gives the b-value in units (1000 s/mm^2). See FSL2MRTrix. Maps to a command-line argument: -grad %s (position: 1).

in_filea pathlike object or string representing an existing file

Diffusion-weighted images. Maps to a command-line argument: %s (position: -3).

argsa unicode 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: {})

noise_level_margina float

Specify the width of the margin on either side of the image to be used to estimate the noise level (default = 10). Maps to a command-line argument: -margin %s.

out_WMProb_filenamea pathlike object or string representing a file

Output WM probability image filename. Maps to a command-line argument: %s (position: -1).

WMprobabilitymapa pathlike object or string representing an existing file

WMprobabilitymap.

MRConvert

Link to code

Bases: CommandLine

Wrapped executable: mrconvert.

Perform conversion between different file types and optionally extract a subset of the input image.

If used correctly, this program can be a very useful workhorse. In addition to converting images between different formats, it can be used to extract specific studies from a data set, extract a specific region of interest, flip the images, or to scale the intensity of the images.

Example

>>> import nipype.interfaces.mrtrix as mrt
>>> mrconvert = mrt.MRConvert()
>>> mrconvert.inputs.in_file = 'dwi_FA.mif'
>>> mrconvert.inputs.out_filename = 'dwi_FA.nii'
>>> mrconvert.run()                                 
in_filea pathlike object or string representing an existing file

Voxel-order data filename. Maps to a command-line argument: %s (position: -2).

argsa unicode 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: {})

extension‘mif’ or ‘nii’ or ‘float’ or ‘char’ or ‘short’ or ‘int’ or ‘long’ or ‘double’

“i.e. Bfloat”. Can be “char”, “short”, “int”, “long”, “float” or “double”. (Nipype default value: mif)

extract_at_axis1 or 2 or 3

“Extract data only at the coordinates specified. This option specifies the Axis. Must be used in conjunction with extract_at_coordinate. Maps to a command-line argument: -coord %s (position: 1).

extract_at_coordinatea list of from 1 to 3 items which are a float

“Extract data only at the coordinates specified. This option specifies the coordinates. Must be used in conjunction with extract_at_axis. Three comma-separated numbers giving the size of each voxel in mm. Maps to a command-line argument: %s (position: 2).

layout‘nii’ or ‘float’ or ‘char’ or ‘short’ or ‘int’ or ‘long’ or ‘double’

Specify the layout of the data in memory. The actual layout produced will depend on whether the output image format can support it. Maps to a command-line argument: -output %s (position: 2).

offset_biasa float

Apply offset to the intensity values. Maps to a command-line argument: -scale %d (position: 3).

out_filenamea pathlike object or string representing a file

Output filename. Maps to a command-line argument: %s (position: -1).

output_datatype‘nii’ or ‘float’ or ‘char’ or ‘short’ or ‘int’ or ‘long’ or ‘double’

“i.e. Bfloat”. Can be “char”, “short”, “int”, “long”, “float” or “double”. Maps to a command-line argument: -output %s (position: 2).

prsa boolean

Assume that the DW gradients are specified in the PRS frame (Siemens DICOM only). Maps to a command-line argument: -prs (position: 3).

replace_NaN_with_zeroa boolean

Replace all NaN values with zero. Maps to a command-line argument: -zero (position: 3).

resamplea float

Apply scaling to the intensity values. Maps to a command-line argument: -scale %d (position: 3).

voxel_dimsa list of from 3 to 3 items which are a float

Three comma-separated numbers giving the size of each voxel in mm. Maps to a command-line argument: -vox %s (position: 3).

converteda pathlike object or string representing an existing file

Path/name of 4D volume in voxel order.

MRMultiply

Link to code

Bases: CommandLine

Wrapped executable: mrmult.

Multiplies two images.

Example

>>> import nipype.interfaces.mrtrix as mrt
>>> MRmult = mrt.MRMultiply()
>>> MRmult.inputs.in_files = ['dwi.mif', 'dwi_WMProb.mif']
>>> MRmult.run()                                             
in_filesa list of items which are a pathlike object or string representing an existing file

Input images to be multiplied. Maps to a command-line argument: %s (position: -2).

argsa unicode string

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

debuga boolean

Display debugging messages. Maps to a command-line argument: -debug (position: 1).

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_filenamea pathlike object or string representing a file

Output image filename. Maps to a command-line argument: %s (position: -1).

quieta boolean

Do not display information messages or progress status. Maps to a command-line argument: -quiet (position: 1).

out_filea pathlike object or string representing an existing file

The output image of the multiplication.

MRTransform

Link to code

Bases: CommandLine

Wrapped executable: mrtransform.

Apply spatial transformations or reslice images

Example

>>> MRxform = MRTransform()
>>> MRxform.inputs.in_files = 'anat_coreg.mif'
>>> MRxform.run()                                   
in_filesa list of items which are a pathlike object or string representing an existing file

Input images to be transformed. Maps to a command-line argument: %s (position: -2).

argsa unicode string

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

debuga boolean

Display debugging messages. Maps to a command-line argument: -debug (position: 1).

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: {})

flip_xa boolean

Assume the transform is supplied assuming a coordinate system with the x-axis reversed relative to the MRtrix convention (i.e. x increases from right to left). This is required to handle transform matrices produced by FSL’s FLIRT command. This is only used in conjunction with the -reference option. Maps to a command-line argument: -flipx (position: 1).

inverta boolean

Invert the specified transform before using it. Maps to a command-line argument: -inverse (position: 1).

out_filenamea pathlike object or string representing a file

Output image. Maps to a command-line argument: %s (position: -1).

quieta boolean

Do not display information messages or progress status. Maps to a command-line argument: -quiet (position: 1).

reference_imagea pathlike object or string representing an existing file

In case the transform supplied maps from the input image onto a reference image, use this option to specify the reference. Note that this implicitly sets the -replace option. Maps to a command-line argument: -reference %s (position: 1).

replace_transforma boolean

Replace the current transform by that specified, rather than applying it to the current transform. Maps to a command-line argument: -replace (position: 1).

template_imagea pathlike object or string representing an existing file

Reslice the input image to match the specified template image. Maps to a command-line argument: -template %s (position: 1).

transformation_filea pathlike object or string representing an existing file

The transform to apply, in the form of a 4x4 ascii file. Maps to a command-line argument: -transform %s (position: 1).

out_filea pathlike object or string representing an existing file

The output image of the transformation.

MRTrixInfo

Link to code

Bases: CommandLine

Wrapped executable: mrinfo.

Prints out relevant header information found in the image specified.

Example

>>> import nipype.interfaces.mrtrix as mrt
>>> MRinfo = mrt.MRTrixInfo()
>>> MRinfo.inputs.in_file = 'dwi.mif'
>>> MRinfo.run()                                    
in_filea pathlike object or string representing an existing file

Input images to be read. Maps to a command-line argument: %s (position: -2).

argsa unicode 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: {})

MRTrixViewer

Link to code

Bases: CommandLine

Wrapped executable: mrview.

Loads the input images in the MRTrix Viewer.

Example

>>> import nipype.interfaces.mrtrix as mrt
>>> MRview = mrt.MRTrixViewer()
>>> MRview.inputs.in_files = 'dwi.mif'
>>> MRview.run()                                    
in_filesa list of items which are a pathlike object or string representing an existing file

Input images to be viewed. Maps to a command-line argument: %s (position: -2).

argsa unicode string

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

debuga boolean

Display debugging messages. Maps to a command-line argument: -debug (position: 1).

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: {})

quieta boolean

Do not display information messages or progress status. Maps to a command-line argument: -quiet (position: 1).

MedianFilter3D

Link to code

Bases: CommandLine

Wrapped executable: median3D.

Smooth images using a 3x3x3 median filter.

Example

>>> import nipype.interfaces.mrtrix as mrt
>>> median3d = mrt.MedianFilter3D()
>>> median3d.inputs.in_file = 'mask.mif'
>>> median3d.run()                                  
in_filea pathlike object or string representing an existing file

Input images to be smoothed. Maps to a command-line argument: %s (position: -2).

argsa unicode string

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

debuga boolean

Display debugging messages. Maps to a command-line argument: -debug (position: 1).

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_filenamea pathlike object or string representing a file

Output image filename. Maps to a command-line argument: %s (position: -1).

quieta boolean

Do not display information messages or progress status. Maps to a command-line argument: -quiet (position: 1).

out_filea pathlike object or string representing an existing file

The output image.

Tensor2ApparentDiffusion

Link to code

Bases: CommandLine

Wrapped executable: tensor2ADC.

Generates a map of the apparent diffusion coefficient (ADC) in each voxel

Example

>>> import nipype.interfaces.mrtrix as mrt
>>> tensor2ADC = mrt.Tensor2ApparentDiffusion()
>>> tensor2ADC.inputs.in_file = 'dwi_tensor.mif'
>>> tensor2ADC.run()                                
in_filea pathlike object or string representing an existing file

Diffusion tensor image. Maps to a command-line argument: %s (position: -2).

argsa unicode string

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

debuga boolean

Display debugging messages. Maps to a command-line argument: -debug (position: 1).

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_filenamea pathlike object or string representing a file

Output Fractional Anisotropy filename. Maps to a command-line argument: %s (position: -1).

quieta boolean

Do not display information messages or progress status. Maps to a command-line argument: -quiet (position: 1).

ADCa pathlike object or string representing an existing file

The output image of the major eigenvectors of the diffusion tensor image.

Tensor2FractionalAnisotropy

Link to code

Bases: CommandLine

Wrapped executable: tensor2FA.

Generates a map of the fractional anisotropy in each voxel.

Example

>>> import nipype.interfaces.mrtrix as mrt
>>> tensor2FA = mrt.Tensor2FractionalAnisotropy()
>>> tensor2FA.inputs.in_file = 'dwi_tensor.mif'
>>> tensor2FA.run()                                 
in_filea pathlike object or string representing an existing file

Diffusion tensor image. Maps to a command-line argument: %s (position: -2).

argsa unicode string

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

debuga boolean

Display debugging messages. Maps to a command-line argument: -debug (position: 1).

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_filenamea pathlike object or string representing a file

Output Fractional Anisotropy filename. Maps to a command-line argument: %s (position: -1).

quieta boolean

Do not display information messages or progress status. Maps to a command-line argument: -quiet (position: 1).

FAa pathlike object or string representing an existing file

The output image of the major eigenvectors of the diffusion tensor image.

Tensor2Vector

Link to code

Bases: CommandLine

Wrapped executable: tensor2vector.

Generates a map of the major eigenvectors of the tensors in each voxel.

Example

>>> import nipype.interfaces.mrtrix as mrt
>>> tensor2vector = mrt.Tensor2Vector()
>>> tensor2vector.inputs.in_file = 'dwi_tensor.mif'
>>> tensor2vector.run()                             
in_filea pathlike object or string representing an existing file

Diffusion tensor image. Maps to a command-line argument: %s (position: -2).

argsa unicode string

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

debuga boolean

Display debugging messages. Maps to a command-line argument: -debug (position: 1).

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_filenamea pathlike object or string representing a file

Output vector filename. Maps to a command-line argument: %s (position: -1).

quieta boolean

Do not display information messages or progress status. Maps to a command-line argument: -quiet (position: 1).

vectora pathlike object or string representing an existing file

The output image of the major eigenvectors of the diffusion tensor image.

Threshold

Link to code

Bases: CommandLine

Wrapped executable: threshold.

Create bitwise image by thresholding image intensity.

By default, the threshold level is determined using a histogram analysis to cut out the background. Otherwise, the threshold intensity can be specified using command line options. Note that only the first study is used for thresholding.

Example

>>> import nipype.interfaces.mrtrix as mrt
>>> thresh = mrt.Threshold()
>>> thresh.inputs.in_file = 'wm_mask.mif'
>>> thresh.run()                                             
in_filea pathlike object or string representing an existing file

The input image to be thresholded. Maps to a command-line argument: %s (position: -2).

absolute_threshold_valuea float

Specify threshold value as absolute intensity. Maps to a command-line argument: -abs %s.

argsa unicode string

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

debuga boolean

Display debugging messages. Maps to a command-line argument: -debug (position: 1).

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: {})

inverta boolean

Invert output binary mask. Maps to a command-line argument: -invert (position: 1).

out_filenamea pathlike object or string representing a file

The output binary image mask. Maps to a command-line argument: %s (position: -1).

percentage_threshold_valuea float

Specify threshold value as a percentage of the peak intensity in the input image. Maps to a command-line argument: -percent %s.

quieta boolean

Do not display information messages or progress status. Maps to a command-line argument: -quiet (position: 1).

replace_zeros_with_NaNa boolean

Replace all zero values with NaN. Maps to a command-line argument: -nan (position: 1).

out_filea pathlike object or string representing an existing file

The output binary image mask.