cmtklib.interfaces.afni module¶

The AFNI module provides Nipype interfaces for the AFNI toolbox missing in nipype or modified.

Bandpass¶

Bases: nipype.interfaces.afni.base.AFNICommand

Wrapped executable: 3dBandpass.

Program to lowpass and/or highpass each voxel time series in a dataset.

Calls the 3dBandpass tool from AFNI, offering more/different options than Fourier

For complete details, see the 3dBandpass Documentation.

Examples
>>> from nipype.interfaces import afni as afni
>>> from nipype.testing import  example_data
>>> bandpass = afni.Bandpass()
>>> bandpass.inputs.in_file = example_data('functional.nii')
>>> bandpass.inputs.highpass = 0.005
>>> bandpass.inputs.lowpass = 0.1
>>> res = bandpass.run() 
highpassa float
Highpass. Maps to a command-line argument: %f (position: -3).

in_filea pathlike object or string representing an existing file
Input file to 3dBandpass. Maps to a command-line argument: %s (position: -1).

lowpassa float
Lowpass. Maps to a command-line argument: %f (position: -2).

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

automaska boolean
Create a mask from the input dataset. Maps to a command-line argument: -automask.

blura float

Blur (inside the mask only) with a filter
width (FWHM) of ‘fff’ millimeters.

Maps to a command-line argument: -blur %f.

despikea boolean

Despike each time series before other processing.

++ Hopefully, you don’t actually need to do this,
which is why it is optional.

Maps to a command-line argument: -despike.

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: {})

localPVa float

Replace each vector by the local Principal Vector

(AKA first singular vector) from a neighborhood of radius ‘rrr’ millimiters.

++ Note that the PV time series is L2 normalized. ++ This option is mostly for Bob Cox to have fun with.

Maps to a command-line argument: -localPV %f.

maska pathlike object or string representing an existing file
Mask file. Maps to a command-line argument: -mask %s (position: 2).

nfftan integer
Set the FFT length [must be a legal value]. Maps to a command-line argument: -nfft %d.

no_detrenda boolean

Skip the quadratic detrending of the input that

occurs before the FFT-based bandpassing.

++ You would only want to do this if the dataset
had been detrended already in some other program.

Maps to a command-line argument: -nodetrend.

normalizea boolean

Make all output time series have L2 norm = 1
++ i.e., sum of squares = 1.

Maps to a command-line argument: -norm.

notransa boolean

Don’t check for initial positive transients in the data:
++ The test is a little slow, so skipping it is OK, if you KNOW the data time series are transient-free.

Maps to a command-line argument: -notrans.

num_threadsan integer
Set number of threads. (Nipype default value: 1)

orthogonalize_dseta pathlike object or string representing an existing file

Orthogonalize each voxel to the corresponding
voxel time series in dataset ‘fset’, which must have the same spatial and temporal grid structure as the main input dataset. ++ At present, only one ‘-dsort’ option is allowed.

Maps to a command-line argument: -dsort %s.

orthogonalize_filea list of items which are a pathlike object or string representing an existing file

Also orthogonalize input to columns in f.1D
++ Multiple ‘-ort’ options are allowed.

Maps to a command-line argument: -ort %s.

out_filea pathlike object or string representing a file
Output file from 3dBandpass. Maps to a command-line argument: -prefix %s (position: 1).

outputtype‘NIFTI’ or ‘AFNI’ or ‘NIFTI_GZ’
AFNI output filetype.

tra float
Set time step (TR) in sec [default=from dataset header]. Maps to a command-line argument: -dt %f.

out_filea pathlike object or string representing an existing file
Output file.

Despike¶

Link to code

Bases: nipype.interfaces.afni.base.AFNICommand

Wrapped executable: 3dDespike.

Removes ‘spikes’ from the 3D+time input dataset.

It calls the 3dDespike tool from AFNI.

For complete details, see the 3dDespike Documentation.

Examples
>>> from nipype.interfaces import afni
>>> despike = afni.Despike()
>>> despike.inputs.in_file = 'functional.nii'
>>> despike.cmdline
'3dDespike -prefix functional_despike functional.nii'
>>> res = despike.run()  
in_filea pathlike object or string representing an existing file
Input file to 3dDespike. Maps to a command-line argument: %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: {})

num_threadsan integer
Set number of threads. (Nipype default value: 1)

out_filea pathlike object or string representing a file
Output image file name. Maps to a command-line argument: -prefix %s.

outputtype‘NIFTI’ or ‘AFNI’ or ‘NIFTI_GZ’
AFNI output filetype.

out_filea pathlike object or string representing an existing file
Output file.