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interfaces.afni.preprocess

Allineate

Link to code

Wraps command 3dAllineate

Program to align one dataset (the ‘source’) to a base dataset

For complete details, see the 3dAllineate Documentation.

Examples

>>> from nipype.interfaces import afni as afni
>>> from nipype.testing import  example_data
>>> allineate = afni.Allineate()
>>> allineate.inputs.infile = example_data('functional.nii')
>>> allineate.inputs.outfile= 'functional_allineate.nii'
>>> allineate.inputs.matrix= example_data('cmatrix.mat')
>>> res = allineate.run() 

Inputs:

[Mandatory]
infile: (an existing file name)
        input file to 3dAllineate
outfile: (a file name)
        output file from 3dAllineate

[Optional]
args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
matrix: (a file name)
        matrix to align input file
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype

Outputs:

args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
out_file: (an existing file name)
        cut file
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype

Automask

Link to code

Wraps command 3dAutomask

Create a brain-only mask of the image using AFNI 3dAutomask command

For complete details, see the 3dAutomask Documentation.

Examples

>>> from nipype.interfaces import afni as afni
>>> from nipype.testing import  example_data
>>> automask = afni.Automask()
>>> automask.inputs.in_file = example_data('functional.nii')
>>> automask.inputs.dilate = 1
>>> res = automask.run() 

Inputs:

[Mandatory]
in_file: (an existing file name)
        input file to 3dAutomask

[Optional]
apply_mask: (a file name)
        output file from 3dAutomask
args: (a string)
        Additional parameters to the command
clfrac: (a float)
        sets the clip level fraction (must be 0.1-0.9). A small value will tend to make the mask
        larger [default = 0.5].
dilate: (an integer)
        dilate the mask outwards
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
erode: (an integer)
        erode the mask inwards
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
options: (a string)
        automask settings
out_file: (a file name)
        output file from 3dAutomask (a brain mask)
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype
suffix: (a string)
        out_file suffix

Outputs:

args: (a string)
        Additional parameters to the command
brain_file: (an existing file name)
        brain file (skull stripped)
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
out_file: (an existing file name)
        mask file
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype

BrickStat

Link to code

Wraps command 3dBrickStat

Compute maximum and/or minimum voxel values of an input dataset

For complete details, see the 3dBrickStat Documentation.

Examples

>>> from nipype.interfaces import afni as afni
>>> from nipype.testing import  example_data
>>> brickstat = afni.BrickStat()
>>> brickstat.inputs.in_file = example_data('functional.nii')
>>> brickstat.inputs.mask = example_data('skeleton_mask.nii.gz')
>>> brickstat.inputs.min = True
>>> res = brickstat.run() 

Inputs:

[Mandatory]
in_file: (an existing file name)
        input file to 3dmaskave

[Optional]
args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
mask: (a file name)
        -mask dset = use dset as mask to include/exclude voxels
min: (a boolean)
        print the minimum value in dataset
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype

Outputs:

args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
min_val: (a float)
        output
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype

Calc

Link to code

Wraps command 3dcalc

This program does voxel-by-voxel arithmetic on 3D datasets

For complete details, see the 3dcalc Documentation.

Examples

>>> from nipype.interfaces import afni as afni
>>> from nipype.testing import  example_data
>>> calc = afni.Calc()
>>> calc.inputs.infile_a = example_data('functional.nii')
>>> calc.inputs.Infile_b = example_data('functional2.nii.gz')
>>> calc.inputs.expr='a*b'
>>> calc.inputs.out_file =  'functional_calc.nii.gz'
>>> res = calc.run() 

Inputs:

[Mandatory]
expr: (a string)
        expr
infile_a: (a file name)
        input file to 3dcalc

[Optional]
args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
infile_b: (a file name)
        operand file to 3dcalc
other: (a file name)
        other options
out_file: (a file name)
        output file from 3dFourier
single_idx: (an integer)
        volume index for infile_a
start_idx: (an integer)
        start index for infile_a
        requires: stop_idx
stop_idx: (an integer)
        stop index for infile_a
        requires: start_idx

Outputs:

out_file: (an existing file name)
         output file

Copy

Link to code

Wraps command 3dcopy

Copies an image of one type to an image of the same or different type using 3dcopy command

For complete details, see the 3dcopy Documentation.

Examples

>>> from nipype.interfaces import afni as afni
>>> from nipype.testing import  example_data
>>> copy = afni.Copy()
>>> copy.inputs.in_file = example_data('functional.nii')
>>> copy.inputs.out_file = 'new_func.nii'
>>> res = copy.run() 

Inputs:

[Mandatory]
in_file: (an existing file name)
        input file to 3dcopy

[Optional]
args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
out_file: (a file name)
        output file from 3dcopy
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype

Outputs:

args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
out_file: (a file name)
        copied file
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype

Despike

Link to code

Wraps command 3dDespike

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

For complete details, see the 3dDespike Documentation.

Examples

>>> from nipype.interfaces import afni as afni
>>> from nipype.testing import  example_data
>>> despike = afni.Despike()
>>> despike.inputs.in_file = example_data('functional.nii')
>>> res = despike.run() 

Inputs:

[Mandatory]
in_file: (an existing file name)
        input file to 3dDespike

[Optional]
args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
options: (a string)
        additional args
out_file: (a file name)
        output file from 3dDespike
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype

Outputs:

args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
out_file: (an existing file name)
        despiked img
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype

Detrend

Link to code

Wraps command 3dDetrend

This program removes components from voxel time series using linear least squares

For complete details, see the 3dDetrend Documentation.

Examples

>>> from nipype.interfaces import afni as afni
>>> from nipype.testing import  example_data
>>> detrend = afni.Detrend()
>>> detrend.inputs.in_file = example_data('functional.nii')
>>> detrend.inputs.options = '-polort 2'
>>> res = detrend.run() 

Inputs:

[Mandatory]
in_file: (an existing file name)
        input file to 3dDetrend

[Optional]
args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
options: (a string)
        selected statistical output
out_file: (a file name)
        output file from 3dDetrend
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype

Outputs:

args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
out_file: (an existing file name)
        statistical file
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype

Fim

Link to code

Wraps command 3dfim+

Program to calculate the cross-correlation of an ideal reference waveform with the measured FMRI time series for each voxel

For complete details, see the 3dfim+ Documentation.

Examples

>>> from nipype.interfaces import afni as afni
>>> from nipype.testing import  example_data
>>> fim = afni.Fim()
>>> fim.inputs.in_file = example_data('functional.nii')
>>> fim.inputs.ideal_file= example_data('seed.1D')
>>> fim.inputs.out_file = 'functional_corr.nii'
>>> fim.inputs.out = 'Correlation'
>>> fim.inputs.fim_thr = 0.0009
>>> res = fim.run() 

Inputs:

[Mandatory]
ideal_file: (a file name)
        output to the file
in_file: (an existing file name)
        input file to 3dfim+

[Optional]
args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
fim_thr: (a float)
        fim internal mask threshold value
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
out: (a string)
        Flag to output the specified parameter
out_file: (a file name)
        output file from 3dfim+
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype

Outputs:

args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
out_file: (an existing file name)
        outfile
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype

Fourier

Link to code

Wraps command 3dFourier

Program to lowpass and/or highpass each voxel time series in a dataset, via the FFT

For complete details, see the 3dFourier Documentation.

Examples

>>> from nipype.interfaces import afni as afni
>>> from nipype.testing import  example_data
>>> fourier = afni.Fourier()
>>> fourier.inputs.in_file = example_data('functional.nii')
>>> fourier.inputs.other = '-retrend'
>>> fourier.inputs.highpass = 0.005
>>> fourier.inputs.lowpass = 0.1
>>> res = fourier.run() 

Inputs:

[Mandatory]
highpass: (a float)
        highpass
in_file: (an existing file name)
        input file to 3dFourier
lowpass: (a float)
        lowpass

[Optional]
args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
other: (a string)
        other options
out_file: (a file name)
        output file from 3dFourier
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype

Outputs:

args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
out_file: (an existing file name)
        band-pass filtered file
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype

Maskave

Link to code

Wraps command 3dmaskave

Computes average of all voxels in the input dataset which satisfy the criterion in the options list

For complete details, see the 3dmaskave Documentation.

Examples

>>> from nipype.interfaces import afni as afni
>>> from nipype.testing import  example_data
>>> maskave = afni.Maskave()
>>> maskave.inputs.in_file = example_data('functional.nii')
>>> maskave.inputs.mask= example_data('seed_mask.nii')
>>> maskave.inputs.quiet= True
>>> maskave.inputs.out_file= 'maskave.1D'
>>> res = maskave.run() 

Inputs:

[Mandatory]
in_file: (an existing file name)
        input file to 3dmaskave

[Optional]
args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
mask: (a file name)
        matrix to align input file
out_file: (a file name)
        output to the file
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype
quiet: (a boolean)
        matrix to align input file

Outputs:

args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
out_file: (an existing file name)
        outfile
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype

Merge

Link to code

Wraps command 3dmerge

Merge or edit volumes using AFNI 3dmerge command

For complete details, see the 3dmerge Documentation.

Examples

>>> from nipype.interfaces import afni as afni
>>> from nipype.testing import  example_data
>>> merge = afni.Merge()
>>> merge.inputs.infile = example_data('functional.nii')
>>> merge.inputs.blurfwhm = 4.0
>>> merge.inputs.doall = True
>>> merge.inputs.outfile = 'e7.nii'
>>> res = merge.run() 

Inputs:

[Mandatory]
infile: (an existing file name)
        input file to 3dvolreg
outfile: (a file name)
        output file from 3dvolreg

[Optional]
args: (a string)
        Additional parameters to the command
blurfwhm: (an integer)
        FWHM blur value (mm)
doall: (a boolean)
        apply options to all sub-bricks in dataset
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
other: (a string)
        other options
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype

Outputs:

args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
out_file: (an existing file name)
        smoothed file
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype

ROIStats

Link to code

Wraps command 3dROIstats

Display statistics over masked regions

For complete details, see the 3dROIstats Documentation.

Examples

>>> from nipype.interfaces import afni as afni
>>> from nipype.testing import  example_data
>>> roistats = afni.ROIStats()
>>> roistats.inputs.in_file = example_data('functional.nii')
>>> roistats.inputs.mask = example_data('skeleton_mask.nii.gz')
>>> roistats.inputs.quiet=True
>>> res = roistats.run() 

Inputs:

[Mandatory]
in_file: (an existing file name)
        input file to 3dROIstats

[Optional]
args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
mask: (a file name)
        input mask
mask_f2short: (a boolean)
        Tells the program to convert a float mask to short integers, by simple rounding.
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype
quiet: (a boolean)
        execute quietly

Outputs:

args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype
stats: (a file name)
        output

Refit

Link to code

Wraps command 3drefit

Changes some of the information inside a 3D dataset’s header

For complete details, see the `3drefit Documentation. <http://afni.nimh.nih.gov/pub/dist/doc/program_help/3drefit.html>

Examples

>>> from nipype.interfaces import afni as afni
>>> from nipype.testing import  example_data
>>> refit = afni.Refit()
>>> refit.inputs.in_file = example_data('structural.nii')
>>> refit.inputs.deoblique=True
>>> res = refit.run() 

Inputs:

[Mandatory]
in_file: (an existing file name)
        input file to 3drefit

[Optional]
args: (a string)
        Additional parameters to the command
deoblique: (a boolean)
        replace current transformation matrix with cardinal matrix
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype
xorigin: (a string)
        x distance for edge voxel offset
yorigin: (a string)
        y distance for edge voxel offset
zorigin: (a string)
        z distance for edge voxel offset

Outputs:

args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
out_file: (an existing file name)
        Same file as original infile with modified matrix
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype

Resample

Link to code

Wraps command 3dresample

Resample or reorient an image using AFNI 3dresample command

For complete details, see the 3dresample Documentation.

Examples

>>> from nipype.interfaces import afni as afni
>>> from nipype.testing import  example_data
>>> resample = afni.Resample()
>>> resample.inputs.in_file = example_data('functional.nii')
>>> resample.inputs.orientation= 'RPI'
>>> res = resample.run() 

Inputs:

[Mandatory]
in_file: (an existing file name)
        input file to 3dresample

[Optional]
args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
orientation: (a string)
        new orientation code
out_file: (a file name)
        output file from 3dresample
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype
suffix: (a string)
        out_file suffix

Outputs:

args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
out_file: (an existing file name)
        reoriented or resampled file
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype

SkullStrip

Link to code

Wraps command 3dSkullStrip

A program to extract the brain from surrounding tissue from MRI T1-weighted images

For complete details, see the 3dSkullStrip Documentation.

Examples

>>> from nipype.interfaces import afni as afni
>>> from nipype.testing import  example_data
>>> skullstrip = afni.Skullstrip()
>>> skullstrip.inputs.in_file = example_data('functional.nii')
>>> skullstrip.inputs.options = '-o_ply'
>>> res = skullstrip.run() 

Inputs:

[Mandatory]
in_file: (an existing file name)
        input file to 3dSkullStrip

[Optional]
args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
options: (a string)
        options
out_file: (a file name)
        output to the file
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype

Outputs:

args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
out_file: (an existing file name)
        outfile
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype

TCat

Link to code

Wraps command 3dTcat

Concatenate sub-bricks from input datasets into one big 3D+time dataset

For complete details, see the 3dTcat Documentation.

Examples

>>> from nipype.interfaces import afni as afni
>>> from nipype.testing import  example_data
>>> tcat = afni.TCat()
>>> tcat.inputs.in_file = example_data('functional.nii')
>>> tcat.inputs.out_file= 'functional_tcat.nii'
>>> tcat.inputs.rlt = '+'
>>> res = tcat.run() 

Inputs:

[Mandatory]
in_file: (an existing file name)
        input file to 3dTcat

[Optional]
args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
out_file: (a file name)
        output to the file
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype
rlt: (a string)
        options

Outputs:

args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
out_file: (an existing file name)
        outfile
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype

TCorrelate

Link to code

Wraps command 3dTcorrelate

Computes the correlation coefficient between corresponding voxel time series in two input 3D+time datasets ‘xset’ and ‘yset’

For complete details, see the 3dTcorrelate Documentation.

Examples

>>> from nipype.interfaces import afni as afni
>>> from nipype.testing import  example_data
>>> tcorrelate = afni.TCorrelate()
>>> tcorrelate.inputs.in_file = example_data('functional.nii')
>>> tcorrelate.inputs.xset= example_data('u_rc1s1_Template.nii')
>>> tcorrelate.inputs.yset = example_data('u_rc1s2_Template.nii')
>>> tcorrelate.inputs.out_file = 'functional_tcorrelate.nii.gz'
>>> tcorrelate.inputs.polort = -1
>>> tcorrelate.inputs.pearson = True
>>> res = tcarrelate.run() 

Inputs:

[Mandatory]
xset: (an existing file name)
        input xset
yset: (an existing file name)
        input yset

[Optional]
args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
options: (a string)
        other options
out_file: (a file name)
        Save output into dataset with prefix
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype
pearson: (a boolean)
        Correlation is the normal Pearson correlation coefficient
polort: (an integer)
        Remove polynomical trend of order m

Outputs:

args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
out_file: (an existing file name)
        outfile
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype

TShift

Link to code

Wraps command 3dTshift

Shifts voxel time series from input so that seperate slices are aligned to the same temporal origin

For complete details, see the `3dTshift Documentation. <http://afni.nimh.nih.gov/pub/dist/doc/program_help/3dTshift.html>

Examples

>>> from nipype.interfaces import afni as afni
>>> from nipype.testing import  example_data
>>> tshift = afni.TShift()
>>> tshift.inputs.in_file = example_data('functional.nii')
>>> tshift.inputs.out_file = 'functional_tshift.nii'
>>> tshift.inputs.tpattern = 'alt+z'
>>> tshift.inputs.tzero = 0.0
>>> res = tshift.run()   

Inputs:

[Mandatory]
in_file: (an existing file name)
        input file to 3dTShift

[Optional]
args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore: (an integer)
        ignore the first set of points specified
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
interp: ('Fourier' or 'linear' or 'cubic' or 'quintic' or 'heptic')
        different interpolation methods (see 3dTShift for details) default = Fourier
out_file: (a file name)
        output file from 3dTshift
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype
rlt: (a boolean)
        Before shifting, remove the mean and linear trend
rltplus: (a boolean)
        Before shifting, remove the mean and linear trend and later put back the mean
suffix: (a string)
        out_file suffix
tpattern: ('alt+z' or 'alt+z2' or 'alt-z' or 'alt-z2' or 'seq+z' or 'seq-z')
        use specified slice time pattern rather than one in header
tr: (a string)
        manually set the TRYou can attach suffix "s" for seconds or "ms" for milliseconds.
tslice: (an integer)
        align each slice to time offset of given slice
        mutually_exclusive: tzero
tzero: (a float)
        align each slice to given time offset
        mutually_exclusive: tslice

Outputs:

args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
out_file: (a file name)
        post slice time shifted 4D image
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype

TStat

Link to code

Wraps command 3dTstat

Compute voxel-wise statistics using AFNI 3dTstat command

For complete details, see the 3dTstat Documentation.

Examples

>>> from nipype.interfaces import afni as afni
>>> from nipype.testing import  example_data
>>> tstat = afni.TStat()
>>> tstat.inputs.in_file = example_data('functional.nii')
>>> tstat.inputs.options= '-mean'
>>> res = tstat.run() 

Inputs:

[Mandatory]
in_file: (an existing file name)
        input file to 3dTstat

[Optional]
args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
options: (a string)
        selected statistical output
out_file: (a file name)
        output file from 3dTstat
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype

Outputs:

args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
out_file: (an existing file name)
        statistical file
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype

To3D

Link to code

Wraps command to3d

Create a 3D dataset from 2D image files using AFNI to3d command

For complete details, see the to3d Documentation

Examples

>>> from nipype.interfaces import afni
>>> To3D = afni.To3D()
>>> To3D.inputs.datatype = 'float'
>>> To3D.inputs.infolder = 'dicomdir'
>>> To3D.inputs.filetype = "anat"
>>> res = To3D.run() 

Inputs:

[Mandatory]
infolder: (an existing directory name)
        folder with DICOM images to convert
outfile: (a file name)
        converted image file

[Optional]
args: (a string)
        Additional parameters to the command
assumemosaic: (a boolean)
        assume that Siemens image is mosaic
datatype: ('short' or 'float' or 'byte' or 'complex')
        set output file datatype
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
filetype: ('spgr' or 'fse' or 'epan' or 'anat' or 'ct' or 'spct' or 'pet' or 'mra' or
         'bmap' or 'diff' or 'omri' or 'abuc' or 'fim' or 'fith' or 'fico' or 'fitt' or 'fift'
         or 'fizt' or 'fict' or 'fibt' or 'fibn' or 'figt' or 'fipt' or 'fbuc')
        type of datafile being converted
funcparams: (a string)
        parameters for functional data
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype
skipoutliers: (a boolean)
        skip the outliers check

Outputs:

out_file: (an existing file name)
        converted file

Volreg

Link to code

Wraps command 3dvolreg

Register input volumes to a base volume using AFNI 3dvolreg command

For complete details, see the 3dvolreg Documentation.

Examples

>>> from nipype.interfaces import afni as afni
>>> from nipype.testing import  example_data
>>> volreg = afni.Volreg()
>>> volreg.inputs.in_file = example_data('functional.nii')
>>> volreg.inputs.other = '-Fourier -twopass'
>>> volreg.inputs.zpad = '4'
>>> res = volreg.run() 

Inputs:

[Mandatory]
in_file: (an existing file name)
        input file to 3dvolreg

[Optional]
args: (a string)
        Additional parameters to the command
basefile: (a file name)
        base file for registration
copyorigin: (a boolean)
        copy base file origin coords to output
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
md1dfile: (a file name)
        max displacement output file
oned_file: (a file name)
        1D movement parameters output file
other: (a string)
        other options
out_file: (a file name)
        output file from 3dvolreg
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype
timeshift: (a boolean)
        time shift to mean slice time offset
verbose: (a boolean)
        more detailed description of the process
zpad: (a file name)
        Zeropad around the edges by 'n' voxels during rotations

Outputs:

args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
md1d_file: (a file name)
        max displacement info file
oned_file: (a file name)
        movement parameters info file
out_file: (an existing file name)
        registered file
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype

Warp

Link to code

Wraps command 3dWarp

Use 3dWarp for spatially transforming a dataset

For complete details, see the 3dWarp Documentation.

Examples

>>> from nipype.interfaces import afni as afni
>>> from nipype.testing import  example_data
>>> warp = afni.Warp()
>>> warp.inputs.in_file = example_data('structural.nii')
>>> warp.inputs.deoblique = True
>>> res = warp.run() 

Inputs:

[Mandatory]
in_file: (an existing file name)
        input file to 3dWarp

[Optional]
args: (a string)
        Additional parameters to the command
deoblique: (a boolean)
        transform dataset from oblique to cardinal
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
gridset: (an existing file name)
        copy grid of specified dataset
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
interp: ('linear' or 'cubic' or 'NN' or 'quintic')
        spatial interpolation methods [default = linear]
matparent: (an existing file name)
        apply transformation from 3dWarpDrive
mni2tta: (a boolean)
        transform dataset from MNI152 to Talaraich
out_file: (a file name)
        output file from 3dWarp
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype
suffix: (a string)
        out_file suffix
tta2mni: (a boolean)
        transform dataset from Talairach to MNI152
zpad: (an integer)
        pad input dataset with N planes of zero on all sides.

Outputs:

args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
out_file: (an existing file name)
        spatially transformed input image
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype

ZCutUp

Link to code

Wraps command 3dZcutup

Cut z-slices from a volume using AFNI 3dZcutup command

For complete details, see the 3dZcutup Documentation.

Examples

>>> from nipype.interfaces import afni as afni
>>> from nipype.testing import  example_data
>>> zcutup = afni.Zcutup()
>>> zcutup.inputs.infile = example_data('functional.nii')
>>> zcutup.inputs.outfile= 'functional_zcutup.nii'
>>> zcutup.inputs.keep= '0 10'
>>> res = zcutup.run() 

Inputs:

[Mandatory]
infile: (an existing file name)
        input file to 3dZcutup
outfile: (a file name)
        output file from 3dZcutup

[Optional]
args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
keep: (a string)
        slice range to keep in output
other: (a string)
        other options
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype

Outputs:

args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
out_file: (an existing file name)
        cut file
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype