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interfaces.afni.preprocess

Allineate

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/afni/preprocess.py#L996

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]
in_file: (an existing file name)
        input file to 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
out_file: (a file name)
        output file from 3dAllineate
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype
suffix: (a string, nipype default value: _allineate)
        out_file suffix

Outputs:

out_file: (an existing file name)
        cut file

Automask

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/afni/preprocess.py#L600

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
apply_suffix: (a string, nipype default value: _masked)
        out_file suffix
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
mask_suffix: (a string, nipype default value: _mask)
        out_file suffix
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

Outputs:

brain_file: (an existing file name)
        brain file (skull stripped)
out_file: (an existing file name)
        mask file

BrickStat

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/afni/preprocess.py#L1371

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:

min_val: (a float)
        output

Calc

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/afni/preprocess.py#L1536

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
in_file_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
in_file_b: (a file name)
        operand file to 3dcalc
other: (a file name)
        other options
out_file: (a file name)
        output file from 3dFourier
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype
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
suffix: (a string, nipype default value: _calc)
        out_file suffix

Outputs:

out_file: (an existing file name)
         output file

Copy

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/afni/preprocess.py#L812

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
suffix: (a string, nipype default value: _copy)
        out_file suffix

Outputs:

out_file: (a file name)
        copied file

Despike

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/afni/preprocess.py#L522

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
suffix: (a string, nipype default value: _despike)
        out_file suffix

Outputs:

out_file: (an existing file name)
        despiked img

Detrend

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/afni/preprocess.py#L462

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
suffix: (a string, nipype default value: _detrend)
        out_file suffix

Outputs:

out_file: (an existing file name)
        statistical file

Fim

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/afni/preprocess.py#L1237

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
suffix: (a string, nipype default value: _fim)
        out_file suffix

Outputs:

out_file: (an existing file name)
        outfile

Fourier

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/afni/preprocess.py#L877

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
suffix: (a string, nipype default value: _fourier)
        out_file suffix

Outputs:

out_file: (an existing file name)
        band-pass filtered file

Maskave

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/afni/preprocess.py#L1058

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
suffix: (a string, nipype default value: _maskave)
        out_file suffix

Outputs:

out_file: (an existing file name)
        outfile

Merge

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/afni/preprocess.py#L757

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]
in_files: (an existing file name)

[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
out_file: (a file name)
        output file from 3dmerge
outputtype: ('NIFTI_GZ' or 'AFNI' or 'NIFTI')
        AFNI output filetype
suffix: (a string, nipype default value: _merge)
        out_file suffix

Outputs:

out_file: (an existing file name)
        smoothed file

ROIStats

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/afni/preprocess.py#L1448

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:

stats: (a file name)
        output

Refit

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/afni/preprocess.py#L206

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
suffix: (a string, nipype default value: _refit)
        out_file suffix
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:

out_file: (an existing file name)
        Same file as original infile with modified matrix

Resample

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/afni/preprocess.py#L345

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, nipype default value: _resample)
        out_file suffix

Outputs:

out_file: (an existing file name)
        reoriented or resampled file

SkullStrip

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/afni/preprocess.py#L1116

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
suffix: (a string, nipype default value: _skullstrip)
        out_file suffix

Outputs:

out_file: (an existing file name)
        outfile

TCat

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/afni/preprocess.py#L1173

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_files: (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
suffix: (a string, nipype default value: _tcat)
        out_file suffix

Outputs:

out_file: (an existing file name)
        outfile

TCorrelate

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/afni/preprocess.py#L1309

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
suffix: (a string, nipype default value: _tcor)
        out_file suffix

Outputs:

out_file: (an existing file name)
        outfile

TShift

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/afni/preprocess.py#L137

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, nipype default value: _tshift)
        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:

out_file: (a file name)
        post slice time shifted 4D image

TStat

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/afni/preprocess.py#L405

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
suffix: (a string, nipype default value: _tstat)
        out_file suffix

Outputs:

out_file: (an existing file name)
        statistical file

To3D

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/afni/preprocess.py#L59

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
out_file: (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

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/afni/preprocess.py#L687

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
suffix: (a string, nipype default value: _volreg)
        out_file suffix
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:

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

Warp

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/afni/preprocess.py#L284

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, nipype default value: _warp)
        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:

out_file: (an existing file name)
        spatially transformed input image

ZCutUp

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/afni/preprocess.py#L938

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]
in_file: (an existing file name)
        input file to 3dZcutup
out_file: (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
suffix: (a string, nipype default value: _zcutup)
        out_file suffix

Outputs:

out_file: (an existing file name)
        cut file