Code: file:///build/buildd/nipype-0.5.3/nipype/interfaces/afni/preprocess.py#L999
Wraps command 3dAllineate
Program to align one dataset (the ‘source’) to a base dataset
For complete details, see the 3dAllineate Documentation.
>>> 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
Code: file:///build/buildd/nipype-0.5.3/nipype/interfaces/afni/preprocess.py#L614
Wraps command 3dAutomask
Create a brain-only mask of the image using AFNI 3dAutomask command
For complete details, see the 3dAutomask Documentation.
>>> 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
Code: file:///build/buildd/nipype-0.5.3/nipype/interfaces/afni/preprocess.py#L1377
Wraps command 3dBrickStat
Compute maximum and/or minimum voxel values of an input dataset
For complete details, see the 3dBrickStat Documentation.
>>> 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
Code: file:///build/buildd/nipype-0.5.3/nipype/interfaces/afni/preprocess.py#L1541
Wraps command 3dcalc
This program does voxel-by-voxel arithmetic on 3D datasets
For complete details, see the 3dcalc Documentation.
>>> 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
Code: file:///build/buildd/nipype-0.5.3/nipype/interfaces/afni/preprocess.py#L820
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.
>>> 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
Code: file:///build/buildd/nipype-0.5.3/nipype/interfaces/afni/preprocess.py#L534
Wraps command 3dDespike
Removes ‘spikes’ from the 3D+time input dataset
For complete details, see the 3dDespike Documentation.
>>> 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
Code: file:///build/buildd/nipype-0.5.3/nipype/interfaces/afni/preprocess.py#L472
Wraps command 3dDetrend
This program removes components from voxel time series using linear least squares
For complete details, see the 3dDetrend Documentation.
>>> 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
Code: file:///build/buildd/nipype-0.5.3/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.
>>> 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
Code: file:///build/buildd/nipype-0.5.3/nipype/interfaces/afni/preprocess.py#L887
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.
>>> 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
Code: file:///build/buildd/nipype-0.5.3/nipype/interfaces/afni/preprocess.py#L1052
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.
>>> 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
Code: file:///build/buildd/nipype-0.5.3/nipype/interfaces/afni/preprocess.py#L774
Wraps command 3dmerge
Merge or edit volumes using AFNI 3dmerge command
For complete details, see the 3dmerge Documentation.
>>> 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
Code: file:///build/buildd/nipype-0.5.3/nipype/interfaces/afni/preprocess.py#L1454
Wraps command 3dROIstats
Display statistics over masked regions
For complete details, see the 3dROIstats Documentation.
>>> 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
Code: file:///build/buildd/nipype-0.5.3/nipype/interfaces/afni/preprocess.py#L209
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>
>>> 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
Code: file:///build/buildd/nipype-0.5.3/nipype/interfaces/afni/preprocess.py#L349
Wraps command 3dresample
Resample or reorient an image using AFNI 3dresample command
For complete details, see the 3dresample Documentation.
>>> 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
Code: file:///build/buildd/nipype-0.5.3/nipype/interfaces/afni/preprocess.py#L1112
Wraps command 3dSkullStrip
A program to extract the brain from surrounding tissue from MRI T1-weighted images
For complete details, see the 3dSkullStrip Documentation.
>>> 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
Code: file:///build/buildd/nipype-0.5.3/nipype/interfaces/afni/preprocess.py#L1170
Wraps command 3dTcat
Concatenate sub-bricks from input datasets into one big 3D+time dataset
For complete details, see the 3dTcat Documentation.
>>> 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
Code: file:///build/buildd/nipype-0.5.3/nipype/interfaces/afni/preprocess.py#L1314
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.
>>> 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
Code: file:///build/buildd/nipype-0.5.3/nipype/interfaces/afni/preprocess.py#L138
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>
>>> 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
Code: file:///build/buildd/nipype-0.5.3/nipype/interfaces/afni/preprocess.py#L414
Wraps command 3dTstat
Compute voxel-wise statistics using AFNI 3dTstat command
For complete details, see the 3dTstat Documentation.
>>> 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
Code: file:///build/buildd/nipype-0.5.3/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
>>> 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
Code: file:///build/buildd/nipype-0.5.3/nipype/interfaces/afni/preprocess.py#L700
Wraps command 3dvolreg
Register input volumes to a base volume using AFNI 3dvolreg command
For complete details, see the 3dvolreg Documentation.
>>> 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
Code: file:///build/buildd/nipype-0.5.3/nipype/interfaces/afni/preprocess.py#L283
Wraps command 3dWarp
Use 3dWarp for spatially transforming a dataset
For complete details, see the 3dWarp Documentation.
>>> 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
Code: file:///build/buildd/nipype-0.5.3/nipype/interfaces/afni/preprocess.py#L950
Wraps command 3dZcutup
Cut z-slices from a volume using AFNI 3dZcutup command
For complete details, see the 3dZcutup Documentation.
>>> 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