Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/fsl/utils.py#L476
Wraps command avscale
Use FSL avscale command to extract info from mat file output of FLIRT
avscale = AvScale() avscale.inputs.mat_file = ‘flirt.mat’ res = avscale.run() # doctest: +SKIP
Inputs:
[Mandatory]
[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
mat_file: (an existing file name)
mat file to read
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
FSL output type
Outputs:
average_scaling
Average Scaling
backward_half_transform
Backwards Half Transform
determinant
Determinant
forward_half_transform
Forward Half Transform
left_right_orientation_preserved: (a boolean)
True if LR orientation preserved
rotation_translation_matrix
Rotation and Translation Matrix
scales
Scales (x,y,z)
skews
Skews
Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/fsl/utils.py#L907
Wraps command convert_xfm
Use the FSL utility convert_xfm to modify FLIRT transformation matrices.
>>> import nipype.interfaces.fsl as fsl
>>> invt = fsl.ConvertXFM()
>>> invt.inputs.in_file = "flirt.mat"
>>> invt.inputs.invert_xfm = True
>>> invt.inputs.out_file = 'flirt_inv.mat'
>>> invt.cmdline
'convert_xfm -omat flirt_inv.mat -inverse flirt.mat'
Inputs:
[Mandatory]
in_file: (an existing file name)
input transformation matrix
[Optional]
args: (a string)
Additional parameters to the command
concat_xfm: (a boolean)
write joint transformation of two input matrices
mutually_exclusive: invert_xfm, concat_xfm, fix_scale_skew
requires: in_file2
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
fix_scale_skew: (a boolean)
use secondary matrix to fix scale and skew
mutually_exclusive: invert_xfm, concat_xfm, fix_scale_skew
requires: in_file2
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_file2: (an existing file name)
second input matrix (for use with fix_scale_skew or concat_xfm
invert_xfm: (a boolean)
invert input transformation
mutually_exclusive: invert_xfm, concat_xfm, fix_scale_skew
out_file: (a file name)
final transformation matrix
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
FSL output type
Outputs:
out_file: (an existing file name)
output transformation matrix
Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/fsl/utils.py#L1090
Wraps command epidewarp.fsl
Wraps fieldmap unwarping script from Freesurfer’s epidewarp.fsl_
>>> dewarp = EPIDeWarp()
>>> dewarp.inputs.epi_file = "functional.nii"
>>> dewarp.inputs.mag_file = "magnitude.nii"
>>> dewarp.inputs.dph_file = "phase.nii"
>>> res = dewarp.run()
_epidewarp.fsl: http://surfer.nmr.mgh.harvard.edu/fswiki/epidewarp.fsl
Inputs:
[Mandatory]
dph_file: (an existing file name)
Phase file assumed to be scaled from 0 to 4095
mag_file: (an existing file name)
Magnitude file
[Optional]
args: (a string)
Additional parameters to the command
cleanup: (a boolean)
cleanup
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
epidw: (a string)
dewarped epi volume
esp: (a float, nipype default value: 0.58)
EPI echo spacing
exfdw: (a string)
dewarped example func volume
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the interface fails to
run
nocleanup: (a boolean, nipype default value: True)
no cleanup
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
FSL output type
sigma: (an integer, nipype default value: 2)
2D spatial gaussing smoothing stdev (default = 2mm)
tediff: (a float, nipype default value: 2.46)
difference in B0 field map TEs
tmpdir: (a string)
tmpdir
vsm: (a string)
voxel shift map
Outputs:
exf_mask: (a file name)
Mask from example functional volume
exfdw: (a file name)
dewarped functional volume example
unwarped_file: (a file name)
unwarped epi file
vsm_file: (a file name)
voxel shift map
Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/fsl/utils.py#L175
Wraps command fslroi
Uses FSL Fslroi command to extract region of interest (ROI) from an image.
You can a) take a 3D ROI from a 3D data set (or if it is 4D, the same ROI is taken from each time point and a new 4D data set is created), b) extract just some time points from a 4D data set, or c) control time and space limits to the ROI. Note that the arguments are minimum index and size (not maximum index). So to extract voxels 10 to 12 inclusive you would specify 10 and 3 (not 10 and 12).
>>> from nipype.interfaces.fsl import ExtractROI
>>> from nipype.testing import anatfile
>>> fslroi = ExtractROI(in_file=anatfile, roi_file='bar.nii', t_min=0, t_size=1)
>>> fslroi.cmdline == 'fslroi %s bar.nii 0 1'%anatfile
True
Inputs:
[Mandatory]
in_file: (an existing file name)
input file
[Optional]
args: (a string)
Additional parameters to the command
crop_list: (a list of items which are a tuple of the form: (an integer, an integer))
mutually_exclusive: x_min, x_size, y_min, y_size, z_min, z_size, t_min, t_size
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
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
FSL output type
roi_file: (a file name)
output file
t_min: (an integer)
t_size: (an integer)
x_min: (an integer)
x_size: (an integer)
y_min: (an integer)
y_size: (an integer)
z_min: (an integer)
z_size: (an integer)
Outputs:
roi_file: (an existing file name)
Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/fsl/utils.py#L356
Wraps command fsl_regfilt
Data de-noising by regressing out part of a design matrix
Uses simple OLS regression on 4D images
Inputs:
[Mandatory]
design_file: (an existing file name)
name of the matrix with time courses (e.g. GLM design or MELODIC mixing matrix)
filter_all: (a boolean)
use all columns in the design file in denoising
mutually_exclusive: filter_columns
filter_columns: (a list of items which are an integer)
(1-based) column indices to filter out of the data
mutually_exclusive: filter_all
in_file: (an existing file name)
input file name (4D image)
[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: (an existing file name)
mask image file name
out_file: (a file name)
output file name for the filtered data
out_vnscales: (a boolean)
output scaling factors for variance normalization
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
FSL output type
var_norm: (a boolean)
perform variance-normalization on data
Outputs:
out_file: (an existing file name)
output file name for the filtered data
Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/fsl/utils.py#L297
Wraps command fslmaths
Use FSL fslmaths command to allow mathematical manipulation of images
>>> from nipype.interfaces import fsl
>>> from nipype.testing import anatfile
>>> maths = fsl.ImageMaths(in_file=anatfile, op_string= '-add 5', out_file='foo_maths.nii')
>>> maths.cmdline == 'fslmaths %s -add 5 foo_maths.nii'%anatfile
True
Inputs:
[Mandatory]
in_file: (an existing file name)
[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_file2: (an existing file name)
op_string: (a string)
string defining the operation, i. e. -add
out_data_type: ('char' or 'short' or 'int' or 'float' or 'double' or 'input')
output datatype, one of (char, short, int, float, double, input)
out_file: (a file name)
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
FSL output type
suffix: (a string)
out_file suffix
Outputs:
out_file: (an existing file name)
Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/fsl/utils.py#L52
Wraps command fslmeants
Use fslmeants for printing the average timeseries (intensities) to the screen (or saves to a file). The average is taken over all voxels in the mask (or all voxels in the image if no mask is specified)
Inputs:
[Mandatory]
in_file: (an existing file name)
input file for computing the average timeseries
[Optional]
args: (a string)
Additional parameters to the command
eig: (a boolean)
calculate Eigenvariate(s) instead of mean (output will have 0 mean)
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: (an existing file name)
input 3D mask
nobin: (a boolean)
do not binarise the mask for calculation of Eigenvariates
order: (an integer, nipype default value: 1)
select number of Eigenvariates
out_file: (a file name)
name of output text matrix
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
FSL output type
show_all: (a boolean)
show all voxel time series (within mask) instead of averaging
spatial_coord: (a list of items which are an integer)
<x y z> requested spatial coordinate (instead of mask)
transpose: (a boolean)
output results in transpose format (one row per voxel/mean)
use_mm: (a boolean)
use mm instead of voxel coordinates (for -c option)
Outputs:
out_file: (an existing file name)
path/name of output text matrix
Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/fsl/utils.py#L406
Wraps command fslstats
Use FSL fslstats command to calculate stats from images
>>> from nipype.interfaces.fsl import ImageStats
>>> from nipype.testing import funcfile
>>> stats = ImageStats(in_file=funcfile, op_string= '-M')
>>> stats.cmdline == 'fslstats %s -M'%funcfile
True
Inputs:
[Mandatory]
in_file: (an existing file name)
input file to generate stats of
op_string: (a string)
string defining the operation, options are applied in order, e.g. -M -l 10 -M will
report the non-zero mean, apply athreshold and then report the new nonzero mean
[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_file: (an existing file name)
mask file used for option -k %s
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
FSL output type
split_4d: (a boolean)
give a separate output line for each 3D volume of a 4D timeseries
Outputs:
out_stat
stats output
Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/fsl/utils.py#L129
Wraps command fslmerge
Use fslmerge to concatenate images
Inputs:
[Mandatory]
dimension: ('t' or 'x' or 'y' or 'z')
dimension along which the file will be merged
in_files: (a list of items which are an existing file name)
[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
merged_file: (a file name)
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
FSL output type
Outputs:
merged_file: (an existing file name)
Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/fsl/utils.py#L556
Wraps command overlay
Use FSL’s overlay command to combine background and statistical images into one volume
>>> from nipype.interfaces import fsl
>>> combine = fsl.Overlay()
>>> combine.inputs.background_image = 'mean_func.nii.gz'
>>> combine.inputs.auto_thresh_bg = True
>>> combine.inputs.stat_image = 'zstat1.nii.gz'
>>> combine.inputs.stat_thresh = (3.5, 10)
>>> combine.inputs.show_negative_stats = True
>>> res = combine.run()
Inputs:
[Mandatory]
auto_thresh_bg: (a boolean)
automatically threhsold the background image
mutually_exclusive: auto_thresh_bg, full_bg_range, bg_thresh
background_image: (an existing file name)
image to use as background
bg_thresh: (a tuple of the form: (a float, a float))
min and max values for background intensity
mutually_exclusive: auto_thresh_bg, full_bg_range, bg_thresh
full_bg_range: (a boolean)
use full range of background image
mutually_exclusive: auto_thresh_bg, full_bg_range, bg_thresh
stat_image: (an existing file name)
statistical image to overlay in color
stat_thresh: (a tuple of the form: (a float, a float))
min and max values for the statistical overlay
[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)
combined image volume
out_type: ('float' or 'int', nipype default value: float)
write output with float or int
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
FSL output type
show_negative_stats: (a boolean)
display negative statistics in overlay
mutually_exclusive: stat_image2
stat_image2: (an existing file name)
second statistical image to overlay in color
mutually_exclusive: show_negative_stats
stat_thresh2: (a tuple of the form: (a float, a float))
min and max values for second statistical overlay
transparency: (a boolean, nipype default value: True)
make overlay colors semi-transparent
use_checkerboard: (a boolean)
use checkerboard mask for overlay
Outputs:
out_file: (an existing file name)
combined image volume
Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/fsl/utils.py#L807
Wraps command fsl_tsplot
Use fsl_tsplot to plot the estimated motion parameters from a realignment program.
>>> import nipype.interfaces.fsl as fsl
>>> plotter = fsl.PlotMotionParams()
>>> plotter.inputs.in_file = 'functional.par'
>>> plotter.inputs.in_source = 'fsl'
>>> plotter.inputs.plot_type = 'rotations'
>>> res = plotter.run()
The ‘in_source’ attribute determines the order of columns that are expected in the source file. FSL prints motion parameters in the order rotations, translations, while SPM prints them in the opposite order. This interface should be able to plot timecourses of motion parameters generated from other sources as long as they fall under one of these two patterns. For more flexibilty, see the fsl.PlotTimeSeries interface.
Inputs:
[Mandatory]
in_file: (an existing file name or a list of items which are an existing file name)
file with motion parameters
in_source: ('spm' or 'fsl')
which program generated the motion parameter file - fsl, spm
plot_type: ('rotations' or 'translations' or 'displacement')
which motion type to plot - rotations, translations, displacement
[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)
image to write
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
FSL output type
plot_size: (a tuple of the form: (an integer, an integer))
plot image height and width
Outputs:
out_file: (an existing file name)
image to write
Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/fsl/utils.py#L730
Wraps command fsl_tsplot
Use fsl_tsplot to create images of time course plots.
>>> import nipype.interfaces.fsl as fsl
>>> plotter = fsl.PlotTimeSeries()
>>> plotter.inputs.in_file = 'functional.par'
>>> plotter.inputs.title = 'Functional timeseries'
>>> plotter.inputs.labels = ['run1', 'run2']
>>> plotter.run()
Inputs:
[Mandatory]
in_file: (an existing file name or a list of items which are an existing file name)
file or list of files with columns of timecourse information
[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
labels: (a string or a list of items which are a string)
label or list of labels
legend_file: (an existing file name)
legend file
out_file: (a file name)
image to write
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
FSL output type
plot_finish: (an integer)
final column from in-file to plot
mutually_exclusive: plot_range
plot_range: (a tuple of the form: (an integer, an integer))
first and last columns from the in-file to plot
mutually_exclusive: plot_start, plot_finish
plot_size: (a tuple of the form: (an integer, an integer))
plot image height and width
plot_start: (an integer)
first column from in-file to plot
mutually_exclusive: plot_range
sci_notation: (a boolean)
switch on scientific notation
title: (a string)
plot title
x_precision: (an integer)
precision of x-axis labels
x_units: (an integer, nipype default value: 1)
scaling units for x-axis (between 1 and length of in file)
y_max: (a float)
maximum y value
mutually_exclusive: y_range
y_min: (a float)
minumum y value
mutually_exclusive: y_range
y_range: (a tuple of the form: (a float, a float))
min and max y axis values
mutually_exclusive: y_min, y_max
Outputs:
out_file: (an existing file name)
image to write
Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/fsl/utils.py#L1014
Wraps command fslpspec
Use FSL PowerSpectrum command for power spectrum estimation.
>>> from nipype.interfaces import fsl
>>> pspec = fsl.PowerSpectrum()
>>> pspec.inputs.in_file = 'functional.nii'
>>> res = pspec.run()
Inputs:
[Mandatory]
in_file: (an existing file name)
input 4D file to estimate the power spectrum
[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)
name of output 4D file for power spectrum
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
FSL output type
Outputs:
out_file: (an existing file name)
path/name of the output 4D power spectrum file
Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/fsl/utils.py#L652
Wraps command slicer
Use FSL’s slicer command to output a png image from a volume.
>>> from nipype.interfaces import fsl
>>> from nipype.testing import example_data
>>> slice = fsl.Slicer()
>>> slice.inputs.in_file = example_data('functional.nii')
>>> slice.inputs.all_axial = True
>>> slice.inputs.image_width = 750
>>> res = slice.run()
Inputs:
[Mandatory]
in_file: (an existing file name)
input volume
[Optional]
all_axial: (a boolean)
output all axial slices into one picture
mutually_exclusive: single_slice, middle_slices, all_axial, sample_axial
requires: image_width
args: (a string)
Additional parameters to the command
colour_map: (an existing file name)
use different colour map from that stored in nifti header
dither_edges: (a boolean)
produce semi-transparaent (dithered) edges
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
image_edges: (an existing file name)
volume to display edge overlay for (useful for checking registration
image_width: (an integer)
max picture width
intensity_range: (a tuple of the form: (a float, a float))
min and max intensities to display
label_slices: (a boolean, nipype default value: True)
display slice number
middle_slices: (a boolean)
output picture of mid-sagital, axial, and coronal slices
mutually_exclusive: single_slice, middle_slices, all_axial, sample_axial
nearest_neighbour: (a boolean)
use nearest neighbour interpolation for output
out_file: (a file name)
picture to write
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
FSL output type
sample_axial: (an integer)
output every n axial slices into one picture
mutually_exclusive: single_slice, middle_slices, all_axial, sample_axial
requires: image_width
scaling: (a float)
image scale
show_orientation: (a boolean, nipype default value: True)
label left-right orientation
single_slice: ('x' or 'y' or 'z')
output picture of single slice in the x, y, or z plane
mutually_exclusive: single_slice, middle_slices, all_axial, sample_axial
requires: slice_number
slice_number: (an integer)
slice number to save in picture
threshold_edges: (a float)
use threshold for edges
Outputs:
out_file: (an existing file name)
picture to write
Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/fsl/utils.py#L89
Wraps command fslmaths
Use fslmaths to smooth the image
Inputs:
[Mandatory]
fwhm: (a float)
in_file: (an existing file name)
[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
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
FSL output type
smoothed_file: (a file name)
Outputs:
smoothed_file: (an existing file name)
Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/fsl/utils.py#L248
Wraps command fslsplit
Uses FSL Fslsplit command to separate a volume into images in time, x, y or z dimension.
Inputs:
[Mandatory]
dimension: ('t' or 'x' or 'y' or 'z')
dimension along which the file will be split
in_file: (an existing file name)
input filename
[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_base_name: (a string)
outputs prefix
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
FSL output type
Outputs:
out_files: (an existing file name)
Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/fsl/utils.py#L972
Wraps command fslswapdim
Use fslswapdim to alter the orientation of an image.
This interface accepts a three-tuple corresponding to the new orientation. You may either provide dimension ids in the form of (-)x, (-)y, or (-z), or nifti-syle dimension codes (RL, LR, AP, PA, IS, SI).
Inputs:
[Mandatory]
in_file: (an existing file name)
input image
new_dims: (a tuple of the form: ('x' or '-x' or 'y' or '-y' or 'z' or '-z' or 'RL' or
'LR' or 'AP' or 'PA' or 'IS' or 'SI', 'x' or '-x' or 'y' or '-y' or 'z' or '-z' or 'RL'
or 'LR' or 'AP' or 'PA' or 'IS' or 'SI', 'x' or '-x' or 'y' or '-y' or 'z' or '-z' or
'RL' or 'LR' or 'AP' or 'PA' or 'IS' or 'SI'))
3-tuple of new dimension order
[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)
image to write
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
FSL output type
Outputs:
out_file: (an existing file name)
image with new dimensions