interfaces.fsl.utils¶
AvScale¶
Wraps command avscale
Use FSL avscale command to extract info from mat file output of FLIRT
Examples¶
>>> avscale = AvScale()
>>> avscale.inputs.mat_file = 'flirt.mat'
>>> res = avscale.run()
Inputs:
[Mandatory]
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
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
flag: %s, position: 0
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
'NIFTI')
FSL output type
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
average_scaling: (any value)
Average Scaling
backward_half_transform: (any value)
Backwards Half Transform
determinant: (any value)
Determinant
forward_half_transform: (any value)
Forward Half Transform
left_right_orientation_preserved: (a boolean)
True if LR orientation preserved
rotation_translation_matrix: (any value)
Rotation and Translation Matrix
scales: (any value)
Scales (x,y,z)
skews: (any value)
Skews
Complex¶
Wraps command fslcomplex
fslcomplex is a tool for converting complex data
Examples¶
>>> cplx = Complex()
>>> cplx.inputs.complex_in_file = "complex.nii"
>>> cplx.real_polar = True
>>> res = cplx.run()
Inputs:
[Mandatory]
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
complex_cartesian: (a boolean)
flag: -complex, position: 1
mutually_exclusive: real_polar, real_cartesian, complex_cartesian,
complex_polar, complex_split, complex_merge
complex_in_file: (an existing file name)
flag: %s, position: 2
complex_in_file2: (an existing file name)
flag: %s, position: 3
complex_merge: (a boolean)
flag: -complexmerge, position: 1
mutually_exclusive: real_polar, real_cartesian, complex_cartesian,
complex_polar, complex_split, complex_merge, start_vol, end_vol
complex_out_file: (a file name)
flag: %s, position: -3
mutually_exclusive: complex_out_file, magnitude_out_file,
phase_out_file, real_out_file, imaginary_out_file, real_polar,
real_cartesian
complex_polar: (a boolean)
flag: -complexpolar, position: 1
mutually_exclusive: real_polar, real_cartesian, complex_cartesian,
complex_polar, complex_split, complex_merge
complex_split: (a boolean)
flag: -complexsplit, position: 1
mutually_exclusive: real_polar, real_cartesian, complex_cartesian,
complex_polar, complex_split, complex_merge
end_vol: (an integer (int or long))
flag: %d, position: -1
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
imaginary_in_file: (an existing file name)
flag: %s, position: 3
imaginary_out_file: (a file name)
flag: %s, position: -3
mutually_exclusive: complex_out_file, magnitude_out_file,
phase_out_file, real_polar, complex_cartesian, complex_polar,
complex_split, complex_merge
magnitude_in_file: (an existing file name)
flag: %s, position: 2
magnitude_out_file: (a file name)
flag: %s, position: -4
mutually_exclusive: complex_out_file, real_out_file,
imaginary_out_file, real_cartesian, complex_cartesian,
complex_polar, complex_split, complex_merge
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
'NIFTI')
FSL output type
phase_in_file: (an existing file name)
flag: %s, position: 3
phase_out_file: (a file name)
flag: %s, position: -3
mutually_exclusive: complex_out_file, real_out_file,
imaginary_out_file, real_cartesian, complex_cartesian,
complex_polar, complex_split, complex_merge
real_cartesian: (a boolean)
flag: -realcartesian, position: 1
mutually_exclusive: real_polar, real_cartesian, complex_cartesian,
complex_polar, complex_split, complex_merge
real_in_file: (an existing file name)
flag: %s, position: 2
real_out_file: (a file name)
flag: %s, position: -4
mutually_exclusive: complex_out_file, magnitude_out_file,
phase_out_file, real_polar, complex_cartesian, complex_polar,
complex_split, complex_merge
real_polar: (a boolean)
flag: -realpolar, position: 1
mutually_exclusive: real_polar, real_cartesian, complex_cartesian,
complex_polar, complex_split, complex_merge
start_vol: (an integer (int or long))
flag: %d, position: -2
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
complex_out_file: (a file name)
imaginary_out_file: (a file name)
magnitude_out_file: (a file name)
phase_out_file: (a file name)
real_out_file: (a file name)
ConvertWarp¶
Wraps command convertwarp
Use FSL convertwarp for combining multiple transforms into one.
Examples¶
>>> from nipype.interfaces.fsl import ConvertWarp
>>> warputils = ConvertWarp()
>>> warputils.inputs.warp1 = "warpfield.nii"
>>> warputils.inputs.reference = "T1.nii"
>>> warputils.inputs.relwarp = True
>>> warputils.inputs.output_type = "NIFTI_GZ"
>>> warputils.cmdline
'convertwarp --ref=T1.nii --rel --warp1=warpfield.nii --out=T1_concatwarp.nii.gz'
>>> res = warputils.run()
Inputs:
[Mandatory]
reference: (an existing file name)
Name of a file in target space of the full transform.
flag: --ref=%s, position: 1
[Optional]
abswarp: (a boolean)
If set it indicates that the warps in --warp1 and --warp2 should be
interpreted as absolute. I.e. the values in --warp1/2 are the
coordinates in the next space, rather than displacements. This flag
is ignored if --warp1/2 was created by fnirt, which always creates
relative displacements.
flag: --abs
mutually_exclusive: relwarp
args: (a string)
Additional parameters to the command
flag: %s
cons_jacobian: (a boolean)
Constrain the Jacobian of the warpfield to lie within specified
min/max limits.
flag: --constrainj
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
jacobian_max: (a float)
Maximum acceptable Jacobian value for constraint (default 100.0)
flag: --jmax=%f
jacobian_min: (a float)
Minimum acceptable Jacobian value for constraint (default 0.01)
flag: --jmin=%f
midmat: (an existing file name)
Name of file containing mid-warp-affine transform
flag: --midmat=%s
out_abswarp: (a boolean)
If set it indicates that the warps in --out should be absolute, i.e.
the values in --out are displacements from the coordinates in --ref.
flag: --absout
mutually_exclusive: out_relwarp
out_file: (a file name)
Name of output file, containing warps that are the combination of
all those given as arguments. The format of this will be a field-
file (rather than spline coefficients) with any affine components
included.
flag: --out=%s, position: -1
out_relwarp: (a boolean)
If set it indicates that the warps in --out should be relative, i.e.
the values in --out are displacements from the coordinates in --ref.
flag: --relout
mutually_exclusive: out_abswarp
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
'NIFTI')
FSL output type
postmat: (an existing file name)
Name of file containing an affine transform (applied last). It could
e.g. be an affine transform that maps the MNI152-space into a better
approximation to the Talairach-space (if indeed there is one).
flag: --postmat=%s
premat: (an existing file name)
filename for pre-transform (affine matrix)
flag: --premat=%s
relwarp: (a boolean)
If set it indicates that the warps in --warp1/2 should be
interpreted as relative. I.e. the values in --warp1/2 are
displacements from the coordinates in the next space.
flag: --rel
mutually_exclusive: abswarp
shift_direction: ('y-' or 'y' or 'x' or 'x-' or 'z' or 'z-')
Indicates the direction that the distortions from --shiftmap goes.
It depends on the direction and polarity of the phase-encoding in
the EPI sequence.
flag: --shiftdir=%s
requires: shift_in_file
shift_in_file: (an existing file name)
Name of file containing a "shiftmap", a non-linear transform with
displacements only in one direction (applied first, before premat).
This would typically be a fieldmap that has been pre-processed using
fugue that maps a subjects functional (EPI) data onto an undistorted
space (i.e. a space that corresponds to his/her true anatomy).
flag: --shiftmap=%s
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
warp1: (an existing file name)
Name of file containing initial warp-fields/coefficients (follows
premat). This could e.g. be a fnirt-transform from a subjects
structural scan to an average of a group of subjects.
flag: --warp1=%s
warp2: (an existing file name)
Name of file containing secondary warp-fields/coefficients (after
warp1/midmat but before postmat). This could e.g. be a fnirt-
transform from the average of a group of subjects to some standard
space (e.g. MNI152).
flag: --warp2=%s
Outputs:
out_file: (an existing file name)
Name of output file, containing the warp as field or coefficients.
ConvertXFM¶
Wraps command convert_xfm
Use the FSL utility convert_xfm to modify FLIRT transformation matrices.
Examples¶
>>> 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
flag: %s, position: -1
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
concat_xfm: (a boolean)
write joint transformation of two input matrices
flag: -concat, position: -3
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
flag: -fixscaleskew, position: -3
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
flag: %s, position: -2
invert_xfm: (a boolean)
invert input transformation
flag: -inverse, position: -3
mutually_exclusive: invert_xfm, concat_xfm, fix_scale_skew
out_file: (a file name)
final transformation matrix
flag: -omat %s, position: 1
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
'NIFTI')
FSL output type
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
out_file: (an existing file name)
output transformation matrix
CopyGeom¶
Wraps command fslcpgeom
Use fslcpgeom to copy the header geometry information to another image. Copy certain parts of the header information (image dimensions, voxel dimensions, voxel dimensions units string, image orientation/origin or qform/sform info) from one image to another. Note that only copies from Analyze to Analyze or Nifti to Nifti will work properly. Copying from different files will result in loss of information or potentially incorrect settings.
Inputs:
[Mandatory]
dest_file: (an existing file name)
destination image
flag: %s, position: 1
in_file: (an existing file name)
source image
flag: %s, position: 0
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
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_dims: (a boolean)
Do not copy image dimensions
flag: -d, position: -1
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
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
out_file: (an existing file name)
image with new geometry header
ExtractROI¶
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).
Examples¶
>>> 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
flag: %s, position: 0
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
crop_list: (a list of items which are a tuple of the form: (an
integer (int or long), an integer (int or long)))
list of two tuples specifying crop options
flag: %s, position: 2
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
flag: %s, position: 1
t_min: (an integer (int or long))
flag: %d, position: 8
t_size: (an integer (int or long))
flag: %d, position: 9
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
x_min: (an integer (int or long))
flag: %d, position: 2
x_size: (an integer (int or long))
flag: %d, position: 3
y_min: (an integer (int or long))
flag: %d, position: 4
y_size: (an integer (int or long))
flag: %d, position: 5
z_min: (an integer (int or long))
flag: %d, position: 6
z_size: (an integer (int or long))
flag: %d, position: 7
Outputs:
roi_file: (an existing file name)
FilterRegressor¶
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)
flag: -d %s, position: 3
filter_all: (a boolean)
use all columns in the design file in denoising
flag: -f '%s', position: 4
mutually_exclusive: filter_columns
filter_columns: (a list of items which are an integer (int or long))
(1-based) column indices to filter out of the data
flag: -f '%s', position: 4
mutually_exclusive: filter_all
in_file: (an existing file name)
input file name (4D image)
flag: -i %s, position: 1
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
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
flag: -m %s
out_file: (a file name)
output file name for the filtered data
flag: -o %s, position: 2
out_vnscales: (a boolean)
output scaling factors for variance normalization
flag: --out_vnscales
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
'NIFTI')
FSL output type
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
var_norm: (a boolean)
perform variance-normalization on data
flag: --vn
Outputs:
out_file: (an existing file name)
output file name for the filtered data
ImageMaths¶
Wraps command fslmaths
Use FSL fslmaths command to allow mathematical manipulation of images FSL info
Examples¶
>>> 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)
flag: %s, position: 1
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
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)
flag: %s, position: 3
op_string: (a string)
string defining the operation, i. e. -add
flag: %s, position: 2
out_data_type: ('char' or 'short' or 'int' or 'float' or 'double' or
'input')
output datatype, one of (char, short, int, float, double, input)
flag: -odt %s, position: 5
out_file: (a file name)
flag: %s, position: 4
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
'NIFTI')
FSL output type
suffix: (a string)
out_file suffix
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
out_file: (an existing file name)
ImageMeants¶
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
flag: -i %s, position: 0
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
eig: (a boolean)
calculate Eigenvariate(s) instead of mean (output will have 0 mean)
flag: --eig
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
flag: -m %s
nobin: (a boolean)
do not binarise the mask for calculation of Eigenvariates
flag: --no_bin
order: (an integer (int or long), nipype default value: 1)
select number of Eigenvariates
flag: --order=%d
out_file: (a file name)
name of output text matrix
flag: -o %s
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
flag: --showall
spatial_coord: (a list of items which are an integer (int or long))
<x y z> requested spatial coordinate (instead of mask)
flag: -c %s
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
transpose: (a boolean)
output results in transpose format (one row per voxel/mean)
flag: --transpose
use_mm: (a boolean)
use mm instead of voxel coordinates (for -c option)
flag: --usemm
Outputs:
out_file: (an existing file name)
path/name of output text matrix
ImageStats¶
Wraps command fslstats
Use FSL fslstats command to calculate stats from images FSL info
Examples¶
>>> 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
flag: %s, position: 2
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 a threshold and then
report the new nonzero mean
flag: %s, position: 3
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
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
flag: -t, position: 1
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
out_stat: (any value)
stats output
InvWarp¶
Wraps command invwarp
Use FSL Invwarp to invert a FNIRT warp
Examples¶
>>> from nipype.interfaces.fsl import InvWarp
>>> invwarp = InvWarp()
>>> invwarp.inputs.warp = "struct2mni.nii"
>>> invwarp.inputs.reference = "anatomical.nii"
>>> invwarp.inputs.output_type = "NIFTI_GZ"
>>> invwarp.cmdline
'invwarp --out=struct2mni_inverse.nii.gz --ref=anatomical.nii --warp=struct2mni.nii'
>>> res = invwarp.run()
Inputs:
[Mandatory]
reference: (an existing file name)
Name of a file in target space. Note that the target space is now
different from the target space that was used to create the --warp
file. It would typically be the file that was specified with the
--in argument when running fnirt.
flag: --ref=%s
warp: (an existing file name)
Name of file containing warp-coefficients/fields. This would
typically be the output from the --cout switch of fnirt (but can
also use fields, like the output from --fout).
flag: --warp=%s
[Optional]
absolute: (a boolean)
If set it indicates that the warps in --warp should be interpreted
as absolute, provided that it is not created by fnirt (which always
uses relative warps). If set it also indicates that the output --out
should be absolute.
flag: --abs
mutually_exclusive: relative
args: (a string)
Additional parameters to the command
flag: %s
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
inverse_warp: (a file name)
Name of output file, containing warps that are the "reverse" of
those in --warp. This will be a field-file (rather than a file of
spline coefficients), and it will have any affine component included
as part of the displacements.
flag: --out=%s
jacobian_max: (a float)
Maximum acceptable Jacobian value for constraint (default 100.0)
flag: --jmax=%f
jacobian_min: (a float)
Minimum acceptable Jacobian value for constraint (default 0.01)
flag: --jmin=%f
niter: (an integer (int or long))
Determines how many iterations of the gradient-descent search that
should be run.
flag: --niter=%d
noconstraint: (a boolean)
Do not apply Jacobian constraint
flag: --noconstraint
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
'NIFTI')
FSL output type
regularise: (a float)
Regularization strength (deafult=1.0).
flag: --regularise=%f
relative: (a boolean)
If set it indicates that the warps in --warp should be interpreted
as relative. I.e. the values in --warp are displacements from the
coordinates in the --ref space. If set it also indicates that the
output --out should be relative.
flag: --rel
mutually_exclusive: absolute
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
inverse_warp: (an existing file name)
Name of output file, containing warps that are the "reverse" of
those in --warp.
Merge¶
Wraps command fslmerge
Use fslmerge to concatenate images
Images can be concatenated across time, x, y, or z dimensions. Across the time (t) dimension the TR is set by default to 1 sec.
Note: to set the TR to a different value, specify ‘t’ for dimension and specify the TR value in seconds for the tr input. The dimension will be automatically updated to ‘tr’.
Examples¶
>>> from nipype.interfaces.fsl import Merge
>>> merger = Merge()
>>> merger.inputs.in_files = ['functional2.nii', 'functional3.nii']
>>> merger.inputs.dimension = 't'
>>> merger.inputs.output_type = 'NIFTI_GZ'
>>> merger.cmdline
'fslmerge -t functional2_merged.nii.gz functional2.nii functional3.nii'
>>> merger.inputs.tr = 2.25
>>> merger.cmdline
'fslmerge -tr functional2_merged.nii.gz functional2.nii functional3.nii 2.25'
Inputs:
[Mandatory]
dimension: ('t' or 'x' or 'y' or 'z' or 'a')
dimension along which to merge, optionally set tr input when
dimension is t
flag: -%s, position: 0
in_files: (a list of items which are an existing file name)
flag: %s, position: 2
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
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)
flag: %s, position: 1
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
'NIFTI')
FSL output type
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
tr: (a float)
use to specify TR in seconds (default is 1.00 sec), overrides
dimension and sets it to tr
flag: %.2f, position: -1
Outputs:
merged_file: (an existing file name)
MotionOutliers¶
Wraps command fsl_motion_outliers
Use FSL fsl_motion_outliers`http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLMotionOutliers`_ to find outliers in timeseries (4d) data. Examples ~~~~~~~~ >>> from nipype.interfaces.fsl import MotionOutliers >>> mo = MotionOutliers() >>> mo.inputs.in_file = “epi.nii” >>> mo.cmdline # doctest: +ELLIPSIS ‘fsl_motion_outliers -i epi.nii -o epi_outliers.txt -p epi_metrics.png -s epi_metrics.txt’ >>> res = mo.run() # doctest: +SKIP
Inputs:
[Mandatory]
in_file: (an existing file name)
unfiltered 4D image
flag: -i %s
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
dummy: (an integer (int or long))
number of dummy scans to delete (before running anything and
creating EVs)
flag: --dummy=%d
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 for calculating metric
flag: -m %s
metric: ('refrms' or 'dvars' or 'refmse' or 'fd' or 'fdrms')
metrics: refrms - RMS intensity difference to reference volume as
metric [default metric], refmse - Mean Square Error version of
refrms (used in original version of fsl_motion_outliers), dvars -
DVARS, fd - frame displacement, fdrms - FD with RMS matrix
calculation
flag: --%s
no_motion_correction: (a boolean)
do not run motion correction (assumed already done)
flag: --nomoco
out_file: (a file name)
output outlier file name
flag: -o %s
out_metric_plot: (a file name)
output metric values plot (DVARS etc.) file name
flag: -p %s
out_metric_values: (a file name)
output metric values (DVARS etc.) file name
flag: -s %s
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
'NIFTI')
FSL output type
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
threshold: (a float)
specify absolute threshold value (otherwise use box-plot cutoff =
P75 + 1.5*IQR)
flag: --thresh=%g
Outputs:
out_file: (an existing file name)
out_metric_plot: (an existing file name)
out_metric_values: (an existing file name)
Overlay¶
Wraps command overlay
- Use FSL’s overlay command to combine background and statistical images
- into one volume
Examples¶
>>> 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 threshold the background image
flag: -a, position: 5
mutually_exclusive: auto_thresh_bg, full_bg_range, bg_thresh
background_image: (an existing file name)
image to use as background
flag: %s, position: 4
bg_thresh: (a tuple of the form: (a float, a float))
min and max values for background intensity
flag: %.3f %.3f, position: 5
mutually_exclusive: auto_thresh_bg, full_bg_range, bg_thresh
full_bg_range: (a boolean)
use full range of background image
flag: -A, position: 5
mutually_exclusive: auto_thresh_bg, full_bg_range, bg_thresh
stat_image: (an existing file name)
statistical image to overlay in color
flag: %s, position: 6
stat_thresh: (a tuple of the form: (a float, a float))
min and max values for the statistical overlay
flag: %.2f %.2f, position: 7
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
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
flag: %s, position: -1
out_type: ('float' or 'int', nipype default value: float)
write output with float or int
flag: %s, position: 2
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
flag: %s, position: 8
mutually_exclusive: stat_image2
stat_image2: (an existing file name)
second statistical image to overlay in color
flag: %s, position: 9
mutually_exclusive: show_negative_stats
stat_thresh2: (a tuple of the form: (a float, a float))
min and max values for second statistical overlay
flag: %.2f %.2f, position: 10
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
transparency: (a boolean, nipype default value: True)
make overlay colors semi-transparent
flag: %s, position: 1
use_checkerboard: (a boolean)
use checkerboard mask for overlay
flag: -c, position: 3
Outputs:
out_file: (an existing file name)
combined image volume
PlotMotionParams¶
Wraps command fsl_tsplot
Use fsl_tsplot to plot the estimated motion parameters from a realignment program.
Examples¶
>>> 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()
Notes¶
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
flag: %s, position: 1
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
flag: %s
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
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
flag: -o %s
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 (int or long), an
integer (int or long)))
plot image height and width
flag: %s
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
out_file: (an existing file name)
image to write
PlotTimeSeries¶
Wraps command fsl_tsplot
Use fsl_tsplot to create images of time course plots.
Examples¶
>>> 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
flag: %s, position: 1
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
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
flag: %s
legend_file: (an existing file name)
legend file
flag: --legend=%s
out_file: (a file name)
image to write
flag: -o %s
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
'NIFTI')
FSL output type
plot_finish: (an integer (int or long))
final column from in-file to plot
flag: --finish=%d
mutually_exclusive: plot_range
plot_range: (a tuple of the form: (an integer (int or long), an
integer (int or long)))
first and last columns from the in-file to plot
flag: %s
mutually_exclusive: plot_start, plot_finish
plot_size: (a tuple of the form: (an integer (int or long), an
integer (int or long)))
plot image height and width
flag: %s
plot_start: (an integer (int or long))
first column from in-file to plot
flag: --start=%d
mutually_exclusive: plot_range
sci_notation: (a boolean)
switch on scientific notation
flag: --sci
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
title: (a string)
plot title
flag: %s
x_precision: (an integer (int or long))
precision of x-axis labels
flag: --precision=%d
x_units: (an integer (int or long), nipype default value: 1)
scaling units for x-axis (between 1 and length of in file)
flag: -u %d
y_max: (a float)
maximum y value
flag: --ymax=%.2f
mutually_exclusive: y_range
y_min: (a float)
minumum y value
flag: --ymin=%.2f
mutually_exclusive: y_range
y_range: (a tuple of the form: (a float, a float))
min and max y axis values
flag: %s
mutually_exclusive: y_min, y_max
Outputs:
out_file: (an existing file name)
image to write
PowerSpectrum¶
Wraps command fslpspec
Use FSL PowerSpectrum command for power spectrum estimation.
Examples¶
>>> 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
flag: %s, position: 0
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
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
flag: %s, position: 1
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
'NIFTI')
FSL output type
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
out_file: (an existing file name)
path/name of the output 4D power spectrum file
Reorient2Std¶
Wraps command fslreorient2std
fslreorient2std is a tool for reorienting the image to match the approximate orientation of the standard template images (MNI152).
Examples¶
>>> reorient = Reorient2Std()
>>> reorient.inputs.in_file = "functional.nii"
>>> res = reorient.run()
Inputs:
[Mandatory]
in_file: (an existing file name)
flag: %s
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
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)
flag: %s
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
'NIFTI')
FSL output type
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
out_file: (an existing file name)
RobustFOV¶
Wraps command robustfov
Inputs:
[Mandatory]
in_file: (an existing file name)
input filename
flag: -i %s, position: 0
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
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_roi: (a file name)
ROI volume output name
flag: -r %s
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
'NIFTI')
FSL output type
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
out_roi: (an existing file name)
ROI volume output name
SigLoss¶
Wraps command sigloss
Estimates signal loss from a field map (in rad/s)
Examples¶
>>> sigloss = SigLoss()
>>> sigloss.inputs.in_file = "phase.nii"
>>> sigloss.inputs.echo_time = 0.03
>>> res = sigloss.run()
Inputs:
[Mandatory]
in_file: (an existing file name)
b0 fieldmap file
flag: -i %s
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
echo_time: (a float)
echo time in seconds
flag: --te=%f
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)
brain mask file
flag: -m %s
out_file: (a file name)
output signal loss estimate file
flag: -s %s
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
'NIFTI')
FSL output type
slice_direction: ('x' or 'y' or 'z')
slicing direction
flag: -d %s
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
out_file: (an existing file name)
signal loss estimate file
Slicer¶
Wraps command slicer
Use FSL’s slicer command to output a png image from a volume.
Examples¶
>>> 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
flag: %s, position: 1
[Optional]
all_axial: (a boolean)
output all axial slices into one picture
flag: -A, position: 10
mutually_exclusive: single_slice, middle_slices, all_axial,
sample_axial
requires: image_width
args: (a string)
Additional parameters to the command
flag: %s
colour_map: (an existing file name)
use different colour map from that stored in nifti header
flag: -l %s, position: 4
dither_edges: (a boolean)
produce semi-transparent (dithered) edges
flag: -t, position: 7
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
flag: %s, position: 2
image_width: (an integer (int or long))
max picture width
flag: %d, position: -2
intensity_range: (a tuple of the form: (a float, a float))
min and max intensities to display
flag: -i %.3f %.3f, position: 5
label_slices: (a boolean, nipype default value: True)
display slice number
flag: -L, position: 3
middle_slices: (a boolean)
output picture of mid-sagittal, axial, and coronal slices
flag: -a, position: 10
mutually_exclusive: single_slice, middle_slices, all_axial,
sample_axial
nearest_neighbour: (a boolean)
use nearest neighbor interpolation for output
flag: -n, position: 8
out_file: (a file name)
picture to write
flag: %s, position: -1
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
'NIFTI')
FSL output type
sample_axial: (an integer (int or long))
output every n axial slices into one picture
flag: -S %d, position: 10
mutually_exclusive: single_slice, middle_slices, all_axial,
sample_axial
requires: image_width
scaling: (a float)
image scale
flag: -s %f, position: 0
show_orientation: (a boolean, nipype default value: True)
label left-right orientation
flag: %s, position: 9
single_slice: ('x' or 'y' or 'z')
output picture of single slice in the x, y, or z plane
flag: -%s, position: 10
mutually_exclusive: single_slice, middle_slices, all_axial,
sample_axial
requires: slice_number
slice_number: (an integer (int or long))
slice number to save in picture
flag: -%d, position: 11
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
threshold_edges: (a float)
use threshold for edges
flag: -e %.3f, position: 6
Outputs:
out_file: (an existing file name)
picture to write
Smooth¶
Wraps command fslmaths
Use fslmaths to smooth the image
Examples¶
Setting the kernel width using sigma:
>>> sm = Smooth()
>>> sm.inputs.output_type = 'NIFTI_GZ'
>>> sm.inputs.in_file = 'functional2.nii'
>>> sm.inputs.sigma = 8.0
>>> sm.cmdline
'fslmaths functional2.nii -kernel gauss 8.000 -fmean functional2_smooth.nii.gz'
Setting the kernel width using fwhm:
>>> sm = Smooth()
>>> sm.inputs.output_type = 'NIFTI_GZ'
>>> sm.inputs.in_file = 'functional2.nii'
>>> sm.inputs.fwhm = 8.0
>>> sm.cmdline
'fslmaths functional2.nii -kernel gauss 3.397 -fmean functional2_smooth.nii.gz'
One of sigma or fwhm must be set:
>>> from nipype.interfaces.fsl import Smooth
>>> sm = Smooth()
>>> sm.inputs.output_type = 'NIFTI_GZ'
>>> sm.inputs.in_file = 'functional2.nii'
>>> sm.cmdline
Traceback (most recent call last):
~~~
ValueError: Smooth requires a value for one of the inputs ...
Inputs:
[Mandatory]
fwhm: (a float)
gaussian kernel fwhm, will be converted to sigma in mm (not voxels)
flag: -kernel gauss %.03f -fmean, position: 1
mutually_exclusive: sigma
in_file: (an existing file name)
flag: %s, position: 0
sigma: (a float)
gaussian kernel sigma in mm (not voxels)
flag: -kernel gauss %.03f -fmean, position: 1
mutually_exclusive: fwhm
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
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)
flag: %s, position: 2
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
smoothed_file: (an existing file name)
Split¶
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
flag: -%s, position: 2
in_file: (an existing file name)
input filename
flag: %s, position: 0
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
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
flag: %s, position: 1
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
'NIFTI')
FSL output type
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
out_files: (a list of items which are an existing file name)
SwapDimensions¶
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
flag: %s, position: 1
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
flag: %s %s %s
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
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
flag: %s
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
'NIFTI')
FSL output type
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
out_file: (an existing file name)
image with new dimensions
WarpPoints¶
Wraps command img2imgcoord
Use FSL img2imgcoord to transform point sets. Accepts plain text files and vtk files.
Note
transformation of TrackVis trk files is not yet implemented
Examples¶
>>> from nipype.interfaces.fsl import WarpPoints
>>> warppoints = WarpPoints()
>>> warppoints.inputs.in_coords = 'surf.txt'
>>> warppoints.inputs.src_file = 'epi.nii'
>>> warppoints.inputs.dest_file = 'T1.nii'
>>> warppoints.inputs.warp_file = 'warpfield.nii'
>>> warppoints.inputs.coord_mm = True
>>> warppoints.cmdline
'img2imgcoord -mm -dest T1.nii -src epi.nii -warp warpfield.nii surf.txt'
>>> res = warppoints.run()
Inputs:
[Mandatory]
dest_file: (an existing file name)
filename of destination image
flag: -dest %s
in_coords: (an existing file name)
filename of file containing coordinates
flag: %s, position: -1
src_file: (an existing file name)
filename of source image
flag: -src %s
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
coord_mm: (a boolean)
all coordinates in mm
flag: -mm
mutually_exclusive: coord_vox
coord_vox: (a boolean)
all coordinates in voxels - default
flag: -vox
mutually_exclusive: coord_mm
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 name
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
warp_file: (an existing file name)
filename of warpfield (e.g. intermediate2dest_warp.nii.gz)
flag: -warp %s
mutually_exclusive: xfm_file
xfm_file: (an existing file name)
filename of affine transform (e.g. source2dest.mat)
flag: -xfm %s
mutually_exclusive: warp_file
Outputs:
out_file: (an existing file name)
Name of output file, containing the warp as field or coefficients.
WarpPointsToStd¶
Wraps command img2stdcoord
Use FSL img2stdcoord to transform point sets to standard space coordinates. Accepts plain text files and vtk files.
Note
transformation of TrackVis trk files is not yet implemented
Examples¶
>>> from nipype.interfaces.fsl import WarpPointsToStd
>>> warppoints = WarpPointsToStd()
>>> warppoints.inputs.in_coords = 'surf.txt'
>>> warppoints.inputs.img_file = 'T1.nii'
>>> warppoints.inputs.std_file = 'mni.nii'
>>> warppoints.inputs.warp_file = 'warpfield.nii'
>>> warppoints.inputs.coord_mm = True
>>> warppoints.cmdline
'img2stdcoord -mm -img T1.nii -std mni.nii -warp warpfield.nii surf.txt'
>>> res = warppoints.run()
Inputs:
[Mandatory]
img_file: (an existing file name)
filename of input image
flag: -img %s
in_coords: (an existing file name)
filename of file containing coordinates
flag: %s, position: -1
std_file: (an existing file name)
filename of destination image
flag: -std %s
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
coord_mm: (a boolean)
all coordinates in mm
flag: -mm
mutually_exclusive: coord_vox
coord_vox: (a boolean)
all coordinates in voxels - default
flag: -vox
mutually_exclusive: coord_mm
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 name
premat_file: (an existing file name)
filename of pre-warp affine transform (e.g.
example_func2highres.mat)
flag: -premat %s
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
warp_file: (an existing file name)
filename of warpfield (e.g. intermediate2dest_warp.nii.gz)
flag: -warp %s
mutually_exclusive: xfm_file
xfm_file: (an existing file name)
filename of affine transform (e.g. source2dest.mat)
flag: -xfm %s
mutually_exclusive: warp_file
Outputs:
out_file: (an existing file name)
Name of output file, containing the warp as field or coefficients.
WarpUtils¶
Wraps command fnirtfileutils
Use FSL fnirtfileutils to convert field->coefficients, coefficients->field, coefficients->other_coefficients etc
Examples¶
>>> from nipype.interfaces.fsl import WarpUtils
>>> warputils = WarpUtils()
>>> warputils.inputs.in_file = "warpfield.nii"
>>> warputils.inputs.reference = "T1.nii"
>>> warputils.inputs.out_format = 'spline'
>>> warputils.inputs.warp_resolution = (10,10,10)
>>> warputils.inputs.output_type = "NIFTI_GZ"
>>> warputils.cmdline
'fnirtfileutils --in=warpfield.nii --outformat=spline --ref=T1.nii --warpres=10.0000,10.0000,10.0000 --out=warpfield_coeffs.nii.gz'
>>> res = invwarp.run()
Inputs:
[Mandatory]
in_file: (an existing file name)
Name of file containing warp-coefficients/fields. This would
typically be the output from the --cout switch of fnirt (but can
also use fields, like the output from --fout).
flag: --in=%s
reference: (an existing file name)
Name of a file in target space. Note that the target space is now
different from the target space that was used to create the --warp
file. It would typically be the file that was specified with the
--in argument when running fnirt.
flag: --ref=%s
write_jacobian: (a boolean, nipype default value: False)
Switch on --jac flag with automatically generated filename
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
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
knot_space: (a tuple of the form: (an integer (int or long), an
integer (int or long), an integer (int or long)))
Alternative (to --warpres) specification of the resolution of the
output spline-field.
flag: --knotspace=%d,%d,%d
out_file: (a file name)
Name of output file. The format of the output depends on what other
parameters are set. The default format is a (4D) field-file. If the
--outformat is set to spline the format will be a (4D) file of
spline coefficients.
flag: --out=%s, position: -1
out_format: ('spline' or 'field')
Specifies the output format. If set to field (default) the output
will be a (4D) field-file. If set to spline the format will be a
(4D) file of spline coefficients.
flag: --outformat=%s
out_jacobian: (a file name)
Specifies that a (3D) file of Jacobian determinants corresponding to
--in should be produced and written to filename.
flag: --jac=%s
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
'NIFTI')
FSL output type
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
warp_resolution: (a tuple of the form: (a float, a float, a float))
Specifies the resolution/knot-spacing of the splines pertaining to
the coefficients in the --out file. This parameter is only relevant
if --outformat is set to spline. It should be noted that if the --in
file has a higher resolution, the resulting coefficients will
pertain to the closest (in a least-squares sense) file in the space
of fields with the --warpres resolution. It should also be noted
that the resolution will always be an integer multiple of the voxel
size.
flag: --warpres=%0.4f,%0.4f,%0.4f
with_affine: (a boolean)
Specifies that the affine transform (i.e. that which was specified
for the --aff parameter in fnirt) should be included as
displacements in the --out file. That can be useful for interfacing
with software that cannot decode FSL/fnirt coefficient-files (where
the affine transform is stored separately from the displacements).
flag: --withaff
Outputs:
out_file: (a file name)
Name of output file, containing the warp as field or coefficients.
out_jacobian: (a file name)
Name of output file, containing the map of the determinant of the
Jacobian