Code: file:///build/buildd/nipype-0.5.3/nipype/interfaces/camino/dti.py#L702
Wraps command dteig
Computes the eigensystem from tensor fitted data.
Reads diffusion tensor (single, two-tensor, three-tensor or multitensor) data from the standard input, computes the eigenvalues and eigenvectors of each tensor and outputs the results to the standard output. For multiple-tensor data the program outputs the eigensystem of each tensor. For each tensor the program outputs: {l_1, e_11, e_12, e_13, l_2, e_21, e_22, e_33, l_3, e_31, e_32, e_33}, where l_1 >= l_2 >= l_3 and e_i = (e_i1, e_i2, e_i3) is the eigenvector with eigenvalue l_i. For three-tensor data, for example, the output contains thirty-six values per voxel.
>>> import nipype.interfaces.camino as cmon
>>> dteig = cmon.ComputeEigensystem()
>>> dteig.inputs.in_file = 'tensor_fitted_data.Bfloat'
>>> dteig.run()
Inputs:
[Mandatory]
in_file: (an existing file name)
Tensor-fitted data 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
inputdatatype: ('double' or 'char' or 'short' or 'int' or 'long' or 'float')
Specifies the data type of the input file. The data type can be any of the following
strings: "char", "short", "int", "long", "float" or "double".
inputmodel: ('dt' or 'multitensor')
Specifies the model that the input data contains parameters for. Possible model types
are: "dt" (diffusion-tensor data) and "multitensor"
maxcomponents: (an integer)
The maximum number of tensor components in a voxel of the input data.
out_file: (a file name)
outputdatatype: ('double' or 'char' or 'short' or 'int' or 'long' or 'float')
Specifies the data type of the output data. The data type can be any of the following
strings: "char", "short", "int", "long", "float" or "double".
Outputs:
eigen: (an existing file name)
Trace of the diffusion tensor
Code: file:///build/buildd/nipype-0.5.3/nipype/interfaces/camino/dti.py#L594
Wraps command fa
Computes the fractional anisotropy of tensors.
Reads diffusion tensor (single, two-tensor or three-tensor) data from the standard input, computes the fractional anisotropy (FA) of each tensor and outputs the results to the standard output. For multiple-tensor data the program outputs the FA of each tensor, so for three-tensor data, for example, the output contains three fractional anisotropy values per voxel.
>>> import nipype.interfaces.camino as cmon
>>> fa = cmon.ComputeFractionalAnisotropy()
>>> fa.inputs.in_file = 'tensor_fitted_data.Bfloat'
>>> fa.inputs.scheme_file = 'A.scheme'
>>> fa.run()
Inputs:
[Mandatory]
in_file: (an existing file name)
Tensor-fitted data 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
inputdatatype: ('char' or 'short' or 'int' or 'long' or 'float' or 'double')
Specifies the data type of the input file. The data type can be any of thefollowing
strings: "char", "short", "int", "long", "float" or "double".
inputmodel: ('dt' or 'twotensor' or 'threetensor' or 'multitensor')
Specifies the model that the input tensor data contains parameters for.Possible model
types are: "dt" (diffusion-tensor data), "twotensor" (two-tensor data), "threetensor"
(three-tensor data). By default, the program assumes that the input data contains a
single diffusion tensor in each voxel.
out_file: (a file name)
outputdatatype: ('char' or 'short' or 'int' or 'long' or 'float' or 'double')
Specifies the data type of the output data. The data type can be any of thefollowing
strings: "char", "short", "int", "long", "float" or "double".
Outputs:
fa: (an existing file name)
Fractional Anisotropy Map
Code: file:///build/buildd/nipype-0.5.3/nipype/interfaces/camino/dti.py#L541
Wraps command md
Computes the mean diffusivity (trace/3) from diffusion tensors.
>>> import nipype.interfaces.camino as cmon
>>> md = cmon.ComputeMeanDiffusivity()
>>> md.inputs.in_file = 'tensor_fitted_data.Bfloat'
>>> md.inputs.scheme_file = 'A.scheme'
>>> md.run()
Inputs:
[Mandatory]
in_file: (an existing file name)
Tensor-fitted data 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
inputdatatype: ('char' or 'short' or 'int' or 'long' or 'float' or 'double')
Specifies the data type of the input file. The data type can be any of thefollowing
strings: "char", "short", "int", "long", "float" or "double".
inputmodel: ('dt' or 'twotensor' or 'threetensor')
Specifies the model that the input tensor data contains parameters for.Possible model
types are: "dt" (diffusion-tensor data), "twotensor" (two-tensor data), "threetensor"
(three-tensor data). By default, the program assumes that the input data contains a
single diffusion tensor in each voxel.
out_file: (a file name)
outputdatatype: ('char' or 'short' or 'int' or 'long' or 'float' or 'double')
Specifies the data type of the output data. The data type can be any of thefollowing
strings: "char", "short", "int", "long", "float" or "double".
Outputs:
md: (an existing file name)
Mean Diffusivity Map
Code: file:///build/buildd/nipype-0.5.3/nipype/interfaces/camino/dti.py#L653
Wraps command trd
Computes the trace of tensors.
Reads diffusion tensor (single, two-tensor or three-tensor) data from the standard input, computes the trace of each tensor, i.e., three times the mean diffusivity, and outputs the results to the standard output. For multiple-tensor data the program outputs the trace of each tensor, so for three-tensor data, for example, the output contains three values per voxel.
Divide the output by three to get the mean diffusivity.
>>> import nipype.interfaces.camino as cmon
>>> trace = cmon.ComputeTensorTrace()
>>> trace.inputs.in_file = 'tensor_fitted_data.Bfloat'
>>> trace.inputs.scheme_file = 'A.scheme'
>>> trace.run()
Inputs:
[Mandatory]
in_file: (an existing file name)
Tensor-fitted data 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
inputdatatype: ('char' or 'short' or 'int' or 'long' or 'float' or 'double')
Specifies the data type of the input file. The data type can be any of thefollowing
strings: "char", "short", "int", "long", "float" or "double".
inputmodel: ('dt' or 'twotensor' or 'threetensor' or 'multitensor')
Specifies the model that the input tensor data contains parameters for.Possible model
types are: "dt" (diffusion-tensor data), "twotensor" (two-tensor data), "threetensor"
(three-tensor data). By default, the program assumes that the input data contains a
single diffusion tensor in each voxel.
out_file: (a file name)
outputdatatype: ('char' or 'short' or 'int' or 'long' or 'float' or 'double')
Specifies the data type of the output data. The data type can be any of thefollowing
strings: "char", "short", "int", "long", "float" or "double".
Outputs:
trace: (an existing file name)
Trace of the diffusion tensor
Code: file:///build/buildd/nipype-0.5.3/nipype/interfaces/camino/dti.py#L28
Wraps command dtfit
Reads diffusion MRI data, acquired using the acquisition scheme detailed in the scheme file, from the data file.
Use non-linear fitting instead of the default linear regression to the log measurements. The data file stores the diffusion MRI data in voxel order with the measurements stored in big-endian format and ordered as in the scheme file. The default input data type is four-byte float. The default output data type is eight-byte double. See modelfit and camino for the format of the data file and scheme file. The program fits the diffusion tensor to each voxel and outputs the results, in voxel order and as big-endian eight-byte doubles, to the standard output. The program outputs eight values in each voxel: [exit code, ln(S(0)), D_xx, D_xy, D_xz, D_yy, D_yz, D_zz]. An exit code of zero indicates no problems. For a list of other exit codes, see modelfit(1). The entry S(0) is an estimate of the signal at q=0.
>>> import nipype.interfaces.camino as cmon
>>> fit = cmon.DTIFit()
>>> fit.inputs.scheme_file = 'A.scheme'
>>> fit.inputs.in_file = 'tensor_fitted_data.Bfloat'
>>> fit.run()
Inputs:
[Mandatory]
in_file: (an existing file name)
voxel-order data filename
scheme_file: (an existing file name)
Camino scheme file (b values / vectors, see camino.fsl2scheme)
[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
non_linear: (a boolean)
Use non-linear fitting instead of the default linear regression to the log measurements.
out_file: (a file name)
Outputs:
tensor_fitted: (an existing file name)
path/name of 4D volume in voxel order
Code: file:///build/buildd/nipype-0.5.3/nipype/interfaces/camino/dti.py#L195
Wraps command dtlutgen
Calibrates the PDFs for PICo probabilistic tractography.
This program needs to be run once for every acquisition scheme. It outputs a lookup table that is used by the dtpicoparams program to find PICo PDF parameters for an image. The default single tensor LUT contains parameters of the Bingham distribution and is generated by supplying a scheme file and an estimated signal to noise in white matter regions of the (q=0) image. The default inversion is linear (inversion index 1).
Advanced users can control several options, including the extent and resolution of the LUT, the inversion index, and the type of PDF. See dtlutgen(1) for details.
>>> import nipype.interfaces.camino as cmon
>>> dtl = cmon.DTLUTGen()
>>> dtl.inputs.snr = 16
>>> dtl.inputs.scheme_file = 'A.scheme'
>>> dtl.inputs.in_file = 'tensor_fitted_data.Bfloat'
>>> dtl.run()
Inputs:
[Mandatory]
scheme_file: (a file name)
The scheme file of the images to be processed using this LUT.
[Optional]
acg: (a boolean)
Compute a LUT for the ACG PDF.
args: (a string)
Additional parameters to the command
bingham: (a boolean)
Compute a LUT for the Bingham PDF. This is the default.
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
frange: (a list of from 2 to 2 items which are a float)
Index to two-tensor LUTs. This is the fractional anisotropy of the two tensors.
The default is 0.3 to 0.94
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the interface fails to
run
inversion: (an integer)
Index of the inversion to use. The default is 1 (linear single tensor inversion).
lrange: (a list of from 2 to 2 items which are a float)
Index to one-tensor LUTs. This is the ratio L1/L3 and L2 / L3.The LUT is square, with
half the values calculated (because L2 / L3 cannot be less than L1 / L3 by
definition).The minimum must be >= 1. For comparison, a ratio L1 / L3 = 10 with L2 / L3
= 1 corresponds to an FA of 0.891, and L1 / L3 = 15 with L2 / L3 = 1 corresponds to an
FA of 0.929. The default range is 1 to 10.
out_file: (a file name)
samples: (an integer)
The number of synthetic measurements to generate at each point in the LUT. The default
is 2000.
snr: (a float)
The signal to noise ratio of the unweighted (q = 0) measurements.This should match the
SNR (in white matter) of the images that the LUTs are used with.
step: (a float)
Distance between points in the LUT.For example, if lrange is 1 to 10 and the step is
0.1, LUT entries will be computed at L1 / L3 = 1, 1.1, 1.2 ... 10.0 and at L2 / L3 =
1.0, 1.1 ... L1 / L3.For single tensor LUTs, the default step is 0.2, for two-tensor
LUTs it is 0.02.
trace: (a float)
Trace of the diffusion tensor(s) used in the test function in the LUT generation. The
default is 2100E-12 m^2 s^-1.
watson: (a boolean)
Compute a LUT for the Watson PDF.
Outputs:
dtLUT: (an existing file name)
Lookup Table
Code: file:///build/buildd/nipype-0.5.3/nipype/interfaces/camino/dti.py#L115
Wraps command modelfit
Fits models of the spin-displacement density to diffusion MRI measurements.
This is an interface to various model fitting routines for diffusion MRI data that fit models of the spin-displacement density function. In particular, it will fit the diffusion tensor to a set of measurements as well as various other models including two or three-tensor models. The program can read input data from a file or can generate synthetic data using various test functions for testing and simulations.
>>> import nipype.interfaces.camino as cmon
>>> fit = cmon.ModelFit()
>>> fit.model = 'dt'
>>> fit.inputs.scheme_file = 'A.scheme'
>>> fit.inputs.in_file = 'tensor_fitted_data.Bfloat'
>>> fit.run()
Inputs:
[Mandatory]
in_file: (an existing file name)
voxel-order data filename
model: ('dt' or 'restore' or 'algdt' or 'nldt_pos' or 'nldt' or 'ldt_wtd' or 'adc' or
'ball_stick' or 'cylcyl dt' or 'cylcyl restore' or 'cylcyl algdt' or 'cylcyl nldt_pos'
or 'cylcyl nldt' or 'cylcyl ldt_wtd' or 'cylcyl adc' or 'cylcyl ball_stick' or
'cylcyl_eq dt' or 'cylcyl_eq restore' or 'cylcyl_eq algdt' or 'cylcyl_eq nldt_pos' or
'cylcyl_eq nldt' or 'cylcyl_eq ldt_wtd' or 'cylcyl_eq adc' or 'cylcyl_eq ball_stick' or
'pospos dt' or 'pospos restore' or 'pospos algdt' or 'pospos nldt_pos' or 'pospos nldt'
or 'pospos ldt_wtd' or 'pospos adc' or 'pospos ball_stick' or 'pospos_eq dt' or
'pospos_eq restore' or 'pospos_eq algdt' or 'pospos_eq nldt_pos' or 'pospos_eq nldt' or
'pospos_eq ldt_wtd' or 'pospos_eq adc' or 'pospos_eq ball_stick' or 'poscyl dt' or
'poscyl restore' or 'poscyl algdt' or 'poscyl nldt_pos' or 'poscyl nldt' or 'poscyl
ldt_wtd' or 'poscyl adc' or 'poscyl ball_stick' or 'poscyl_eq dt' or 'poscyl_eq
restore' or 'poscyl_eq algdt' or 'poscyl_eq nldt_pos' or 'poscyl_eq nldt' or 'poscyl_eq
ldt_wtd' or 'poscyl_eq adc' or 'poscyl_eq ball_stick' or 'cylcylcyl dt' or 'cylcylcyl
restore' or 'cylcylcyl algdt' or 'cylcylcyl nldt_pos' or 'cylcylcyl nldt' or 'cylcylcyl
ldt_wtd' or 'cylcylcyl adc' or 'cylcylcyl ball_stick' or 'cylcylcyl_eq dt' or
'cylcylcyl_eq restore' or 'cylcylcyl_eq algdt' or 'cylcylcyl_eq nldt_pos' or
'cylcylcyl_eq nldt' or 'cylcylcyl_eq ldt_wtd' or 'cylcylcyl_eq adc' or 'cylcylcyl_eq
ball_stick' or 'pospospos dt' or 'pospospos restore' or 'pospospos algdt' or 'pospospos
nldt_pos' or 'pospospos nldt' or 'pospospos ldt_wtd' or 'pospospos adc' or 'pospospos
ball_stick' or 'pospospos_eq dt' or 'pospospos_eq restore' or 'pospospos_eq algdt' or
'pospospos_eq nldt_pos' or 'pospospos_eq nldt' or 'pospospos_eq ldt_wtd' or
'pospospos_eq adc' or 'pospospos_eq ball_stick' or 'posposcyl dt' or 'posposcyl
restore' or 'posposcyl algdt' or 'posposcyl nldt_pos' or 'posposcyl nldt' or 'posposcyl
ldt_wtd' or 'posposcyl adc' or 'posposcyl ball_stick' or 'posposcyl_eq dt' or
'posposcyl_eq restore' or 'posposcyl_eq algdt' or 'posposcyl_eq nldt_pos' or
'posposcyl_eq nldt' or 'posposcyl_eq ldt_wtd' or 'posposcyl_eq adc' or 'posposcyl_eq
ball_stick' or 'poscylcyl dt' or 'poscylcyl restore' or 'poscylcyl algdt' or 'poscylcyl
nldt_pos' or 'poscylcyl nldt' or 'poscylcyl ldt_wtd' or 'poscylcyl adc' or 'poscylcyl
ball_stick' or 'poscylcyl_eq dt' or 'poscylcyl_eq restore' or 'poscylcyl_eq algdt' or
'poscylcyl_eq nldt_pos' or 'poscylcyl_eq nldt' or 'poscylcyl_eq ldt_wtd' or
'poscylcyl_eq adc' or 'poscylcyl_eq ball_stick')
Specifies the model to be fit to the data.
scheme_file: (an existing file name)
Camino scheme file (b values / vectors, see camino.fsl2scheme)
[Optional]
args: (a string)
Additional parameters to the command
bgmask: (an existing file name)
Provides the name of a file containing a background mask computed using, for example,
FSL's bet2 program. The mask file contains zero in background voxels and non-zero in
foreground.
bgthresh: (a float)
Sets a threshold on the average q=0 measurement to separate foreground and background.
The program does not process background voxels, but outputs the same number of values in
background voxels and foreground voxels. Each value is zero in background voxels apart
from the exit code which is -1.
cfthresh: (a float)
Sets a threshold on the average q=0 measurement to determine which voxels are CSF. This
program does not treat CSF voxels any different to other voxels.
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
fixedbvalue: (a list of from 3 to 3 items which are a float)
As above, but specifies <M> <N> <b>. The resulting scheme is the same whether you
specify b directly or indirectly using -fixedmodq.
fixedmodq: (a list of from 4 to 4 items which are a float)
Specifies <M> <N> <Q> <tau> a spherical acquisition scheme with M measurements with q=0
and N measurements with |q|=Q and diffusion time tau. The N measurements with |q|=Q have
unique directions. The program reads in the directions from the files in directory
PointSets.
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the interface fails to
run
inputdatatype: ('float' or 'char' or 'short' or 'int' or 'long' or 'double')
Specifies the data type of the input file: "char", "short", "int", "long", "float" or
"double". The input file must have BIG-ENDIAN ordering. By default, the input type is
"float".
noisemap: (an existing file name)
Specifies the name of the file to contain the estimated noise variance on the diffusion-
weighted signal, generated by a weighted tensor fit. The data type of this file is big-
endian double.
out_file: (a file name)
outlier: (an existing file name)
Specifies the name of the file to contain the outlier map generated by the RESTORE
algorithm.
outputfile: (a file name)
Filename of the output file.
residualmap: (an existing file name)
Specifies the name of the file to contain the weighted residual errors after computing a
weighted linear tensor fit. One value is produced per measurement, in voxel order.The
data type of this file is big-endian double. Images of the residuals for each
measurement can be extracted with shredder.
sigma: (a float)
Specifies the standard deviation of the noise in the data. Required by the RESTORE
algorithm.
tau: (a float)
Sets the diffusion time separately. This overrides the diffusion time specified in a
scheme file or by a scheme index for both the acquisition scheme and in the data
synthesis.
Outputs:
fitted_data: (an existing file name)
output file of 4D volume in voxel order
Code: file:///build/buildd/nipype-0.5.3/nipype/interfaces/camino/dti.py#L266
Wraps command picopdfs
Constructs a spherical PDF in each voxel for probabilistic tractography.
>>> import nipype.interfaces.camino as cmon
>>> pdf = cmon.PicoPDFs()
>>> pdf.inputs.inputmodel = 'dt'
>>> pdf.inputs.luts = 'lut_file'
>>> pdf.inputs.in_file = 'voxel-order_data.Bfloat'
>>> pdf.run()
Inputs:
[Mandatory]
in_file: (an existing file name)
voxel-order data filename
[Optional]
args: (a string)
Additional parameters to the command
directmap: (a boolean)
Only applicable when using pds as the inputmodel. Use direct mapping between the
eigenvalues and the distribution parameters instead of the log of the eigenvalues.
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
inputmodel: ('dt' or 'multitensor' or 'pds', nipype default value: dt)
input model type
maxcomponents: (an integer)
The maximum number of tensor components in a voxel (default 2) for multitensor
data.Currently, only the default is supported, but future releases may allow the input
of three-tensor data using this option.
numpds: (an integer)
The maximum number of PDs in a voxel (default 3) for PD data.This option determines the
size of the input and output voxels.This means that the data file may be large enough to
accomodate three or more PDs,but does not mean that any of the voxels are classified as
containing three or more PDs.
out_file: (a file name)
pdf: ('watson' or 'bingham' or 'acg', nipype default value: watson)
Specifies the PDF to use. There are three choices:watson - The Watson distribution.
This distribution is rotationally symmetric.bingham - The Bingham distributionn, which
allows elliptical probability density contours.acg - The Angular Central Gaussian
distribution, which also allows elliptical probability density contours
Outputs:
pdfs: (an existing file name)
path/name of 4D volume in voxel order
Code: file:///build/buildd/nipype-0.5.3/nipype/interfaces/camino/dti.py#L337
Wraps command track
Performs tractography using one of the following models: dt’, ‘multitensor’, ‘pds’, ‘pico’, ‘bootstrap’, ‘ballstick’, ‘bayesdirac’
>>> import nipype.interfaces.camino as cmon
>>> track = cmon.Track()
>>> track.inputs.inputmodel = 'dt'
>>> track.inputs.in_file = 'data.Bfloat'
>>> track.inputs.seed_file = 'seed_mask.nii'
>>> track.run()
Inputs:
[Mandatory]
in_file: (an existing file name)
input data file
[Optional]
anisfile: (an existing file name)
File containing the anisotropy map. This is required to apply an anisotropy threshold
with non tensor data. If the map issupplied it is always used, even in tensor data.
anisthresh: (a float)
Terminate fibres that enter a voxel with lower anisotropy than the threshold.
args: (a string)
Additional parameters to the command
curvethresh: (a float)
Curvature threshold for tracking, expressed as the maximum angle (in degrees) between
between two streamline orientations calculated over the length of a voxel. If the angle
is greater than this, then the streamline terminates.
data_dims: (a list of from 3 to 3 items which are an integer)
data dimensions in voxels
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
gzip: (a boolean)
save the output image in gzip format
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the interface fails to
run
inputdatatype: ('float' or 'double')
input file type
inputmodel: ('dt' or 'multitensor' or 'pds' or 'pico' or 'bootstrap' or 'ballstick' or
'bayesdirac', nipype default value: dt)
input model type
ipthresh: (a float)
Curvature threshold for tracking, expressed as the minimum dot product between two
streamline orientations calculated over the length of a voxel. If the dot product
between the previous and current directions is less than this threshold, then the
streamline terminates. The default setting will terminate fibres that curve by more than
80 degrees. Set this to -1.0 to disable curvature checking completely.
maxcomponents: (an integer)
The maximum number of tensor components in a voxel. This determines the size of the
input file and does not say anything about the voxel classification. The default is 2 if
the input model is multitensor and 1 if the input model is dt.
out_file: (a file name)
output data file
outputtracts: ('float' or 'double' or 'oogl')
output tract file type
voxel_dims: (a list of from 3 to 3 items which are a float)
voxel dimensions in mm
Outputs:
tracked: (an existing file name)
output file containing reconstructed tracts
Code: file:///build/buildd/nipype-0.5.3/nipype/interfaces/camino/dti.py#L458
Wraps command track
Performs streamline tractography using ball-stick fitted data
>>> import nipype.interfaces.camino as cmon
>>> track = cmon.TrackBallStick()
>>> track.inputs.in_file = 'ballstickfit_data.Bfloat'
>>> track.inputs.seed_file = 'seed_mask.nii'
>>> track.run()
Inputs:
[Mandatory]
in_file: (an existing file name)
input data file
[Optional]
anisfile: (an existing file name)
File containing the anisotropy map. This is required to apply an anisotropy threshold
with non tensor data. If the map issupplied it is always used, even in tensor data.
anisthresh: (a float)
Terminate fibres that enter a voxel with lower anisotropy than the threshold.
args: (a string)
Additional parameters to the command
curvethresh: (a float)
Curvature threshold for tracking, expressed as the maximum angle (in degrees) between
between two streamline orientations calculated over the length of a voxel. If the angle
is greater than this, then the streamline terminates.
data_dims: (a list of from 3 to 3 items which are an integer)
data dimensions in voxels
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
gzip: (a boolean)
save the output image in gzip format
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the interface fails to
run
inputdatatype: ('float' or 'double')
input file type
inputmodel: ('dt' or 'multitensor' or 'pds' or 'pico' or 'bootstrap' or 'ballstick' or
'bayesdirac', nipype default value: dt)
input model type
ipthresh: (a float)
Curvature threshold for tracking, expressed as the minimum dot product between two
streamline orientations calculated over the length of a voxel. If the dot product
between the previous and current directions is less than this threshold, then the
streamline terminates. The default setting will terminate fibres that curve by more than
80 degrees. Set this to -1.0 to disable curvature checking completely.
maxcomponents: (an integer)
The maximum number of tensor components in a voxel. This determines the size of the
input file and does not say anything about the voxel classification. The default is 2 if
the input model is multitensor and 1 if the input model is dt.
out_file: (a file name)
output data file
outputtracts: ('float' or 'double' or 'oogl')
output tract file type
voxel_dims: (a list of from 3 to 3 items which are a float)
voxel dimensions in mm
Outputs:
tracked: (an existing file name)
output file containing reconstructed tracts
Code: file:///build/buildd/nipype-0.5.3/nipype/interfaces/camino/dti.py#L437
Wraps command track
Performs streamline tractography using a Bayesian tracking with Dirac priors
>>> import nipype.interfaces.camino as cmon
>>> track = cmon.TrackBayesDirac()
>>> track.inputs.in_file = 'tensor_fitted_data.Bfloat'
>>> track.inputs.seed_file = 'seed_mask.nii'
>>> track.inputs.scheme_file = 'bvecs.scheme'
>>> track.run()
Inputs:
[Mandatory]
in_file: (an existing file name)
input data file
scheme_file: (a file name)
The scheme file corresponding to the data being processed.
[Optional]
anisfile: (an existing file name)
File containing the anisotropy map. This is required to apply an anisotropy threshold
with non tensor data. If the map issupplied it is always used, even in tensor data.
anisthresh: (a float)
Terminate fibres that enter a voxel with lower anisotropy than the threshold.
args: (a string)
Additional parameters to the command
curvepriorg: (a float)
Concentration parameter for the prior distribution on fibre orientations given the fibre
orientation at the previous step. Larger values of g make curvature less likely.
curvepriork: (a float)
Concentration parameter for the prior distribution on fibre orientations given the fibre
orientation at the previous step. Larger values of k make curvature less likely.
curvethresh: (a float)
Curvature threshold for tracking, expressed as the maximum angle (in degrees) between
between two streamline orientations calculated over the length of a voxel. If the angle
is greater than this, then the streamline terminates.
data_dims: (a list of from 3 to 3 items which are an integer)
data dimensions in voxels
datamodel: ('cylsymmdt' or 'ballstick')
Model of the data for Bayesian tracking. The default model is "cylsymmdt", a diffusion
tensor with cylindrical symmetry about e_1, ie L1 >= L_2 = L_3. The other model is
"ballstick", the partial volume model (see ballstickfit).
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
extpriordatatype: ('float' or 'double')
Datatype of the prior image. The default is "double".
extpriorfile: (an existing file name)
Path to a PICo image produced by picopdfs. The PDF in each voxel is used as a prior for
the fibre orientation in Bayesian tracking. The prior image must be in the same space as
the diffusion data.
gzip: (a boolean)
save the output image in gzip format
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the interface fails to
run
inputdatatype: ('float' or 'double')
input file type
inputmodel: ('dt' or 'multitensor' or 'pds' or 'pico' or 'bootstrap' or 'ballstick' or
'bayesdirac', nipype default value: dt)
input model type
ipthresh: (a float)
Curvature threshold for tracking, expressed as the minimum dot product between two
streamline orientations calculated over the length of a voxel. If the dot product
between the previous and current directions is less than this threshold, then the
streamline terminates. The default setting will terminate fibres that curve by more than
80 degrees. Set this to -1.0 to disable curvature checking completely.
iterations: (an integer)
Number of streamlines to generate at each seed point. The default is 5000.
maxcomponents: (an integer)
The maximum number of tensor components in a voxel. This determines the size of the
input file and does not say anything about the voxel classification. The default is 2 if
the input model is multitensor and 1 if the input model is dt.
out_file: (a file name)
output data file
outputtracts: ('float' or 'double' or 'oogl')
output tract file type
pdf: ('bingham' or 'watson' or 'acg')
Specifies the model for PICo priors (not the curvature priors). The default is
"bingham".
pointset: (an integer)
Index to the point set to use for Bayesian likelihood calculation. The index specifies a
set of evenly distributed points on the unit sphere, where each point x defines two
possible step directions (x or -x) for the streamline path. A larger number indexes a
larger point set, which gives higher angular resolution at the expense of computation
time. The default is index 1, which gives 1922 points, index 0 gives 1082 points, index
2 gives 3002 points.
voxel_dims: (a list of from 3 to 3 items which are a float)
voxel dimensions in mm
Outputs:
tracked: (an existing file name)
output file containing reconstructed tracts
Code: file:///build/buildd/nipype-0.5.3/nipype/interfaces/camino/dti.py#L491
Wraps command track
Performs bootstrap streamline tractography using mulitple scans of the same subject
>>> import nipype.interfaces.camino as cmon
>>> track = cmon.TrackBootstrap()
>>> track.inputs.scheme_file = 'bvecs.scheme'
>>> track.inputs.bsdatafiles = ['fitted_data1.Bfloat', 'fitted_data2.Bfloat']
>>> track.inputs.seed_file = 'seed_mask.nii'
>>> track.run()
Inputs:
[Mandatory]
bsdatafiles: (a list of items which are a file name)
Specifies files containing raw data for repetition bootstrapping. Use -inputfile for
wild bootstrap data.
in_file: (an existing file name)
input data file
scheme_file: (a file name)
The scheme file corresponding to the data being processed.
[Optional]
anisfile: (an existing file name)
File containing the anisotropy map. This is required to apply an anisotropy threshold
with non tensor data. If the map issupplied it is always used, even in tensor data.
anisthresh: (a float)
Terminate fibres that enter a voxel with lower anisotropy than the threshold.
args: (a string)
Additional parameters to the command
bgmask: (an existing file name)
Provides the name of a file containing a background mask computed using, for example,
FSL's bet2 program. The mask file contains zero in background voxels and non-zero in
foreground.
bsmodel: ('dt' or 'multitensor')
Model to fit to bootstrap data. This is used for repetition bootstrapping. May be "dt"
(default) or "multitensor". This option may be omitted if -inversion is specified.
curvethresh: (a float)
Curvature threshold for tracking, expressed as the maximum angle (in degrees) between
between two streamline orientations calculated over the length of a voxel. If the angle
is greater than this, then the streamline terminates.
data_dims: (a list of from 3 to 3 items which are an integer)
data dimensions in voxels
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
gzip: (a boolean)
save the output image in gzip format
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the interface fails to
run
inputdatatype: ('float' or 'double')
input file type
inputmodel: ('dt' or 'multitensor' or 'pds' or 'pico' or 'bootstrap' or 'ballstick' or
'bayesdirac', nipype default value: dt)
input model type
inversion: (an integer)
Tensor reconstruction algorithm for repetition bootstrapping. Default is 1 (linear
reconstruction, single tensor).
ipthresh: (a float)
Curvature threshold for tracking, expressed as the minimum dot product between two
streamline orientations calculated over the length of a voxel. If the dot product
between the previous and current directions is less than this threshold, then the
streamline terminates. The default setting will terminate fibres that curve by more than
80 degrees. Set this to -1.0 to disable curvature checking completely.
iterations: (an integer)
Number of streamlines to generate at each seed point.
maxcomponents: (an integer)
The maximum number of tensor components in a voxel. This determines the size of the
input file and does not say anything about the voxel classification. The default is 2 if
the input model is multitensor and 1 if the input model is dt.
out_file: (a file name)
output data file
outputtracts: ('float' or 'double' or 'oogl')
output tract file type
voxel_dims: (a list of from 3 to 3 items which are a float)
voxel dimensions in mm
wildbsmodel: ('dt')
The model to fit to the data, for wild bootstrapping. The same model is used to generate
the the wild bootstrap data. Must be "dt", which is the default.
Outputs:
tracked: (an existing file name)
output file containing reconstructed tracts
Code: file:///build/buildd/nipype-0.5.3/nipype/interfaces/camino/dti.py#L373
Wraps command track
Performs streamline tractography using tensor data
>>> import nipype.interfaces.camino as cmon
>>> track = cmon.TrackDT()
>>> track.inputs.in_file = 'tensor_fitted_data.Bfloat'
>>> track.inputs.seed_file = 'seed_mask.nii'
>>> track.run()
Inputs:
[Mandatory]
in_file: (an existing file name)
input data file
[Optional]
anisfile: (an existing file name)
File containing the anisotropy map. This is required to apply an anisotropy threshold
with non tensor data. If the map issupplied it is always used, even in tensor data.
anisthresh: (a float)
Terminate fibres that enter a voxel with lower anisotropy than the threshold.
args: (a string)
Additional parameters to the command
curvethresh: (a float)
Curvature threshold for tracking, expressed as the maximum angle (in degrees) between
between two streamline orientations calculated over the length of a voxel. If the angle
is greater than this, then the streamline terminates.
data_dims: (a list of from 3 to 3 items which are an integer)
data dimensions in voxels
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
gzip: (a boolean)
save the output image in gzip format
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the interface fails to
run
inputdatatype: ('float' or 'double')
input file type
inputmodel: ('dt' or 'multitensor' or 'pds' or 'pico' or 'bootstrap' or 'ballstick' or
'bayesdirac', nipype default value: dt)
input model type
ipthresh: (a float)
Curvature threshold for tracking, expressed as the minimum dot product between two
streamline orientations calculated over the length of a voxel. If the dot product
between the previous and current directions is less than this threshold, then the
streamline terminates. The default setting will terminate fibres that curve by more than
80 degrees. Set this to -1.0 to disable curvature checking completely.
maxcomponents: (an integer)
The maximum number of tensor components in a voxel. This determines the size of the
input file and does not say anything about the voxel classification. The default is 2 if
the input model is multitensor and 1 if the input model is dt.
out_file: (a file name)
output data file
outputtracts: ('float' or 'double' or 'oogl')
output tract file type
voxel_dims: (a list of from 3 to 3 items which are a float)
voxel dimensions in mm
Outputs:
tracked: (an existing file name)
output file containing reconstructed tracts
Code: file:///build/buildd/nipype-0.5.3/nipype/interfaces/camino/dti.py#L398
Wraps command track
Performs streamline tractography using the Probabilistic Index of Connectivity (PICo) algorithm
>>> import nipype.interfaces.camino as cmon
>>> track = cmon.TrackPICo()
>>> track.inputs.in_file = 'pdfs.Bfloat'
>>> track.inputs.seed_file = 'seed_mask.nii'
>>> track.run()
Inputs:
[Mandatory]
in_file: (an existing file name)
input data file
[Optional]
anisfile: (an existing file name)
File containing the anisotropy map. This is required to apply an anisotropy threshold
with non tensor data. If the map issupplied it is always used, even in tensor data.
anisthresh: (a float)
Terminate fibres that enter a voxel with lower anisotropy than the threshold.
args: (a string)
Additional parameters to the command
curvethresh: (a float)
Curvature threshold for tracking, expressed as the maximum angle (in degrees) between
between two streamline orientations calculated over the length of a voxel. If the angle
is greater than this, then the streamline terminates.
data_dims: (a list of from 3 to 3 items which are an integer)
data dimensions in voxels
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
gzip: (a boolean)
save the output image in gzip format
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the interface fails to
run
inputdatatype: ('float' or 'double')
input file type
inputmodel: ('dt' or 'multitensor' or 'pds' or 'pico' or 'bootstrap' or 'ballstick' or
'bayesdirac', nipype default value: dt)
input model type
ipthresh: (a float)
Curvature threshold for tracking, expressed as the minimum dot product between two
streamline orientations calculated over the length of a voxel. If the dot product
between the previous and current directions is less than this threshold, then the
streamline terminates. The default setting will terminate fibres that curve by more than
80 degrees. Set this to -1.0 to disable curvature checking completely.
iterations: (an integer)
Number of streamlines to generate at each seed point. The default is 5000.
maxcomponents: (an integer)
The maximum number of tensor components in a voxel. This determines the size of the
input file and does not say anything about the voxel classification. The default is 2 if
the input model is multitensor and 1 if the input model is dt.
numpds: (an integer)
The maximum number of PDs in a voxel. The default is 1 for input model pico. This option
determines the size of the voxels in the input file and does not affect tracking.
out_file: (a file name)
output data file
outputtracts: ('float' or 'double' or 'oogl')
output tract file type
pdf: ('bingham' or 'watson' or 'acg')
Specifies the model for PICo parameters. The default is "bingham.
voxel_dims: (a list of from 3 to 3 items which are a float)
voxel dimensions in mm
Outputs:
tracked: (an existing file name)
output file containing reconstructed tracts