Wraps command bedpostx
Deprecated! Please use create_bedpostx_pipeline instead
>>> from nipype.interfaces import fsl
>>> bedp = fsl.BEDPOSTX(bpx_directory='subjdir', bvecs='bvecs', bvals='bvals', dwi='diffusion.nii', mask='mask.nii', fibres=1)
>>> bedp.cmdline
'bedpostx subjdir -n 1'
Inputs:
[Mandatory]
bvals : (an existing file name)
b values file
bvecs : (an existing file name)
b vectors file
dwi : (an existing file name)
diffusion weighted image data file
mask : (an existing file name)
bet binary mask file
[Optional]
args : (a string)
Additional parameters to the command
bpx_directory : (a directory name)
the name for this subjects bedpostx folder
burn_period : (an integer)
burnin period
environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
Environment variables
fibres : (an integer)
number of fibres per voxel
ignore_exception : (a boolean)
Print an error message instead of throwing an exception in case the interface fails to run
jumps : (an integer)
number of jumps
output_type : ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
FSL output type
sampling : (an integer)
sample every
weight : (a float)
ARD weight, more weight means less secondary fibres per voxel
Outputs:
bpx_out_directory : (an existing directory name)
path/name of directory with all bedpostx output files for this subject
dyads : (a list of items which are a file name)
a list of path/name of mean of PDD distribution in vector form
mean_fsamples : (a list of items which are a file name)
a list of path/name of 3D volume with mean of distribution on f anisotropy
mean_phsamples : (a list of items which are a file name)
a list of path/name of 3D volume with mean of distribution on phi
mean_thsamples : (a list of items which are a file name)
a list of path/name of 3D volume with mean of distribution on theta
merged_fsamples : (a list of items which are a file name)
a list of path/name of 4D volume with samples from the distribution on anisotropic volume fraction
merged_phsamples : (a list of items which are a file name)
a list of path/name of file with samples from the distribution on phi
merged_thsamples : (a list of items which are a file name)
a list of path/name of 4D volume with samples from the distribution on theta
xfms_directory : (an existing directory name)
path/name of directory with the tranformation matrices
Wraps command dtifit
Use FSL dtifit command for fitting a diffusion tensor model at each voxel
>>> from nipype.interfaces import fsl
>>> dti = fsl.DTIFit()
>>> dti.inputs.dwi = 'diffusion.nii'
>>> dti.inputs.bvecs = 'bvecs'
>>> dti.inputs.bvals = 'bvals'
>>> dti.inputs.base_name = 'TP'
>>> dti.inputs.mask = 'mask.nii'
>>> dti.cmdline
'dtifit -k diffusion.nii -o TP -m mask.nii -r bvecs -b bvals'
Inputs:
[Mandatory]
bvals : (an existing file name)
b values file
bvecs : (an existing file name)
b vectors file
dwi : (an existing file name)
diffusion weighted image data file
mask : (an existing file name)
bet binary mask file
[Optional]
args : (a string)
Additional parameters to the command
base_name : (a string)
base_name that all output files will start with
cni : (an existing file name)
input counfound regressors
environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
Environment variables
ignore_exception : (a boolean)
Print an error message instead of throwing an exception in case the interface fails to run
little_bit : (a boolean)
only process small area of brain
max_x : (an integer)
max x
max_y : (an integer)
max y
max_z : (an integer)
max z
min_x : (an integer)
min x
min_y : (an integer)
min y
min_z : (an integer)
min z
output_type : ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
FSL output type
save_tensor : (a boolean)
save the elements of the tensor
sse : (a boolean)
output sum of squared errors
Outputs:
FA : (an existing file name)
path/name of file with the fractional anisotropy
L1 : (an existing file name)
path/name of file with the 1st eigenvalue
L2 : (an existing file name)
path/name of file with the 2nd eigenvalue
L3 : (an existing file name)
path/name of file with the 3rd eigenvalue
MD : (an existing file name)
path/name of file with the mean diffusivity
MO : (an existing file name)
path/name of file with the mode of anisotropy
S0 : (an existing file name)
path/name of file with the raw T2 signal with no diffusion weighting
V1 : (an existing file name)
path/name of file with the 1st eigenvector
V2 : (an existing file name)
path/name of file with the 2nd eigenvector
V3 : (an existing file name)
path/name of file with the 3rd eigenvector
tensor : (an existing file name)
path/name of file with the 4D tensor volume
Wraps command distancemap
Use FSL’s distancemap to generate a map of the distance to the nearest nonzero voxel.
import nipype.interfaces.fsl as fsl mapper = fsl.DistanceMap() mapper.inputs.in_file = “skeleton_mask.nii.gz” mapper.run() # doctest: +SKIP
Inputs:
[Mandatory]
in_file : (an existing file name)
image to calculate distance values for
[Optional]
args : (a string)
Additional parameters to the command
distance_map : (a file name)
distance map to write
environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
Environment variables
ignore_exception : (a boolean)
Print an error message instead of throwing an exception in case the interface fails to run
invert_input : (a boolean)
invert input image
local_max_file : (a boolean or a file name)
write an image of the local maxima
mask_file : (an existing file name)
binary mask to contrain calculations
output_type : ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
FSL output type
Outputs:
distance_map : (an existing file name)
value is distance to nearest nonzero voxels
local_max_file : (a file name)
image of local maxima
Wraps command eddy_correct
Deprecated! Please use create_eddy_correct_pipeline instead
>>> from nipype.interfaces import fsl
>>> eddyc = fsl.EddyCorrect(in_file='diffusion.nii',out_file="diffusion_edc.nii", ref_num=0)
>>> eddyc.cmdline
'eddy_correct diffusion.nii diffusion_edc.nii 0'
Inputs:
[Mandatory]
in_file : (an existing file name)
4D input file
ref_num : (an integer)
reference number
[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')
Environment variables
ignore_exception : (a boolean)
Print an error message instead of throwing an exception in case the interface fails to run
out_file : (a file name)
4D output file
output_type : ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
FSL output type
Outputs:
eddy_corrected : (an existing file name)
path/name of 4D eddy corrected output file
Wraps command find_the_biggest
Use FSL find_the_biggest for performing hard segmentation on the outputs of connectivity-based thresholding in probtrack. For complete details, see the FDT Documentation.
>>> from nipype.interfaces import fsl
>>> ldir = ['seeds_to_M1.nii', 'seeds_to_M2.nii']
>>> fBig = fsl.FindTheBiggest(in_files=ldir, out_file='biggestSegmentation')
>>> fBig.cmdline
'find_the_biggest seeds_to_M1.nii seeds_to_M2.nii biggestSegmentation'
Inputs:
[Mandatory]
in_files : (a list of items which are a file name)
a list of input volumes or a singleMatrixFile
[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')
Environment variables
ignore_exception : (a boolean)
Print an error message instead of throwing an exception in case the interface fails to run
out_file : (a file name)
file with the resulting segmentation
output_type : ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
FSL output type
Outputs:
out_file : (an existing file name)
output file indexed in order of input files
Wraps command make_dyadic_vectors
Create vector volume representing mean principal diffusion direction and its uncertainty (dispersion)
Inputs:
[Mandatory]
phi_vol : (an existing file name)
Unknown
theta_vol : (an existing file name)
Unknown
[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')
Environment variables
ignore_exception : (a boolean)
Print an error message instead of throwing an exception in case the interface fails to run
mask : (an existing file name)
Unknown
output : (a file name)
Unknown
output_type : ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
FSL output type
perc : (a float)
the {perc}% angle of the output cone of uncertainty (output will be in degrees)
Outputs:
dispersion : (an existing file name)
Unknown
dyads : (an existing file name)
Unknown
Wraps command probtrackx
Use FSL probtrackx for tractography on bedpostx results
>>> from nipype.interfaces import fsl
>>> pbx = fsl.ProbTrackX(samples_base_name='merged', mask='mask.nii', seed='MASK_average_thal_right.nii', mode='seedmask', xfm='trans.mat', n_samples=3, n_steps=10, force_dir=True, opd=True, os2t=True, target_masks = ['targets_MASK1.nii','targets_MASK2.nii'], thsamples='merged_thsamples.nii', fsamples='merged_fsamples.nii', phsamples='merged_phsamples.nii', out_dir='.')
>>> pbx.cmdline
'probtrackx --forcedir -m mask.nii --mode=seedmask --nsamples=3 --nsteps=10 --opd --os2t --dir=. --samples=merged --seed=MASK_average_thal_right.nii --targetmasks=targets.txt --xfm=trans.mat'
Inputs:
[Mandatory]
fsamples : (an existing file name)
Unknown
mask : (an existing file name)
bet binary mask file in diffusion space
phsamples : (an existing file name)
Unknown
seed : (an existing file name or a list of items which are an existing file name or a list of items which are a list of from 3 to 3 items which are an integer)
seed volume(s), or voxel(s)or freesurfer label file
thsamples : (an existing file name)
Unknown
[Optional]
args : (a string)
Additional parameters to the command
avoid_mp : (an existing file name)
reject pathways passing through locations given by this mask
c_thresh : (a float)
curvature threshold - default=0.2
correct_path_distribution : (a boolean)
correct path distribution for the length of the pathways
dist_thresh : (a float)
discards samples shorter than this threshold (in mm - default=0)
environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
Environment variables
fibst : (an integer)
force a starting fibre for tracking - default=1, i.e. first fibre orientation. Only works if randfib==0
force_dir : (a boolean)
use the actual directory name given - i.e. do not add + to make a new directory
ignore_exception : (a boolean)
Print an error message instead of throwing an exception in case the interface fails to run
inv_xfm : (a file name)
transformation matrix taking DTI space to seed space (compulsory when using a warp_field for seeds_to_dti)
loop_check : (a boolean)
perform loop_checks on paths - slower, but allows lower curvature threshold
mask2 : (an existing file name)
second bet binary mask (in diffusion space) in twomask_symm mode
mesh : (an existing file name)
Freesurfer-type surface descriptor (in ascii format)
mod_euler : (a boolean)
use modified euler streamlining
mode : ('simple' or 'two_mask_symm' or 'seedmask')
options: simple (single seed voxel), seedmask (mask of seed voxels),twomask_symm (two bet binary masks)
n_samples : (an integer)
number of samples - default=5000
n_steps : (an integer)
number of steps per sample - default=2000
network : (a boolean)
activate network mode - only keep paths going through at least one seed mask (required if multiple seed masks)
opd : (a boolean)
outputs path distributions
os2t : (a boolean)
Outputs seeds to targets
out_dir : (an existing directory name)
directory to put the final volumes in
output_type : ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
FSL output type
rand_fib : (0 or 1 or 2 or 3)
options: 0 - default, 1 - to randomly sample initial fibres (with f > fibthresh), 2 - to sample in proportion fibres (with f>fibthresh) to f, 3 - to sample ALL populations at random (even if f<fibthresh)
random_seed : (a boolean)
random seed
s2tastext : (a boolean)
output seed-to-target counts as a text file (useful when seeding from a mesh)
sample_random_points : (a boolean)
sample random points within seed voxels
samples_base_name : (a string)
the rootname/base_name for samples files
seed_ref : (an existing file name)
reference vol to define seed space in simple mode - diffusion space assumed if absent
step_length : (a float)
step_length in mm - default=0.5
stop_mask : (an existing file name)
stop tracking at locations given by this mask file
target_masks : (a file name)
list of target masks - required for seeds_to_targets classification
use_anisotropy : (a boolean)
use anisotropy to constrain tracking
verbose : (0 or 1 or 2)
Verbose level, [0-2]
waypoints : (an existing file name)
waypoint mask or ascii list of waypoint masks - only keep paths going through ALL the masks
xfm : (an existing file name)
transformation matrix taking seed space to DTI space (either FLIRT matrix or FNIRT warp_field) - default is identity
Outputs:
fdt_paths : (an existing file name)
path/name of a 3D image file containing the output connectivity distribution to the seed mask
log : (an existing file name)
path/name of a text record of the command that was run
particle_files : (a list of items which are a file name)
Unknown
targets : (a list of items which are a file name)
a list with all generated seeds_to_target files
way_total : (an existing file name)
path/name of a text file containing a single number corresponding to the total number of generated tracts that have not been rejected by inclusion/exclusion mask criteria
Wraps command proj_thresh
Use FSL proj_thresh for thresholding some outputs of probtrack For complete details, see the FDT Documentation <http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_thresh.html>
>>> from nipype.interfaces import fsl
>>> ldir = ['seeds_to_M1.nii', 'seeds_to_M2.nii']
>>> pThresh = fsl.ProjThresh(in_files=ldir,threshold=3)
>>> pThresh.cmdline
'proj_thresh seeds_to_M1.nii seeds_to_M2.nii 3'
Inputs:
[Mandatory]
in_files : (a list of items which are a file name)
a list of input volumes
threshold : (an integer)
threshold indicating minimum number of seed voxels entering this mask region
[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')
Environment variables
ignore_exception : (a boolean)
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
Outputs:
out_files : (a list of items which are a file name)
path/name of output volume after thresholding
Wraps command tbss_skeleton
Use FSL’s tbss_skeleton to skeletonise an FA image or project arbitrary values onto a skeleton.
There are two ways to use this interface. To create a skeleton from an FA image, just supply the in_file and set skeleton_file to True (or specify a skeleton filename. To project values onto a skeleton, you must set project_data to True, and then also supply values for threshold, distance_map, and data_file. The search_mask_file and use_cingulum_mask inputs are also used in data projection, but use_cingulum_mask is set to True by default. This mask controls where the projection algorithm searches within a circular space around a tract, rather than in a single perpindicular direction.
import nipype.interfaces.fsl as fsl skeletor = fsl.TractSkeleton() skeletor.inputs.in_file = “all_FA.nii.gz” skeletor.inputs.skeleton_file = True skeletor.run() # doctest: +SKIP
Inputs:
[Mandatory]
in_file : (an existing file name)
input image (typcially mean FA volume)
[Optional]
alt_data_file : (an existing file name)
4D non-FA data to project onto skeleton
alt_skeleton : (an existing file name)
alternate skeleton to use
args : (a string)
Additional parameters to the command
data_file : (an existing file name)
4D data to project onto skeleton (usually FA)
distance_map : (an existing file name)
distance map image
environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
Environment variables
ignore_exception : (a boolean)
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
project_data : (a boolean)
project data onto skeleton
requires: threshold,distance_map,data_file
projected_data : (a file name)
input data projected onto skeleton
search_mask_file : (an existing file name)
mask in which to use alternate search rule
exclusive: use_cingulum_mask
skeleton_file : (a boolean or a file name)
write out skeleton image
threshold : (a float)
skeleton threshold value
use_cingulum_mask : (a boolean)
perform alternate search using built-in cingulum mask
exclusive: search_mask_file
Outputs:
projected_data : (a file name)
input data projected onto skeleton
skeleton_file : (a file name)
tract skeleton image
Wraps command vecreg
Use FSL vecreg for registering vector data For complete details, see the FDT Documentation <http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_vecreg.html>
>>> from nipype.interfaces import fsl
>>> vreg = fsl.VecReg(in_file='diffusion.nii', affine_mat='trans.mat', ref_vol='mni.nii', out_file='diffusion_vreg.nii')
>>> vreg.cmdline
'vecreg -t trans.mat -i diffusion.nii -o diffusion_vreg.nii -r mni.nii'
Inputs:
[Mandatory]
in_file : (an existing file name)
filename for input vector or tensor field
ref_vol : (an existing file name)
filename for reference (target) volume
[Optional]
affine_mat : (an existing file name)
filename for affine transformation matrix
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')
Environment variables
ignore_exception : (a boolean)
Print an error message instead of throwing an exception in case the interface fails to run
interpolation : ('nearestneighbour' or 'trilinear' or 'sinc' or 'spline')
interpolation method : nearestneighbour, trilinear (default), sinc or spline
mask : (an existing file name)
brain mask in input space
out_file : (a file name)
filename for output registered vector or tensor field
output_type : ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
FSL output type
ref_mask : (an existing file name)
brain mask in output space (useful for speed up of nonlinear reg)
rotation_mat : (an existing file name)
filename for secondary affine matrixif set, this will be used for the rotation of the vector/tensor field
rotation_warp : (an existing file name)
filename for secondary warp fieldif set, this will be used for the rotation of the vector/tensor field
warp_field : (an existing file name)
filename for 4D warp field for nonlinear registration
Outputs:
out_file : (an existing file name)
path/name of filename for the registered vector or tensor field
Wraps command xfibres
Perform model parameters estimation for local (voxelwise) diffusion parameters
Inputs:
[Mandatory]
bvals : (an existing file name)
Unknown
bvecs : (an existing file name)
Unknown
dwi : (an existing file name)
Unknown
mask : (an existing file name)
Unknown
[Optional]
all_ard : (a boolean)
Turn ARD on on all fibres
exclusive: no_ard,all_ard
args : (a string)
Additional parameters to the command
burn_in : (an integer >= 0)
Total num of jumps at start of MCMC to be discarded
burn_in_no_ard : (an integer >= 0)
num of burnin jumps before the ard is imposed
environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
Environment variables
force_dir : (a boolean)
use the actual directory name given - i.e. do not add + to make a new directory
fudge : (an integer)
ARD fudge factor
ignore_exception : (a boolean)
Print an error message instead of throwing an exception in case the interface fails to run
logdir : (a directory name)
Unknown
model : (an integer)
Which model to use. 1=mono-exponential (default and required for single shell). 2=continous exponential (for multi-shell experiments)
n_fibres : (an integer >= 1)
Maximum nukmber of fibres to fit in each voxel
n_jumps : (an integer >= 1)
Num of jumps to be made by MCMC
no_ard : (a boolean)
Turn ARD off on all fibres
exclusive: no_ard,all_ard
no_spat : (a boolean)
Initialise with tensor, not spatially
exclusive: no_spat,non_linear
non_linear : (a boolean)
Initialise with nonlinear fitting
exclusive: no_spat,non_linear
output_type : ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
FSL output type
sample_every : (an integer >= 0)
Num of jumps for each sample (MCMC)
seed : (an integer)
seed for pseudo random number generator
update_proposal_every : (an integer >= 1)
Num of jumps for each update to the proposal density std (MCMC)
Outputs:
dyads : (an existing file name)
Mean of PDD distribution in vector form.
fsamples : (an existing file name)
Samples from the distribution on anisotropic volume fraction
mean_S0samples : (an existing file name)
Samples from S0 distribution
mean_dsamples : (an existing file name)
Mean of distribution on diffusivity d
mean_fsamples : (an existing file name)
Mean of distribution on f anisotropy
phsamples : (an existing file name)
Samples from the distribution on phi
thsamples : (an existing file name)
Samples from the distribution on theta