nipype.interfaces.fsl.preprocess module

The fsl module provides classes for interfacing with the FSL command line tools. This was written to work with FSL version 4.1.4.

ApplyWarp

Link to code

Bases: FSLCommand

Wrapped executable: applywarp.

FSL’s applywarp wrapper to apply the results of a FNIRT registration

Examples

>>> from nipype.interfaces import fsl
>>> from nipype.testing import example_data
>>> aw = fsl.ApplyWarp()
>>> aw.inputs.in_file = example_data('structural.nii')
>>> aw.inputs.ref_file = example_data('mni.nii')
>>> aw.inputs.field_file = 'my_coefficients_filed.nii' #doctest: +SKIP
>>> res = aw.run() #doctest: +SKIP
in_file : a pathlike object or string representing an existing file
Image to be warped. Maps to a command-line argument: --in=%s (position: 0).
ref_file : a pathlike object or string representing an existing file
Reference image. Maps to a command-line argument: --ref=%s (position: 1).
abswarp : a boolean
Treat warp field as absolute: x’ = w(x). Maps to a command-line argument: --abs. Mutually exclusive with inputs: relwarp.
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
datatype : ‘char’ or ‘short’ or ‘int’ or ‘float’ or ‘double’
Force output data type [char short int float double]. Maps to a command-line argument: --datatype=%s.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
field_file : a pathlike object or string representing an existing file
File containing warp field. Maps to a command-line argument: --warp=%s.
interp : ‘nn’ or ‘trilinear’ or ‘sinc’ or ‘spline’
Interpolation method. Maps to a command-line argument: --interp=%s (position: -2).
mask_file : a pathlike object or string representing an existing file
Filename for mask image (in reference space). Maps to a command-line argument: --mask=%s.
out_file : a pathlike object or string representing a file
Output filename. Maps to a command-line argument: --out=%s (position: 2).
output_type : ‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’
FSL output type.
postmat : a pathlike object or string representing an existing file
Filename for post-transform (affine matrix). Maps to a command-line argument: --postmat=%s.
premat : a pathlike object or string representing an existing file
Filename for pre-transform (affine matrix). Maps to a command-line argument: --premat=%s.
relwarp : a boolean
Treat warp field as relative: x’ = x + w(x). Maps to a command-line argument: --rel (position: -1). Mutually exclusive with inputs: abswarp.
superlevel : ‘a’ or an integer (int or long)
Level of intermediary supersampling, a for ‘automatic’ or integer level. Default = 2. Maps to a command-line argument: --superlevel=%s.
supersample : a boolean
Intermediary supersampling of output, default is off. Maps to a command-line argument: --super.
out_file : a pathlike object or string representing an existing file
Warped output file.

ApplyXFM

Link to code

Bases: FLIRT

Wrapped executable: flirt.

Currently just a light wrapper around FLIRT, with no modifications

ApplyXFM is used to apply an existing tranform to an image

Examples

>>> import nipype.interfaces.fsl as fsl
>>> from nipype.testing import example_data
>>> applyxfm = fsl.preprocess.ApplyXFM()
>>> applyxfm.inputs.in_file = example_data('structural.nii')
>>> applyxfm.inputs.in_matrix_file = example_data('trans.mat')
>>> applyxfm.inputs.out_file = 'newfile.nii'
>>> applyxfm.inputs.reference = example_data('mni.nii')
>>> applyxfm.inputs.apply_xfm = True
>>> result = applyxfm.run() # doctest: +SKIP
in_file : a pathlike object or string representing an existing file
Input file. Maps to a command-line argument: -in %s (position: 0).
reference : a pathlike object or string representing an existing file
Reference file. Maps to a command-line argument: -ref %s (position: 1).
angle_rep : ‘quaternion’ or ‘euler’
Representation of rotation angles. Maps to a command-line argument: -anglerep %s.
apply_isoxfm : a float
As applyxfm but forces isotropic resampling. Maps to a command-line argument: -applyisoxfm %f. Mutually exclusive with inputs: apply_xfm.
apply_xfm : a boolean
Apply transformation supplied by in_matrix_file or uses_qform to use the affine matrix stored in the reference header. Maps to a command-line argument: -applyxfm. (Nipype default value: True)
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
bbrslope : a float
Value of bbr slope. Maps to a command-line argument: -bbrslope %f.
bbrtype : ‘signed’ or ‘global_abs’ or ‘local_abs’
Type of bbr cost function: signed [default], global_abs, local_abs. Maps to a command-line argument: -bbrtype %s.
bgvalue : a float
Use specified background value for points outside FOV. Maps to a command-line argument: -setbackground %f.
bins : an integer (int or long)
Number of histogram bins. Maps to a command-line argument: -bins %d.
coarse_search : an integer (int or long)
Coarse search delta angle. Maps to a command-line argument: -coarsesearch %d.
cost : ‘mutualinfo’ or ‘corratio’ or ‘normcorr’ or ‘normmi’ or ‘leastsq’ or ‘labeldiff’ or ‘bbr’
Cost function. Maps to a command-line argument: -cost %s.
cost_func : ‘mutualinfo’ or ‘corratio’ or ‘normcorr’ or ‘normmi’ or ‘leastsq’ or ‘labeldiff’ or ‘bbr’
Cost function. Maps to a command-line argument: -searchcost %s.
datatype : ‘char’ or ‘short’ or ‘int’ or ‘float’ or ‘double’
Force output data type. Maps to a command-line argument: -datatype %s.
display_init : a boolean
Display initial matrix. Maps to a command-line argument: -displayinit.
dof : an integer (int or long)
Number of transform degrees of freedom. Maps to a command-line argument: -dof %d.
echospacing : a float
Value of EPI echo spacing - units of seconds. Maps to a command-line argument: -echospacing %f.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
fieldmap : a pathlike object or string representing a file
Fieldmap image in rads/s - must be already registered to the reference image. Maps to a command-line argument: -fieldmap %s.
fieldmapmask : a pathlike object or string representing a file
Mask for fieldmap image. Maps to a command-line argument: -fieldmapmask %s.
fine_search : an integer (int or long)
Fine search delta angle. Maps to a command-line argument: -finesearch %d.
force_scaling : a boolean
Force rescaling even for low-res images. Maps to a command-line argument: -forcescaling.
in_matrix_file : a pathlike object or string representing a file
Input 4x4 affine matrix. Maps to a command-line argument: -init %s.
in_weight : a pathlike object or string representing an existing file
File for input weighting volume. Maps to a command-line argument: -inweight %s.
interp : ‘trilinear’ or ‘nearestneighbour’ or ‘sinc’ or ‘spline’
Final interpolation method used in reslicing. Maps to a command-line argument: -interp %s.
min_sampling : a float
Set minimum voxel dimension for sampling. Maps to a command-line argument: -minsampling %f.
no_clamp : a boolean
Do not use intensity clamping. Maps to a command-line argument: -noclamp.
no_resample : a boolean
Do not change input sampling. Maps to a command-line argument: -noresample.
no_resample_blur : a boolean
Do not use blurring on downsampling. Maps to a command-line argument: -noresampblur.
no_search : a boolean
Set all angular searches to ranges 0 to 0. Maps to a command-line argument: -nosearch.
out_file : a pathlike object or string representing a file
Registered output file. Maps to a command-line argument: -out %s (position: 2).
out_log : a pathlike object or string representing a file
Output log. Requires inputs: save_log.
out_matrix_file : a pathlike object or string representing a file
Output affine matrix in 4x4 asciii format. Maps to a command-line argument: -omat %s (position: 3).
output_type : ‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’
FSL output type.
padding_size : an integer (int or long)
For applyxfm: interpolates outside image by size. Maps to a command-line argument: -paddingsize %d.
pedir : an integer (int or long)
Phase encode direction of EPI - 1/2/3=x/y/z & -1/-2/-3=-x/-y/-z. Maps to a command-line argument: -pedir %d.
ref_weight : a pathlike object or string representing an existing file
File for reference weighting volume. Maps to a command-line argument: -refweight %s.
rigid2D : a boolean
Use 2D rigid body mode - ignores dof. Maps to a command-line argument: -2D.
save_log : a boolean
Save to log file.
schedule : a pathlike object or string representing an existing file
Replaces default schedule. Maps to a command-line argument: -schedule %s.
searchr_x : a list of from 2 to 2 items which are an integer (int or long)
Search angles along x-axis, in degrees. Maps to a command-line argument: -searchrx %s.
searchr_y : a list of from 2 to 2 items which are an integer (int or long)
Search angles along y-axis, in degrees. Maps to a command-line argument: -searchry %s.
searchr_z : a list of from 2 to 2 items which are an integer (int or long)
Search angles along z-axis, in degrees. Maps to a command-line argument: -searchrz %s.
sinc_width : an integer (int or long)
Full-width in voxels. Maps to a command-line argument: -sincwidth %d.
sinc_window : ‘rectangular’ or ‘hanning’ or ‘blackman’
Sinc window. Maps to a command-line argument: -sincwindow %s.
uses_qform : a boolean
Initialize using sform or qform. Maps to a command-line argument: -usesqform.
verbose : an integer (int or long)
Verbose mode, 0 is least. Maps to a command-line argument: -verbose %d.
wm_seg : a pathlike object or string representing a file
White matter segmentation volume needed by BBR cost function. Maps to a command-line argument: -wmseg %s.
wmcoords : a pathlike object or string representing a file
White matter boundary coordinates for BBR cost function. Maps to a command-line argument: -wmcoords %s.
wmnorms : a pathlike object or string representing a file
White matter boundary normals for BBR cost function. Maps to a command-line argument: -wmnorms %s.
out_file : a pathlike object or string representing an existing file
Path/name of registered file (if generated).
out_log : a pathlike object or string representing a file
Path/name of output log (if generated).
out_matrix_file : a pathlike object or string representing an existing file
Path/name of calculated affine transform (if generated).

BET

Link to code

Bases: FSLCommand

Wrapped executable: bet.

FSL BET wrapper for skull stripping

For complete details, see the BET Documentation.

Examples

>>> from nipype.interfaces import fsl
>>> btr = fsl.BET()
>>> btr.inputs.in_file = 'structural.nii'
>>> btr.inputs.frac = 0.7
>>> btr.inputs.out_file = 'brain_anat.nii'
>>> btr.cmdline
'bet structural.nii brain_anat.nii -f 0.70'
>>> res = btr.run() # doctest: +SKIP
in_file : a pathlike object or string representing an existing file
Input file to skull strip. Maps to a command-line argument: %s (position: 0).
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
center : a list of at most 3 items which are an integer (int or long)
Center of gravity in voxels. Maps to a command-line argument: -c %s.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
frac : a float
Fractional intensity threshold. Maps to a command-line argument: -f %.2f.
functional : a boolean
Apply to 4D fMRI data. Maps to a command-line argument: -F. Mutually exclusive with inputs: functional, reduce_bias, robust, padding, remove_eyes, surfaces, t2_guided.
mask : a boolean
Create binary mask image. Maps to a command-line argument: -m.
mesh : a boolean
Generate a vtk mesh brain surface. Maps to a command-line argument: -e.
no_output : a boolean
Don’t generate segmented output. Maps to a command-line argument: -n.
out_file : a pathlike object or string representing a file
Name of output skull stripped image. Maps to a command-line argument: %s (position: 1).
outline : a boolean
Create surface outline image. Maps to a command-line argument: -o.
output_type : ‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’
FSL output type.
padding : a boolean
Improve BET if FOV is very small in Z (by temporarily padding end slices). Maps to a command-line argument: -Z. Mutually exclusive with inputs: functional, reduce_bias, robust, padding, remove_eyes, surfaces, t2_guided.
radius : an integer (int or long)
Head radius. Maps to a command-line argument: -r %d.
reduce_bias : a boolean
Bias field and neck cleanup. Maps to a command-line argument: -B. Mutually exclusive with inputs: functional, reduce_bias, robust, padding, remove_eyes, surfaces, t2_guided.
remove_eyes : a boolean
Eye & optic nerve cleanup (can be useful in SIENA). Maps to a command-line argument: -S. Mutually exclusive with inputs: functional, reduce_bias, robust, padding, remove_eyes, surfaces, t2_guided.
robust : a boolean
Robust brain centre estimation (iterates BET several times). Maps to a command-line argument: -R. Mutually exclusive with inputs: functional, reduce_bias, robust, padding, remove_eyes, surfaces, t2_guided.
skull : a boolean
Create skull image. Maps to a command-line argument: -s.
surfaces : a boolean
Run bet2 and then betsurf to get additional skull and scalp surfaces (includes registrations). Maps to a command-line argument: -A. Mutually exclusive with inputs: functional, reduce_bias, robust, padding, remove_eyes, surfaces, t2_guided.
t2_guided : a pathlike object or string representing a file
As with creating surfaces, when also feeding in non-brain-extracted T2 (includes registrations). Maps to a command-line argument: -A2 %s. Mutually exclusive with inputs: functional, reduce_bias, robust, padding, remove_eyes, surfaces, t2_guided.
threshold : a boolean
Apply thresholding to segmented brain image and mask. Maps to a command-line argument: -t.
vertical_gradient : a float
Vertical gradient in fractional intensity threshold (-1, 1). Maps to a command-line argument: -g %.2f.
inskull_mask_file : a pathlike object or string representing a file
Path/name of inskull mask (if generated).
inskull_mesh_file : a pathlike object or string representing a file
Path/name of inskull mesh outline (if generated).
mask_file : a pathlike object or string representing a file
Path/name of binary brain mask (if generated).
meshfile : a pathlike object or string representing a file
Path/name of vtk mesh file (if generated).
out_file : a pathlike object or string representing a file
Path/name of skullstripped file (if generated).
outline_file : a pathlike object or string representing a file
Path/name of outline file (if generated).
outskin_mask_file : a pathlike object or string representing a file
Path/name of outskin mask (if generated).
outskin_mesh_file : a pathlike object or string representing a file
Path/name of outskin mesh outline (if generated).
outskull_mask_file : a pathlike object or string representing a file
Path/name of outskull mask (if generated).
outskull_mesh_file : a pathlike object or string representing a file
Path/name of outskull mesh outline (if generated).
skull_file : a pathlike object or string representing a file
Path/name of skull file (if generated).
skull_mask_file : a pathlike object or string representing a file
Path/name of skull mask (if generated).

FAST

Link to code

Bases: FSLCommand

Wrapped executable: fast.

FSL FAST wrapper for segmentation and bias correction

For complete details, see the FAST Documentation.

Examples

>>> from nipype.interfaces import fsl
>>> fastr = fsl.FAST()
>>> fastr.inputs.in_files = 'structural.nii'
>>> fastr.inputs.out_basename = 'fast_'
>>> fastr.cmdline
'fast -o fast_ -S 1 structural.nii'
>>> out = fastr.run()  # doctest: +SKIP
in_files : a list of items which are a pathlike object or string representing an existing file
Image, or multi-channel set of images, to be segmented. Maps to a command-line argument: %s (position: -1).
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
bias_iters : 1 <= a long integer <= 10
Number of main-loop iterations during bias-field removal. Maps to a command-line argument: -I %d.
bias_lowpass : 4 <= a long integer <= 40
Bias field smoothing extent (FWHM) in mm. Maps to a command-line argument: -l %d.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
hyper : 0.0 <= a floating point number <= 1.0
Segmentation spatial smoothness. Maps to a command-line argument: -H %.2f.
img_type : 1 or 2 or 3
Int specifying type of image: (1 = T1, 2 = T2, 3 = PD). Maps to a command-line argument: -t %d.
init_seg_smooth : 0.0001 <= a floating point number <= 0.1
Initial segmentation spatial smoothness (during bias field estimation). Maps to a command-line argument: -f %.3f.
init_transform : a pathlike object or string representing an existing file
<standard2input.mat> initialise using priors. Maps to a command-line argument: -a %s.
iters_afterbias : 1 <= a long integer <= 20
Number of main-loop iterations after bias-field removal. Maps to a command-line argument: -O %d.
manual_seg : a pathlike object or string representing an existing file
Filename containing intensities. Maps to a command-line argument: -s %s.
mixel_smooth : 0.0 <= a floating point number <= 1.0
Spatial smoothness for mixeltype. Maps to a command-line argument: -R %.2f.
no_bias : a boolean
Do not remove bias field. Maps to a command-line argument: -N.
no_pve : a boolean
Turn off PVE (partial volume estimation). Maps to a command-line argument: --nopve.
number_classes : 1 <= a long integer <= 10
Number of tissue-type classes. Maps to a command-line argument: -n %d.
other_priors : a list of from 3 to 3 items which are a pathlike object or string representing a file
Alternative prior images. Maps to a command-line argument: -A %s.
out_basename : a pathlike object or string representing a file
Base name of output files. Maps to a command-line argument: -o %s.
output_biascorrected : a boolean
Output restored image (bias-corrected image). Maps to a command-line argument: -B.
output_biasfield : a boolean
Output estimated bias field. Maps to a command-line argument: -b.
output_type : ‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’
FSL output type.
probability_maps : a boolean
Outputs individual probability maps. Maps to a command-line argument: -p.
segment_iters : 1 <= a long integer <= 50
Number of segmentation-initialisation iterations. Maps to a command-line argument: -W %d.
segments : a boolean
Outputs a separate binary image for each tissue type. Maps to a command-line argument: -g.
use_priors : a boolean
Use priors throughout. Maps to a command-line argument: -P.
verbose : a boolean
Switch on diagnostic messages. Maps to a command-line argument: -v.

bias_field : a list of items which are a pathlike object or string representing a file mixeltype : a pathlike object or string representing a file

Path/name of mixeltype volume file _mixeltype.

partial_volume_files : a list of items which are a pathlike object or string representing a file partial_volume_map : a pathlike object or string representing a file

Path/name of partial volume file _pveseg.

probability_maps : a list of items which are a pathlike object or string representing a file restored_image : a list of items which are a pathlike object or string representing a file tissue_class_files : a list of items which are a pathlike object or string representing a file tissue_class_map : a pathlike object or string representing an existing file

Path/name of binary segmented volume file one val for each class _seg.

FIRST

Link to code

Bases: FSLCommand

Wrapped executable: run_first_all.

FSL run_first_all wrapper for segmentation of subcortical volumes

http://www.fmrib.ox.ac.uk/fsl/first/index.html

Examples

>>> from nipype.interfaces import fsl
>>> first = fsl.FIRST()
>>> first.inputs.in_file = 'structural.nii'
>>> first.inputs.out_file = 'segmented.nii'
>>> res = first.run() #doctest: +SKIP
in_file : a pathlike object or string representing an existing file
Input data file. Maps to a command-line argument: -i %s (position: -2).
out_file : a pathlike object or string representing a file
Output data file. Maps to a command-line argument: -o %s (position: -1). (Nipype default value: segmented)
affine_file : a pathlike object or string representing an existing file
Affine matrix to use (e.g. img2std.mat) (does not re-run registration). Maps to a command-line argument: -a %s (position: 6).
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
brain_extracted : a boolean
Input structural image is already brain-extracted. Maps to a command-line argument: -b (position: 2).
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
list_of_specific_structures : a list of at least 1 items which are a unicode string
Runs only on the specified structures (e.g. L_Hipp, R_HippL_Accu, R_Accu, L_Amyg, R_AmygL_Caud, R_Caud, L_Pall, R_PallL_Puta, R_Puta, L_Thal, R_Thal, BrStem. Maps to a command-line argument: -s %s (position: 5).
method : ‘auto’ or ‘fast’ or ‘none’
Method must be one of auto, fast, none, or it can be entered using the ‘method_as_numerical_threshold’ input. Maps to a command-line argument: -m %s (position: 4). Mutually exclusive with inputs: method_as_numerical_threshold. (Nipype default value: auto)
method_as_numerical_threshold : a float
Specify a numerical threshold value or use the ‘method’ input to choose auto, fast, or none. Maps to a command-line argument: -m %.4f (position: 4).
no_cleanup : a boolean
Input structural image is already brain-extracted. Maps to a command-line argument: -d (position: 3).
output_type : ‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’
FSL output type.
verbose : a boolean
Use verbose logging. Maps to a command-line argument: -v (position: 1).
bvars : a list of items which are a pathlike object or string representing an existing file
Bvars for each subcortical region.
original_segmentations : a pathlike object or string representing an existing file
3D image file containing the segmented regions as integer values. Uses CMA labelling.
segmentation_file : a pathlike object or string representing an existing file
4D image file containing a single volume per segmented region.
vtk_surfaces : a list of items which are a pathlike object or string representing an existing file
VTK format meshes for each subcortical region.

FLIRT

Link to code

Bases: FSLCommand

Wrapped executable: flirt.

FSL FLIRT wrapper for coregistration

For complete details, see the FLIRT Documentation.

To print out the command line help, use:
fsl.FLIRT().inputs_help()

Examples

>>> from nipype.interfaces import fsl
>>> from nipype.testing import example_data
>>> flt = fsl.FLIRT(bins=640, cost_func='mutualinfo')
>>> flt.inputs.in_file = 'structural.nii'
>>> flt.inputs.reference = 'mni.nii'
>>> flt.inputs.output_type = "NIFTI_GZ"
>>> flt.cmdline # doctest: +ELLIPSIS
'flirt -in structural.nii -ref mni.nii -out structural_flirt.nii.gz -omat structural_flirt.mat -bins 640 -searchcost mutualinfo'
>>> res = flt.run() #doctest: +SKIP
in_file : a pathlike object or string representing an existing file
Input file. Maps to a command-line argument: -in %s (position: 0).
reference : a pathlike object or string representing an existing file
Reference file. Maps to a command-line argument: -ref %s (position: 1).
angle_rep : ‘quaternion’ or ‘euler’
Representation of rotation angles. Maps to a command-line argument: -anglerep %s.
apply_isoxfm : a float
As applyxfm but forces isotropic resampling. Maps to a command-line argument: -applyisoxfm %f. Mutually exclusive with inputs: apply_xfm.
apply_xfm : a boolean
Apply transformation supplied by in_matrix_file or uses_qform to use the affine matrix stored in the reference header. Maps to a command-line argument: -applyxfm.
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
bbrslope : a float
Value of bbr slope. Maps to a command-line argument: -bbrslope %f.
bbrtype : ‘signed’ or ‘global_abs’ or ‘local_abs’
Type of bbr cost function: signed [default], global_abs, local_abs. Maps to a command-line argument: -bbrtype %s.
bgvalue : a float
Use specified background value for points outside FOV. Maps to a command-line argument: -setbackground %f.
bins : an integer (int or long)
Number of histogram bins. Maps to a command-line argument: -bins %d.
coarse_search : an integer (int or long)
Coarse search delta angle. Maps to a command-line argument: -coarsesearch %d.
cost : ‘mutualinfo’ or ‘corratio’ or ‘normcorr’ or ‘normmi’ or ‘leastsq’ or ‘labeldiff’ or ‘bbr’
Cost function. Maps to a command-line argument: -cost %s.
cost_func : ‘mutualinfo’ or ‘corratio’ or ‘normcorr’ or ‘normmi’ or ‘leastsq’ or ‘labeldiff’ or ‘bbr’
Cost function. Maps to a command-line argument: -searchcost %s.
datatype : ‘char’ or ‘short’ or ‘int’ or ‘float’ or ‘double’
Force output data type. Maps to a command-line argument: -datatype %s.
display_init : a boolean
Display initial matrix. Maps to a command-line argument: -displayinit.
dof : an integer (int or long)
Number of transform degrees of freedom. Maps to a command-line argument: -dof %d.
echospacing : a float
Value of EPI echo spacing - units of seconds. Maps to a command-line argument: -echospacing %f.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
fieldmap : a pathlike object or string representing a file
Fieldmap image in rads/s - must be already registered to the reference image. Maps to a command-line argument: -fieldmap %s.
fieldmapmask : a pathlike object or string representing a file
Mask for fieldmap image. Maps to a command-line argument: -fieldmapmask %s.
fine_search : an integer (int or long)
Fine search delta angle. Maps to a command-line argument: -finesearch %d.
force_scaling : a boolean
Force rescaling even for low-res images. Maps to a command-line argument: -forcescaling.
in_matrix_file : a pathlike object or string representing a file
Input 4x4 affine matrix. Maps to a command-line argument: -init %s.
in_weight : a pathlike object or string representing an existing file
File for input weighting volume. Maps to a command-line argument: -inweight %s.
interp : ‘trilinear’ or ‘nearestneighbour’ or ‘sinc’ or ‘spline’
Final interpolation method used in reslicing. Maps to a command-line argument: -interp %s.
min_sampling : a float
Set minimum voxel dimension for sampling. Maps to a command-line argument: -minsampling %f.
no_clamp : a boolean
Do not use intensity clamping. Maps to a command-line argument: -noclamp.
no_resample : a boolean
Do not change input sampling. Maps to a command-line argument: -noresample.
no_resample_blur : a boolean
Do not use blurring on downsampling. Maps to a command-line argument: -noresampblur.
no_search : a boolean
Set all angular searches to ranges 0 to 0. Maps to a command-line argument: -nosearch.
out_file : a pathlike object or string representing a file
Registered output file. Maps to a command-line argument: -out %s (position: 2).
out_log : a pathlike object or string representing a file
Output log. Requires inputs: save_log.
out_matrix_file : a pathlike object or string representing a file
Output affine matrix in 4x4 asciii format. Maps to a command-line argument: -omat %s (position: 3).
output_type : ‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’
FSL output type.
padding_size : an integer (int or long)
For applyxfm: interpolates outside image by size. Maps to a command-line argument: -paddingsize %d.
pedir : an integer (int or long)
Phase encode direction of EPI - 1/2/3=x/y/z & -1/-2/-3=-x/-y/-z. Maps to a command-line argument: -pedir %d.
ref_weight : a pathlike object or string representing an existing file
File for reference weighting volume. Maps to a command-line argument: -refweight %s.
rigid2D : a boolean
Use 2D rigid body mode - ignores dof. Maps to a command-line argument: -2D.
save_log : a boolean
Save to log file.
schedule : a pathlike object or string representing an existing file
Replaces default schedule. Maps to a command-line argument: -schedule %s.
searchr_x : a list of from 2 to 2 items which are an integer (int or long)
Search angles along x-axis, in degrees. Maps to a command-line argument: -searchrx %s.
searchr_y : a list of from 2 to 2 items which are an integer (int or long)
Search angles along y-axis, in degrees. Maps to a command-line argument: -searchry %s.
searchr_z : a list of from 2 to 2 items which are an integer (int or long)
Search angles along z-axis, in degrees. Maps to a command-line argument: -searchrz %s.
sinc_width : an integer (int or long)
Full-width in voxels. Maps to a command-line argument: -sincwidth %d.
sinc_window : ‘rectangular’ or ‘hanning’ or ‘blackman’
Sinc window. Maps to a command-line argument: -sincwindow %s.
uses_qform : a boolean
Initialize using sform or qform. Maps to a command-line argument: -usesqform.
verbose : an integer (int or long)
Verbose mode, 0 is least. Maps to a command-line argument: -verbose %d.
wm_seg : a pathlike object or string representing a file
White matter segmentation volume needed by BBR cost function. Maps to a command-line argument: -wmseg %s.
wmcoords : a pathlike object or string representing a file
White matter boundary coordinates for BBR cost function. Maps to a command-line argument: -wmcoords %s.
wmnorms : a pathlike object or string representing a file
White matter boundary normals for BBR cost function. Maps to a command-line argument: -wmnorms %s.
out_file : a pathlike object or string representing an existing file
Path/name of registered file (if generated).
out_log : a pathlike object or string representing a file
Path/name of output log (if generated).
out_matrix_file : a pathlike object or string representing an existing file
Path/name of calculated affine transform (if generated).
FLIRT.aggregate_outputs(runtime=None, needed_outputs=None)

Collate expected outputs and apply output traits validation.

FNIRT

Link to code

Bases: FSLCommand

Wrapped executable: fnirt.

FSL FNIRT wrapper for non-linear registration

For complete details, see the FNIRT Documentation.

Examples

>>> from nipype.interfaces import fsl
>>> from nipype.testing import example_data
>>> fnt = fsl.FNIRT(affine_file=example_data('trans.mat'))
>>> res = fnt.run(ref_file=example_data('mni.nii', in_file=example_data('structural.nii')) #doctest: +SKIP

T1 -> Mni153

>>> from nipype.interfaces import fsl
>>> fnirt_mprage = fsl.FNIRT()
>>> fnirt_mprage.inputs.in_fwhm = [8, 4, 2, 2]
>>> fnirt_mprage.inputs.subsampling_scheme = [4, 2, 1, 1]

Specify the resolution of the warps

>>> fnirt_mprage.inputs.warp_resolution = (6, 6, 6)
>>> res = fnirt_mprage.run(in_file='structural.nii', ref_file='mni.nii', warped_file='warped.nii', fieldcoeff_file='fieldcoeff.nii')#doctest: +SKIP

We can check the command line and confirm that it’s what we expect.

>>> fnirt_mprage.cmdline  #doctest: +SKIP
'fnirt --cout=fieldcoeff.nii --in=structural.nii --infwhm=8,4,2,2 --ref=mni.nii --subsamp=4,2,1,1 --warpres=6,6,6 --iout=warped.nii'
in_file : a pathlike object or string representing an existing file
Name of input image. Maps to a command-line argument: --in=%s.
ref_file : a pathlike object or string representing an existing file
Name of reference image. Maps to a command-line argument: --ref=%s.
affine_file : a pathlike object or string representing an existing file
Name of file containing affine transform. Maps to a command-line argument: --aff=%s.
apply_inmask : a list of items which are 0 or 1
List of iterations to use input mask on (1 to use, 0 to skip). Maps to a command-line argument: --applyinmask=%s. Mutually exclusive with inputs: skip_inmask.
apply_intensity_mapping : a list of items which are 0 or 1
List of subsampling levels to apply intensity mapping for (0 to skip, 1 to apply). Maps to a command-line argument: --estint=%s. Mutually exclusive with inputs: skip_intensity_mapping.
apply_refmask : a list of items which are 0 or 1
List of iterations to use reference mask on (1 to use, 0 to skip). Maps to a command-line argument: --applyrefmask=%s. Mutually exclusive with inputs: skip_refmask.
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
bias_regularization_lambda : a float
Weight of regularisation for bias-field, default 10000. Maps to a command-line argument: --biaslambda=%f.
biasfield_resolution : a tuple of the form: (an integer (int or long), an integer (int or long), an integer (int or long))
Resolution (in mm) of bias-field modelling local intensities, default 50, 50, 50. Maps to a command-line argument: --biasres=%d,%d,%d.
config_file : ‘T1_2_MNI152_2mm’ or ‘FA_2_FMRIB58_1mm’ or a pathlike object or string representing an existing file
Name of config file specifying command line arguments. Maps to a command-line argument: --config=%s.
derive_from_ref : a boolean
If true, ref image is used to calculate derivatives. Default false. Maps to a command-line argument: --refderiv.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
field_file : a boolean or a pathlike object or string representing a file
Name of output file with field or true. Maps to a command-line argument: --fout=%s.
fieldcoeff_file : a boolean or a pathlike object or string representing a file
Name of output file with field coefficients or true. Maps to a command-line argument: --cout=%s.
hessian_precision : ‘double’ or ‘float’
Precision for representing Hessian, double or float. Default double. Maps to a command-line argument: --numprec=%s.
in_fwhm : a list of items which are an integer (int or long)
FWHM (in mm) of gaussian smoothing kernel for input volume, default [6, 4, 2, 2]. Maps to a command-line argument: --infwhm=%s.
in_intensitymap_file : a list of from 1 to 2 items which are a pathlike object or string representing an existing file
Name of file/files containing initial intensity mapping usually generated by previous fnirt run. Maps to a command-line argument: --intin=%s.
inmask_file : a pathlike object or string representing an existing file
Name of file with mask in input image space. Maps to a command-line argument: --inmask=%s.
inmask_val : a float
Value to mask out in –in image. Default =0.0. Maps to a command-line argument: --impinval=%f.
intensity_mapping_model : ‘none’ or ‘global_linear’ or ‘global_non_linear’ or ‘local_linear’ or ‘global_non_linear_with_bias’ or ‘local_non_linear’
Model for intensity-mapping. Maps to a command-line argument: --intmod=%s.
intensity_mapping_order : an integer (int or long)
Order of poynomial for mapping intensities, default 5. Maps to a command-line argument: --intorder=%d.
inwarp_file : a pathlike object or string representing an existing file
Name of file containing initial non-linear warps. Maps to a command-line argument: --inwarp=%s.
jacobian_file : a boolean or a pathlike object or string representing a file
Name of file for writing out the Jacobian of the field (for diagnostic or VBM purposes). Maps to a command-line argument: --jout=%s.
jacobian_range : a tuple of the form: (a float, a float)
Allowed range of Jacobian determinants, default 0.01, 100.0. Maps to a command-line argument: --jacrange=%f,%f.
log_file : a pathlike object or string representing a file
Name of log-file. Maps to a command-line argument: --logout=%s.
max_nonlin_iter : a list of items which are an integer (int or long)
Max # of non-linear iterations list, default [5, 5, 5, 5]. Maps to a command-line argument: --miter=%s.
modulatedref_file : a boolean or a pathlike object or string representing a file
Name of file for writing out intensity modulated –ref (for diagnostic purposes). Maps to a command-line argument: --refout=%s.
out_intensitymap_file : a boolean or a pathlike object or string representing a file
Name of files for writing information pertaining to intensity mapping. Maps to a command-line argument: --intout=%s.
output_type : ‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’
FSL output type.
ref_fwhm : a list of items which are an integer (int or long)
FWHM (in mm) of gaussian smoothing kernel for ref volume, default [4, 2, 0, 0]. Maps to a command-line argument: --reffwhm=%s.
refmask_file : a pathlike object or string representing an existing file
Name of file with mask in reference space. Maps to a command-line argument: --refmask=%s.
refmask_val : a float
Value to mask out in –ref image. Default =0.0. Maps to a command-line argument: --imprefval=%f.
regularization_lambda : a list of items which are a float
Weight of regularisation, default depending on –ssqlambda and –regmod switches. See user documetation. Maps to a command-line argument: --lambda=%s.
regularization_model : ‘membrane_energy’ or ‘bending_energy’
Model for regularisation of warp-field [membrane_energy bending_energy], default bending_energy. Maps to a command-line argument: --regmod=%s.
skip_implicit_in_masking : a boolean
Skip implicit masking based on value in –in image. Default = 0. Maps to a command-line argument: --impinm=0.
skip_implicit_ref_masking : a boolean
Skip implicit masking based on value in –ref image. Default = 0. Maps to a command-line argument: --imprefm=0.
skip_inmask : a boolean
Skip specified inmask if set, default false. Maps to a command-line argument: --applyinmask=0. Mutually exclusive with inputs: apply_inmask.
skip_intensity_mapping : a boolean
Skip estimate intensity-mapping default false. Maps to a command-line argument: --estint=0. Mutually exclusive with inputs: apply_intensity_mapping.
skip_lambda_ssq : a boolean
If true, lambda is not weighted by current ssq, default false. Maps to a command-line argument: --ssqlambda=0.
skip_refmask : a boolean
Skip specified refmask if set, default false. Maps to a command-line argument: --applyrefmask=0. Mutually exclusive with inputs: apply_refmask.
spline_order : an integer (int or long)
Order of spline, 2->Qadratic spline, 3->Cubic spline. Default=3. Maps to a command-line argument: --splineorder=%d.
subsampling_scheme : a list of items which are an integer (int or long)
Sub-sampling scheme, list, default [4, 2, 1, 1]. Maps to a command-line argument: --subsamp=%s.
warp_resolution : a tuple of the form: (an integer (int or long), an integer (int or long), an integer (int or long))
(approximate) resolution (in mm) of warp basis in x-, y- and z-direction, default 10, 10, 10. Maps to a command-line argument: --warpres=%d,%d,%d.
warped_file : a pathlike object or string representing a file
Name of output image. Maps to a command-line argument: --iout=%s.
field_file : a pathlike object or string representing a file
File with warp field.
fieldcoeff_file : a pathlike object or string representing an existing file
File with field coefficients.
jacobian_file : a pathlike object or string representing a file
File containing Jacobian of the field.
log_file : a pathlike object or string representing a file
Name of log-file.
modulatedref_file : a pathlike object or string representing a file
File containing intensity modulated –ref.
out_intensitymap_file : a list of from 2 to 2 items which are a pathlike object or string representing a file
Files containing info pertaining to intensity mapping.
warped_file : a pathlike object or string representing an existing file
Warped image.
FNIRT.filemap = {'field_file': 'field', 'fieldcoeff_file': 'fieldwarp', 'jacobian_file': 'field_jacobian', 'log_file': 'log.txt', 'modulatedref_file': 'modulated', 'out_intensitymap_file': 'intmap', 'warped_file': 'warped'}
classmethod FNIRT.intensitymap_file_basename(f)

Removes valid intensitymap extensions from f, returning a basename that can refer to both intensitymap files.

FNIRT.write_config(configfile)

Writes out currently set options to specified config file

XX TODO : need to figure out how the config file is written

Parameters:configfile (/path/to/configfile) –

FUGUE

Link to code

Bases: FSLCommand

Wrapped executable: fugue.

FSL FUGUE set of tools for EPI distortion correction

FUGUE is, most generally, a set of tools for EPI distortion correction.

Distortions may be corrected for
  1. improving registration with non-distorted images (e.g. structurals), or
  2. dealing with motion-dependent changes.

FUGUE is designed to deal only with the first case - improving registration.

Examples

Unwarping an input image (shift map is known):

>>> from nipype.interfaces.fsl.preprocess import FUGUE
>>> fugue = FUGUE()
>>> fugue.inputs.in_file = 'epi.nii'
>>> fugue.inputs.mask_file = 'epi_mask.nii'
>>> fugue.inputs.shift_in_file = 'vsm.nii'  # Previously computed with fugue as well
>>> fugue.inputs.unwarp_direction = 'y'
>>> fugue.inputs.output_type = "NIFTI_GZ"
>>> fugue.cmdline # doctest: +ELLIPSIS
'fugue --in=epi.nii --mask=epi_mask.nii --loadshift=vsm.nii --unwarpdir=y --unwarp=epi_unwarped.nii.gz'
>>> fugue.run() #doctest: +SKIP

Warping an input image (shift map is known):

>>> from nipype.interfaces.fsl.preprocess import FUGUE
>>> fugue = FUGUE()
>>> fugue.inputs.in_file = 'epi.nii'
>>> fugue.inputs.forward_warping = True
>>> fugue.inputs.mask_file = 'epi_mask.nii'
>>> fugue.inputs.shift_in_file = 'vsm.nii'  # Previously computed with fugue as well
>>> fugue.inputs.unwarp_direction = 'y'
>>> fugue.inputs.output_type = "NIFTI_GZ"
>>> fugue.cmdline # doctest: +ELLIPSIS
'fugue --in=epi.nii --mask=epi_mask.nii --loadshift=vsm.nii --unwarpdir=y --warp=epi_warped.nii.gz'
>>> fugue.run() #doctest: +SKIP

Computing the vsm (unwrapped phase map is known):

>>> from nipype.interfaces.fsl.preprocess import FUGUE
>>> fugue = FUGUE()
>>> fugue.inputs.phasemap_in_file = 'epi_phasediff.nii'
>>> fugue.inputs.mask_file = 'epi_mask.nii'
>>> fugue.inputs.dwell_to_asym_ratio = (0.77e-3 * 3) / 2.46e-3
>>> fugue.inputs.unwarp_direction = 'y'
>>> fugue.inputs.save_shift = True
>>> fugue.inputs.output_type = "NIFTI_GZ"
>>> fugue.cmdline # doctest: +ELLIPSIS
'fugue --dwelltoasym=0.9390243902 --mask=epi_mask.nii --phasemap=epi_phasediff.nii --saveshift=epi_phasediff_vsm.nii.gz --unwarpdir=y'
>>> fugue.run() #doctest: +SKIP
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
asym_se_time : a float
Set the fieldmap asymmetric spin echo time (sec). Maps to a command-line argument: --asym=%.10f.
despike_2dfilter : a boolean
Apply a 2D de-spiking filter. Maps to a command-line argument: --despike.
despike_threshold : a float
Specify the threshold for de-spiking (default=3.0). Maps to a command-line argument: --despikethreshold=%s.
dwell_time : a float
Set the EPI dwell time per phase-encode line - same as echo spacing - (sec). Maps to a command-line argument: --dwell=%.10f.
dwell_to_asym_ratio : a float
Set the dwell to asym time ratio. Maps to a command-line argument: --dwelltoasym=%.10f.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
fmap_in_file : a pathlike object or string representing an existing file
Filename for loading fieldmap (rad/s). Maps to a command-line argument: --loadfmap=%s.
fmap_out_file : a pathlike object or string representing a file
Filename for saving fieldmap (rad/s). Maps to a command-line argument: --savefmap=%s.
forward_warping : a boolean
Apply forward warping instead of unwarping. (Nipype default value: False)
fourier_order : an integer (int or long)
Apply Fourier (sinusoidal) fitting of order N. Maps to a command-line argument: --fourier=%d.
icorr : a boolean
Apply intensity correction to unwarping (pixel shift method only). Maps to a command-line argument: --icorr. Requires inputs: shift_in_file.
icorr_only : a boolean
Apply intensity correction only. Maps to a command-line argument: --icorronly. Requires inputs: unwarped_file.
in_file : a pathlike object or string representing an existing file
Filename of input volume. Maps to a command-line argument: --in=%s.
mask_file : a pathlike object or string representing an existing file
Filename for loading valid mask. Maps to a command-line argument: --mask=%s.
median_2dfilter : a boolean
Apply 2D median filtering. Maps to a command-line argument: --median.
no_extend : a boolean
Do not apply rigid-body extrapolation to the fieldmap. Maps to a command-line argument: --noextend.
no_gap_fill : a boolean
Do not apply gap-filling measure to the fieldmap. Maps to a command-line argument: --nofill.
nokspace : a boolean
Do not use k-space forward warping. Maps to a command-line argument: --nokspace.
output_type : ‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’
FSL output type.
pava : a boolean
Apply monotonic enforcement via PAVA. Maps to a command-line argument: --pava.
phase_conjugate : a boolean
Apply phase conjugate method of unwarping. Maps to a command-line argument: --phaseconj.
phasemap_in_file : a pathlike object or string representing an existing file
Filename for input phase image. Maps to a command-line argument: --phasemap=%s.
poly_order : an integer (int or long)
Apply polynomial fitting of order N. Maps to a command-line argument: --poly=%d.
save_fmap : a boolean
Write field map volume. Mutually exclusive with inputs: save_unmasked_fmap.
save_shift : a boolean
Write pixel shift volume. Mutually exclusive with inputs: save_unmasked_shift.
save_unmasked_fmap : a boolean
Saves the unmasked fieldmap when using –savefmap. Maps to a command-line argument: --unmaskfmap. Mutually exclusive with inputs: save_fmap.
save_unmasked_shift : a boolean
Saves the unmasked shiftmap when using –saveshift. Maps to a command-line argument: --unmaskshift. Mutually exclusive with inputs: save_shift.
shift_in_file : a pathlike object or string representing an existing file
Filename for reading pixel shift volume. Maps to a command-line argument: --loadshift=%s.
shift_out_file : a pathlike object or string representing a file
Filename for saving pixel shift volume. Maps to a command-line argument: --saveshift=%s.
smooth2d : a float
Apply 2D Gaussian smoothing of sigma N (in mm). Maps to a command-line argument: --smooth2=%.2f.
smooth3d : a float
Apply 3D Gaussian smoothing of sigma N (in mm). Maps to a command-line argument: --smooth3=%.2f.
unwarp_direction : ‘x’ or ‘y’ or ‘z’ or ‘x-‘ or ‘y-‘ or ‘z-‘
Specifies direction of warping (default y). Maps to a command-line argument: --unwarpdir=%s.
unwarped_file : a pathlike object or string representing a file
Apply unwarping and save as filename. Maps to a command-line argument: --unwarp=%s. Mutually exclusive with inputs: warped_file. Requires inputs: in_file.
warped_file : a pathlike object or string representing a file
Apply forward warping and save as filename. Maps to a command-line argument: --warp=%s. Mutually exclusive with inputs: unwarped_file. Requires inputs: in_file.
fmap_out_file : a pathlike object or string representing a file
Fieldmap file.
shift_out_file : a pathlike object or string representing a file
Voxel shift map file.
unwarped_file : a pathlike object or string representing a file
Unwarped file.
warped_file : a pathlike object or string representing a file
Forward warped file.

MCFLIRT

Link to code

Bases: FSLCommand

Wrapped executable: mcflirt.

FSL MCFLIRT wrapper for within-modality motion correction

For complete details, see the MCFLIRT Documentation.

Examples

>>> from nipype.interfaces import fsl
>>> mcflt = fsl.MCFLIRT()
>>> mcflt.inputs.in_file = 'functional.nii'
>>> mcflt.inputs.cost = 'mutualinfo'
>>> mcflt.inputs.out_file = 'moco.nii'
>>> mcflt.cmdline
'mcflirt -in functional.nii -cost mutualinfo -out moco.nii'
>>> res = mcflt.run()  # doctest: +SKIP
in_file : a pathlike object or string representing an existing file
Timeseries to motion-correct. Maps to a command-line argument: -in %s (position: 0).
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
bins : an integer (int or long)
Number of histogram bins. Maps to a command-line argument: -bins %d.
cost : ‘mutualinfo’ or ‘woods’ or ‘corratio’ or ‘normcorr’ or ‘normmi’ or ‘leastsquares’
Cost function to optimize. Maps to a command-line argument: -cost %s.
dof : an integer (int or long)
Degrees of freedom for the transformation. Maps to a command-line argument: -dof %d.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
init : a pathlike object or string representing an existing file
Inital transformation matrix. Maps to a command-line argument: -init %s.
interpolation : ‘spline’ or ‘nn’ or ‘sinc’
Interpolation method for transformation. Maps to a command-line argument: -%s_final.
mean_vol : a boolean
Register to mean volume. Maps to a command-line argument: -meanvol.
out_file : a pathlike object or string representing a file
File to write. Maps to a command-line argument: -out %s.
output_type : ‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’
FSL output type.
ref_file : a pathlike object or string representing an existing file
Target image for motion correction. Maps to a command-line argument: -reffile %s.
ref_vol : an integer (int or long)
Volume to align frames to. Maps to a command-line argument: -refvol %d.
rotation : an integer (int or long)
Scaling factor for rotation tolerances. Maps to a command-line argument: -rotation %d.
save_mats : a boolean
Save transformation matrices. Maps to a command-line argument: -mats.
save_plots : a boolean
Save transformation parameters. Maps to a command-line argument: -plots.
save_rms : a boolean
Save rms displacement parameters. Maps to a command-line argument: -rmsabs -rmsrel.
scaling : a float
Scaling factor to use. Maps to a command-line argument: -scaling %.2f.
smooth : a float
Smoothing factor for the cost function. Maps to a command-line argument: -smooth %.2f.
stages : an integer (int or long)
Stages (if 4, perform final search with sinc interpolation. Maps to a command-line argument: -stages %d.
stats_imgs : a boolean
Produce variance and std. dev. images. Maps to a command-line argument: -stats.
use_contour : a boolean
Run search on contour images. Maps to a command-line argument: -edge.
use_gradient : a boolean
Run search on gradient images. Maps to a command-line argument: -gdt.
mat_file : a list of items which are a pathlike object or string representing an existing file
Transformation matrices.
mean_img : a pathlike object or string representing an existing file
Mean timeseries image (if mean_vol=True).
out_file : a pathlike object or string representing an existing file
Motion-corrected timeseries.
par_file : a pathlike object or string representing an existing file
Text-file with motion parameters.
rms_files : a list of items which are a pathlike object or string representing an existing file
Absolute and relative displacement parameters.
std_img : a pathlike object or string representing an existing file
Standard deviation image.
variance_img : a pathlike object or string representing an existing file
Variance image.

PRELUDE

Link to code

Bases: FSLCommand

Wrapped executable: prelude.

FSL prelude wrapper for phase unwrapping

Examples

Please insert examples for use of this command

complex_phase_file : a pathlike object or string representing an existing file
Complex phase input volume. Maps to a command-line argument: --complex=%s. Mutually exclusive with inputs: magnitude_file, phase_file.
magnitude_file : a pathlike object or string representing an existing file
File containing magnitude image. Maps to a command-line argument: --abs=%s. Mutually exclusive with inputs: complex_phase_file.
phase_file : a pathlike object or string representing an existing file
Raw phase file. Maps to a command-line argument: --phase=%s. Mutually exclusive with inputs: complex_phase_file.
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
end : an integer (int or long)
Final image number to process (default Inf). Maps to a command-line argument: --end=%d.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
label_file : a pathlike object or string representing a file
Saving the area labels output. Maps to a command-line argument: --labels=%s.
labelprocess2d : a boolean
Does label processing in 2D (slice at a time). Maps to a command-line argument: --labelslices.
mask_file : a pathlike object or string representing an existing file
Filename of mask input volume. Maps to a command-line argument: --mask=%s.
num_partitions : an integer (int or long)
Number of phase partitions to use. Maps to a command-line argument: --numphasesplit=%d.
output_type : ‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’
FSL output type.
process2d : a boolean
Does all processing in 2D (slice at a time). Maps to a command-line argument: --slices. Mutually exclusive with inputs: labelprocess2d.
process3d : a boolean
Forces all processing to be full 3D. Maps to a command-line argument: --force3D. Mutually exclusive with inputs: labelprocess2d, process2d.
rawphase_file : a pathlike object or string representing a file
Saving the raw phase output. Maps to a command-line argument: --rawphase=%s.
removeramps : a boolean
Remove phase ramps during unwrapping. Maps to a command-line argument: --removeramps.
savemask_file : a pathlike object or string representing a file
Saving the mask volume. Maps to a command-line argument: --savemask=%s.
start : an integer (int or long)
First image number to process (default 0). Maps to a command-line argument: --start=%d.
threshold : a float
Intensity threshold for masking. Maps to a command-line argument: --thresh=%.10f.
unwrapped_phase_file : a pathlike object or string representing a file
File containing unwrapepd phase. Maps to a command-line argument: --unwrap=%s.
unwrapped_phase_file : a pathlike object or string representing an existing file
Unwrapped phase file.

SUSAN

Link to code

Bases: FSLCommand

Wrapped executable: susan.

FSL SUSAN wrapper to perform smoothing

For complete details, see the SUSAN Documentation.

Examples

>>> from nipype.interfaces import fsl
>>> from nipype.testing import example_data
>>> anatfile  # doctest: +SKIP
anatomical.nii  # doctest: +SKIP
>>> sus = fsl.SUSAN()
>>> sus.inputs.in_file = example_data('structural.nii')
>>> sus.inputs.brightness_threshold = 2000.0
>>> sus.inputs.fwhm = 8.0
>>> result = sus.run()  # doctest: +SKIP
brightness_threshold : a float
Brightness threshold and should be greater than noise level and less than contrast of edges to be preserved. Maps to a command-line argument: %.10f (position: 2).
fwhm : a float
Fwhm of smoothing, in mm, gets converted using sqrt(8*log(2)). Maps to a command-line argument: %.10f (position: 3).
in_file : a pathlike object or string representing an existing file
Filename of input timeseries. Maps to a command-line argument: %s (position: 1).
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
dimension : 3 or 2
Within-plane (2) or fully 3D (3). Maps to a command-line argument: %d (position: 4). (Nipype default value: 3)
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
out_file : a pathlike object or string representing a file
Output file name. Maps to a command-line argument: %s (position: -1).
output_type : ‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’
FSL output type.
usans : a list of at most 2 items which are a tuple of the form: (a pathlike object or string representing an existing file, a float)
Determines whether the smoothing area (USAN) is to be found from secondary images (0, 1 or 2). A negative value for any brightness threshold will auto-set the threshold at 10% of the robust range. (Nipype default value: [])
use_median : 1 or 0
Whether to use a local median filter in the cases where single-point noise is detected. Maps to a command-line argument: %d (position: 5). (Nipype default value: 1)
smoothed_file : a pathlike object or string representing an existing file
Smoothed output file.

SliceTimer

Link to code

Bases: FSLCommand

Wrapped executable: slicetimer.

FSL slicetimer wrapper to perform slice timing correction

Examples

>>> from nipype.interfaces import fsl
>>> from nipype.testing import example_data
>>> st = fsl.SliceTimer()
>>> st.inputs.in_file = example_data('functional.nii')
>>> st.inputs.interleaved = True
>>> result = st.run() #doctest: +SKIP
in_file : a pathlike object or string representing an existing file
Filename of input timeseries. Maps to a command-line argument: --in=%s (position: 0).
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
custom_order : a pathlike object or string representing an existing file
Filename of single-column custom interleave order file (first slice is referred to as 1 not 0). Maps to a command-line argument: --ocustom=%s.
custom_timings : a pathlike object or string representing an existing file
Slice timings, in fractions of TR, range 0:1 (default is 0.5 = no shift). Maps to a command-line argument: --tcustom=%s.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
global_shift : a float
Shift in fraction of TR, range 0:1 (default is 0.5 = no shift). Maps to a command-line argument: --tglobal.
index_dir : a boolean
Slice indexing from top to bottom. Maps to a command-line argument: --down.
interleaved : a boolean
Use interleaved acquisition. Maps to a command-line argument: --odd.
out_file : a pathlike object or string representing a file
Filename of output timeseries. Maps to a command-line argument: --out=%s.
output_type : ‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’
FSL output type.
slice_direction : 1 or 2 or 3
Direction of slice acquisition (x=1, y=2, z=3) - default is z. Maps to a command-line argument: --direction=%d.
time_repetition : a float
Specify TR of data - default is 3s. Maps to a command-line argument: --repeat=%f.
slice_time_corrected_file : a pathlike object or string representing an existing file
Slice time corrected file.