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'
>>> res = aw.run()
in_filea pathlike object or string representing an existing file

Image to be warped. Maps to a command-line argument: --in=%s (position: 0).

ref_filea pathlike object or string representing an existing file

Reference image. Maps to a command-line argument: --ref=%s (position: 1).

abswarpa boolean

Treat warp field as absolute: x’ = w(x). Maps to a command-line argument: --abs. Mutually exclusive with inputs: relwarp.

argsa 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.

environa 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_filea 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_filea pathlike object or string representing an existing file

Filename for mask image (in reference space). Maps to a command-line argument: --mask=%s.

out_filea 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’ or ‘GIFTI’

FSL output type.

postmata pathlike object or string representing an existing file

Filename for post-transform (affine matrix). Maps to a command-line argument: --postmat=%s.

premata pathlike object or string representing an existing file

Filename for pre-transform (affine matrix). Maps to a command-line argument: --premat=%s.

relwarpa 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

Level of intermediary supersampling, a for ‘automatic’ or integer level. Default = 2. Maps to a command-line argument: --superlevel=%s.

supersamplea boolean

Intermediary supersampling of output, default is off. Maps to a command-line argument: --super.

out_filea 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 transform 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()
in_filea pathlike object or string representing an existing file

Input file. Maps to a command-line argument: -in %s (position: 0).

referencea 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_isoxfma float

As applyxfm but forces isotropic resampling. Maps to a command-line argument: -applyisoxfm %f. Mutually exclusive with inputs: apply_xfm.

apply_xfma 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)

argsa string

Additional parameters to the command. Maps to a command-line argument: %s.

bbrslopea 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.

bgvaluea float

Use specified background value for points outside FOV. Maps to a command-line argument: -setbackground %f.

binsan integer

Number of histogram bins. Maps to a command-line argument: -bins %d.

coarse_searchan integer

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_inita boolean

Display initial matrix. Maps to a command-line argument: -displayinit.

dofan integer

Number of transform degrees of freedom. Maps to a command-line argument: -dof %d.

echospacinga float

Value of EPI echo spacing - units of seconds. Maps to a command-line argument: -echospacing %f.

environa 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: {})

fieldmapa 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.

fieldmapmaska pathlike object or string representing a file

Mask for fieldmap image. Maps to a command-line argument: -fieldmapmask %s.

fine_searchan integer

Fine search delta angle. Maps to a command-line argument: -finesearch %d.

force_scalinga boolean

Force rescaling even for low-res images. Maps to a command-line argument: -forcescaling.

in_matrix_filea pathlike object or string representing a file

Input 4x4 affine matrix. Maps to a command-line argument: -init %s.

in_weighta 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_samplinga float

Set minimum voxel dimension for sampling. Maps to a command-line argument: -minsampling %f.

no_clampa boolean

Do not use intensity clamping. Maps to a command-line argument: -noclamp.

no_resamplea boolean

Do not change input sampling. Maps to a command-line argument: -noresample.

no_resample_blura boolean

Do not use blurring on downsampling. Maps to a command-line argument: -noresampblur.

no_searcha boolean

Set all angular searches to ranges 0 to 0. Maps to a command-line argument: -nosearch.

out_filea pathlike object or string representing a file

Registered output file. Maps to a command-line argument: -out %s (position: 2).

out_loga pathlike object or string representing a file

Output log. Requires inputs: save_log.

out_matrix_filea 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’ or ‘GIFTI’

FSL output type.

padding_sizean integer

For applyxfm: interpolates outside image by size. Maps to a command-line argument: -paddingsize %d.

pediran integer

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_weighta pathlike object or string representing an existing file

File for reference weighting volume. Maps to a command-line argument: -refweight %s.

rigid2Da boolean

Use 2D rigid body mode - ignores dof. Maps to a command-line argument: -2D.

save_loga boolean

Save to log file.

schedulea pathlike object or string representing an existing file

Replaces default schedule. Maps to a command-line argument: -schedule %s.

searchr_xa list of from 2 to 2 items which are an integer

Search angles along x-axis, in degrees. Maps to a command-line argument: -searchrx %s.

searchr_ya list of from 2 to 2 items which are an integer

Search angles along y-axis, in degrees. Maps to a command-line argument: -searchry %s.

searchr_za list of from 2 to 2 items which are an integer

Search angles along z-axis, in degrees. Maps to a command-line argument: -searchrz %s.

sinc_widthan integer

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_qforma boolean

Initialize using sform or qform. Maps to a command-line argument: -usesqform.

verbosean integer

Verbose mode, 0 is least. Maps to a command-line argument: -verbose %d.

wm_sega pathlike object or string representing a file

White matter segmentation volume needed by BBR cost function. Maps to a command-line argument: -wmseg %s.

wmcoordsa pathlike object or string representing a file

White matter boundary coordinates for BBR cost function. Maps to a command-line argument: -wmcoords %s.

wmnormsa pathlike object or string representing a file

White matter boundary normals for BBR cost function. Maps to a command-line argument: -wmnorms %s.

out_filea pathlike object or string representing an existing file

Path/name of registered file (if generated).

out_loga pathlike object or string representing a file

Path/name of output log (if generated).

out_matrix_filea 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()
in_filea pathlike object or string representing an existing file

Input file to skull strip. Maps to a command-line argument: %s (position: 0).

argsa string

Additional parameters to the command. Maps to a command-line argument: %s.

centera list of at most 3 items which are an integer

Center of gravity in voxels. Maps to a command-line argument: -c %s.

environa 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: {})

fraca float

Fractional intensity threshold. Maps to a command-line argument: -f %.2f.

functionala 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.

maska boolean

Create binary mask image. Maps to a command-line argument: -m.

mesha boolean

Generate a vtk mesh brain surface. Maps to a command-line argument: -e.

no_outputa boolean

Don’t generate segmented output. Maps to a command-line argument: -n.

out_filea pathlike object or string representing a file

Name of output skull stripped image. Maps to a command-line argument: %s (position: 1).

outlinea 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’ or ‘GIFTI’

FSL output type.

paddinga 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.

radiusan integer

Head radius. Maps to a command-line argument: -r %d.

reduce_biasa 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_eyesa 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.

robusta 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.

skulla boolean

Create skull image. Maps to a command-line argument: -s.

surfacesa 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_guideda 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.

thresholda boolean

Apply thresholding to segmented brain image and mask. Maps to a command-line argument: -t.

vertical_gradienta float

Vertical gradient in fractional intensity threshold (-1, 1). Maps to a command-line argument: -g %.2f.

inskull_mask_filea pathlike object or string representing a file

Path/name of inskull mask (if generated).

inskull_mesh_filea pathlike object or string representing a file

Path/name of inskull mesh outline (if generated).

mask_filea pathlike object or string representing a file

Path/name of binary brain mask (if generated).

meshfilea pathlike object or string representing a file

Path/name of vtk mesh file (if generated).

out_filea pathlike object or string representing a file

Path/name of skullstripped file (if generated).

outline_filea pathlike object or string representing a file

Path/name of outline file (if generated).

outskin_mask_filea pathlike object or string representing a file

Path/name of outskin mask (if generated).

outskin_mesh_filea pathlike object or string representing a file

Path/name of outskin mesh outline (if generated).

outskull_mask_filea pathlike object or string representing a file

Path/name of outskull mask (if generated).

outskull_mesh_filea pathlike object or string representing a file

Path/name of outskull mesh outline (if generated).

skull_filea pathlike object or string representing a file

Path/name of skull file (if generated).

skull_mask_filea 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
>>> fast = fsl.FAST()
>>> fast.inputs.in_files = 'structural.nii'
>>> fast.inputs.out_basename = 'fast_'
>>> fast.cmdline
'fast -o fast_ -S 1 structural.nii'
>>> out = fast.run()
in_filesa 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).

argsa string

Additional parameters to the command. Maps to a command-line argument: %s.

bias_iters1 <= an integer <= 10

Number of main-loop iterations during bias-field removal. Maps to a command-line argument: -I %d.

bias_lowpass4 <= an integer <= 40

Bias field smoothing extent (FWHM) in mm. Maps to a command-line argument: -l %d.

environa 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: {})

hyper0.0 <= a floating point number <= 1.0

Segmentation spatial smoothness. Maps to a command-line argument: -H %.2f.

img_type1 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_smooth0.0001 <= a floating point number <= 0.1

Initial segmentation spatial smoothness (during bias field estimation). Maps to a command-line argument: -f %.3f.

init_transforma pathlike object or string representing an existing file

<standard2input.mat> initialise using priors. Maps to a command-line argument: -a %s.

iters_afterbias1 <= an integer <= 20

Number of main-loop iterations after bias-field removal. Maps to a command-line argument: -O %d.

manual_sega pathlike object or string representing an existing file

Filename containing intensities. Maps to a command-line argument: -s %s.

mixel_smooth0.0 <= a floating point number <= 1.0

Spatial smoothness for mixeltype. Maps to a command-line argument: -R %.2f.

no_biasa boolean

Do not remove bias field. Maps to a command-line argument: -N.

no_pvea boolean

Turn off PVE (partial volume estimation). Maps to a command-line argument: --nopve.

number_classes1 <= an integer <= 10

Number of tissue-type classes. Maps to a command-line argument: -n %d.

other_priorsa 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_basenamea pathlike object or string representing a file

Base name of output files. Maps to a command-line argument: -o %s.

output_biascorrecteda boolean

Output restored image (bias-corrected image). Maps to a command-line argument: -B.

output_biasfielda 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’ or ‘GIFTI’

FSL output type.

probability_mapsa boolean

Outputs individual probability maps. Maps to a command-line argument: -p.

segment_iters1 <= an integer <= 50

Number of segmentation-initialisation iterations. Maps to a command-line argument: -W %d.

segmentsa boolean

Outputs a separate binary image for each tissue type. Maps to a command-line argument: -g.

use_priorsa boolean

Use priors throughout. Maps to a command-line argument: -P.

verbosea 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()
in_filea pathlike object or string representing an existing file

Input data file. Maps to a command-line argument: -i %s (position: -2).

out_filea 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_filea 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).

argsa string

Additional parameters to the command. Maps to a command-line argument: %s.

brain_extracteda boolean

Input structural image is already brain-extracted. Maps to a command-line argument: -b (position: 2).

environa 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_structuresa list of at least 1 items which are a 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_thresholda 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_cleanupa 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’ or ‘GIFTI’

FSL output type.

verbosea boolean

Use verbose logging. Maps to a command-line argument: -v (position: 1).

bvarsa list of items which are a pathlike object or string representing an existing file

Bvars for each subcortical region.

original_segmentationsa pathlike object or string representing an existing file

3D image file containing the segmented regions as integer values. Uses CMA labelling.

segmentation_filea pathlike object or string representing an existing file

4D image file containing a single volume per segmented region.

vtk_surfacesa 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
'flirt -in structural.nii -ref mni.nii -out structural_flirt.nii.gz -omat structural_flirt.mat -bins 640 -searchcost mutualinfo'
>>> res = flt.run()
in_filea pathlike object or string representing an existing file

Input file. Maps to a command-line argument: -in %s (position: 0).

referencea 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_isoxfma float

As applyxfm but forces isotropic resampling. Maps to a command-line argument: -applyisoxfm %f. Mutually exclusive with inputs: apply_xfm.

apply_xfma 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.

argsa string

Additional parameters to the command. Maps to a command-line argument: %s.

bbrslopea 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.

bgvaluea float

Use specified background value for points outside FOV. Maps to a command-line argument: -setbackground %f.

binsan integer

Number of histogram bins. Maps to a command-line argument: -bins %d.

coarse_searchan integer

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_inita boolean

Display initial matrix. Maps to a command-line argument: -displayinit.

dofan integer

Number of transform degrees of freedom. Maps to a command-line argument: -dof %d.

echospacinga float

Value of EPI echo spacing - units of seconds. Maps to a command-line argument: -echospacing %f.

environa 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: {})

fieldmapa 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.

fieldmapmaska pathlike object or string representing a file

Mask for fieldmap image. Maps to a command-line argument: -fieldmapmask %s.

fine_searchan integer

Fine search delta angle. Maps to a command-line argument: -finesearch %d.

force_scalinga boolean

Force rescaling even for low-res images. Maps to a command-line argument: -forcescaling.

in_matrix_filea pathlike object or string representing a file

Input 4x4 affine matrix. Maps to a command-line argument: -init %s.

in_weighta 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_samplinga float

Set minimum voxel dimension for sampling. Maps to a command-line argument: -minsampling %f.

no_clampa boolean

Do not use intensity clamping. Maps to a command-line argument: -noclamp.

no_resamplea boolean

Do not change input sampling. Maps to a command-line argument: -noresample.

no_resample_blura boolean

Do not use blurring on downsampling. Maps to a command-line argument: -noresampblur.

no_searcha boolean

Set all angular searches to ranges 0 to 0. Maps to a command-line argument: -nosearch.

out_filea pathlike object or string representing a file

Registered output file. Maps to a command-line argument: -out %s (position: 2).

out_loga pathlike object or string representing a file

Output log. Requires inputs: save_log.

out_matrix_filea 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’ or ‘GIFTI’

FSL output type.

padding_sizean integer

For applyxfm: interpolates outside image by size. Maps to a command-line argument: -paddingsize %d.

pediran integer

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_weighta pathlike object or string representing an existing file

File for reference weighting volume. Maps to a command-line argument: -refweight %s.

rigid2Da boolean

Use 2D rigid body mode - ignores dof. Maps to a command-line argument: -2D.

save_loga boolean

Save to log file.

schedulea pathlike object or string representing an existing file

Replaces default schedule. Maps to a command-line argument: -schedule %s.

searchr_xa list of from 2 to 2 items which are an integer

Search angles along x-axis, in degrees. Maps to a command-line argument: -searchrx %s.

searchr_ya list of from 2 to 2 items which are an integer

Search angles along y-axis, in degrees. Maps to a command-line argument: -searchry %s.

searchr_za list of from 2 to 2 items which are an integer

Search angles along z-axis, in degrees. Maps to a command-line argument: -searchrz %s.

sinc_widthan integer

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_qforma boolean

Initialize using sform or qform. Maps to a command-line argument: -usesqform.

verbosean integer

Verbose mode, 0 is least. Maps to a command-line argument: -verbose %d.

wm_sega pathlike object or string representing a file

White matter segmentation volume needed by BBR cost function. Maps to a command-line argument: -wmseg %s.

wmcoordsa pathlike object or string representing a file

White matter boundary coordinates for BBR cost function. Maps to a command-line argument: -wmcoords %s.

wmnormsa pathlike object or string representing a file

White matter boundary normals for BBR cost function. Maps to a command-line argument: -wmnorms %s.

out_filea pathlike object or string representing an existing file

Path/name of registered file (if generated).

out_loga pathlike object or string representing a file

Path/name of output log (if generated).

out_matrix_filea 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'))

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')

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

>>> fnirt_mprage.cmdline
'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_filea pathlike object or string representing an existing file

Name of input image. Maps to a command-line argument: --in=%s.

ref_filea pathlike object or string representing an existing file

Name of reference image. Maps to a command-line argument: --ref=%s.

affine_filea pathlike object or string representing an existing file

Name of file containing affine transform. Maps to a command-line argument: --aff=%s.

apply_inmaska 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_mappinga 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_refmaska 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.

argsa string

Additional parameters to the command. Maps to a command-line argument: %s.

bias_regularization_lambdaa float

Weight of regularisation for bias-field, default 10000. Maps to a command-line argument: --biaslambda=%f.

biasfield_resolutiona tuple of the form: (an integer, an integer, an integer)

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_refa boolean

If true, ref image is used to calculate derivatives. Default false. Maps to a command-line argument: --refderiv.

environa 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_filea 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_filea 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_fwhma list of items which are an integer

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_filea 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_filea 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_vala 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_orderan integer

Order of poynomial for mapping intensities, default 5. Maps to a command-line argument: --intorder=%d.

inwarp_filea 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_filea 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_rangea 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_filea pathlike object or string representing a file

Name of log-file. Maps to a command-line argument: --logout=%s.

max_nonlin_itera list of items which are an integer

Max # of non-linear iterations list, default [5, 5, 5, 5]. Maps to a command-line argument: --miter=%s.

modulatedref_filea 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_filea 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’ or ‘GIFTI’

FSL output type.

ref_fwhma list of items which are an integer

FWHM (in mm) of gaussian smoothing kernel for ref volume, default [4, 2, 0, 0]. Maps to a command-line argument: --reffwhm=%s.

refmask_filea 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_vala float

Value to mask out in –ref image. Default =0.0. Maps to a command-line argument: --imprefval=%f.

regularization_lambdaa list of items which are a float

Weight of regularisation, default depending on –ssqlambda and –regmod switches. See user documentation. 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_maskinga boolean

Skip implicit masking based on value in –in image. Default = 0. Maps to a command-line argument: --impinm=0.

skip_implicit_ref_maskinga boolean

Skip implicit masking based on value in –ref image. Default = 0. Maps to a command-line argument: --imprefm=0.

skip_inmaska boolean

Skip specified inmask if set, default false. Maps to a command-line argument: --applyinmask=0. Mutually exclusive with inputs: apply_inmask.

skip_intensity_mappinga boolean

Skip estimate intensity-mapping default false. Maps to a command-line argument: --estint=0. Mutually exclusive with inputs: apply_intensity_mapping.

skip_lambda_ssqa boolean

If true, lambda is not weighted by current ssq, default false. Maps to a command-line argument: --ssqlambda=0.

skip_refmaska boolean

Skip specified refmask if set, default false. Maps to a command-line argument: --applyrefmask=0. Mutually exclusive with inputs: apply_refmask.

spline_orderan integer

Order of spline, 2->Qadratic spline, 3->Cubic spline. Default=3. Maps to a command-line argument: --splineorder=%d.

subsampling_schemea list of items which are an integer

Sub-sampling scheme, list, default [4, 2, 1, 1]. Maps to a command-line argument: --subsamp=%s.

warp_resolutiona tuple of the form: (an integer, an integer, an integer)

(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_filea pathlike object or string representing a file

Name of output image. Maps to a command-line argument: --iout=%s.

field_filea pathlike object or string representing a file

File with warp field.

fieldcoeff_filea pathlike object or string representing an existing file

File with field coefficients.

jacobian_filea pathlike object or string representing a file

File containing Jacobian of the field.

log_filea pathlike object or string representing a file

Name of log-file.

modulatedref_filea pathlike object or string representing a file

File containing intensity modulated –ref.

out_intensitymap_filea 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_filea 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
'fugue --in=epi.nii --mask=epi_mask.nii --loadshift=vsm.nii --unwarpdir=y --unwarp=epi_unwarped.nii.gz'
>>> fugue.run()

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
'fugue --in=epi.nii --mask=epi_mask.nii --loadshift=vsm.nii --unwarpdir=y --warp=epi_warped.nii.gz'
>>> fugue.run()

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
'fugue --dwelltoasym=0.9390243902 --mask=epi_mask.nii --phasemap=epi_phasediff.nii --saveshift=epi_phasediff_vsm.nii.gz --unwarpdir=y'
>>> fugue.run()
argsa string

Additional parameters to the command. Maps to a command-line argument: %s.

asym_se_timea float

Set the fieldmap asymmetric spin echo time (sec). Maps to a command-line argument: --asym=%.10f.

despike_2dfiltera boolean

Apply a 2D de-spiking filter. Maps to a command-line argument: --despike.

despike_thresholda float

Specify the threshold for de-spiking (default=3.0). Maps to a command-line argument: --despikethreshold=%s.

dwell_timea 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_ratioa float

Set the dwell to asym time ratio. Maps to a command-line argument: --dwelltoasym=%.10f.

environa 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_filea pathlike object or string representing an existing file

Filename for loading fieldmap (rad/s). Maps to a command-line argument: --loadfmap=%s.

fmap_out_filea pathlike object or string representing a file

Filename for saving fieldmap (rad/s). Maps to a command-line argument: --savefmap=%s.

forward_warpinga boolean

Apply forward warping instead of unwarping. (Nipype default value: False)

fourier_orderan integer

Apply Fourier (sinusoidal) fitting of order N. Maps to a command-line argument: --fourier=%d.

icorra boolean

Apply intensity correction to unwarping (pixel shift method only). Maps to a command-line argument: --icorr. Requires inputs: shift_in_file.

icorr_onlya boolean

Apply intensity correction only. Maps to a command-line argument: --icorronly. Requires inputs: unwarped_file.

in_filea pathlike object or string representing an existing file

Filename of input volume. Maps to a command-line argument: --in=%s.

mask_filea pathlike object or string representing an existing file

Filename for loading valid mask. Maps to a command-line argument: --mask=%s.

median_2dfiltera boolean

Apply 2D median filtering. Maps to a command-line argument: --median.

no_extenda boolean

Do not apply rigid-body extrapolation to the fieldmap. Maps to a command-line argument: --noextend.

no_gap_filla boolean

Do not apply gap-filling measure to the fieldmap. Maps to a command-line argument: --nofill.

nokspacea 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’ or ‘GIFTI’

FSL output type.

pavaa boolean

Apply monotonic enforcement via PAVA. Maps to a command-line argument: --pava.

phase_conjugatea boolean

Apply phase conjugate method of unwarping. Maps to a command-line argument: --phaseconj.

phasemap_in_filea pathlike object or string representing an existing file

Filename for input phase image. Maps to a command-line argument: --phasemap=%s.

poly_orderan integer

Apply polynomial fitting of order N. Maps to a command-line argument: --poly=%d.

save_fmapa boolean

Write field map volume. Mutually exclusive with inputs: save_unmasked_fmap.

save_shifta boolean

Write pixel shift volume. Mutually exclusive with inputs: save_unmasked_shift.

save_unmasked_fmapa boolean

Saves the unmasked fieldmap when using –savefmap. Maps to a command-line argument: --unmaskfmap. Mutually exclusive with inputs: save_fmap.

save_unmasked_shifta boolean

Saves the unmasked shiftmap when using –saveshift. Maps to a command-line argument: --unmaskshift. Mutually exclusive with inputs: save_shift.

shift_in_filea pathlike object or string representing an existing file

Filename for reading pixel shift volume. Maps to a command-line argument: --loadshift=%s.

shift_out_filea pathlike object or string representing a file

Filename for saving pixel shift volume. Maps to a command-line argument: --saveshift=%s.

smooth2da float

Apply 2D Gaussian smoothing of sigma N (in mm). Maps to a command-line argument: --smooth2=%.2f.

smooth3da 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_filea 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_filea 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_filea pathlike object or string representing a file

Fieldmap file.

shift_out_filea pathlike object or string representing a file

Voxel shift map file.

unwarped_filea pathlike object or string representing a file

Unwarped file.

warped_filea 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()
in_filea pathlike object or string representing an existing file

Timeseries to motion-correct. Maps to a command-line argument: -in %s (position: 0).

argsa string

Additional parameters to the command. Maps to a command-line argument: %s.

binsan integer

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.

dofan integer

Degrees of freedom for the transformation. Maps to a command-line argument: -dof %d.

environa 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: {})

inita pathlike object or string representing an existing file

Initial 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_vola boolean

Register to mean volume. Maps to a command-line argument: -meanvol.

out_filea 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’ or ‘GIFTI’

FSL output type.

ref_filea pathlike object or string representing an existing file

Target image for motion correction. Maps to a command-line argument: -reffile %s.

ref_volan integer

Volume to align frames to. Maps to a command-line argument: -refvol %d.

rotationan integer

Scaling factor for rotation tolerances. Maps to a command-line argument: -rotation %d.

save_matsa boolean

Save transformation matrices. Maps to a command-line argument: -mats.

save_plotsa boolean

Save transformation parameters. Maps to a command-line argument: -plots.

save_rmsa boolean

Save rms displacement parameters. Maps to a command-line argument: -rmsabs -rmsrel.

scalinga float

Scaling factor to use. Maps to a command-line argument: -scaling %.2f.

smootha float

Smoothing factor for the cost function. Maps to a command-line argument: -smooth %.2f.

stagesan integer

Stages (if 4, perform final search with sinc interpolation. Maps to a command-line argument: -stages %d.

stats_imgsa boolean

Produce variance and std. dev. images. Maps to a command-line argument: -stats.

use_contoura boolean

Run search on contour images. Maps to a command-line argument: -edge.

use_gradienta boolean

Run search on gradient images. Maps to a command-line argument: -gdt.

mat_filea list of items which are a pathlike object or string representing an existing file

Transformation matrices.

mean_imga pathlike object or string representing an existing file

Mean timeseries image (if mean_vol=True).

out_filea pathlike object or string representing an existing file

Motion-corrected timeseries.

par_filea pathlike object or string representing an existing file

Text-file with motion parameters.

rms_filesa list of items which are a pathlike object or string representing an existing file

Absolute and relative displacement parameters.

std_imga pathlike object or string representing an existing file

Standard deviation image.

variance_imga 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_filea 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_filea 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_filea 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.

argsa string

Additional parameters to the command. Maps to a command-line argument: %s.

endan integer

Final image number to process (default Inf). Maps to a command-line argument: --end=%d.

environa 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_filea pathlike object or string representing a file

Saving the area labels output. Maps to a command-line argument: --labels=%s.

labelprocess2da boolean

Does label processing in 2D (slice at a time). Maps to a command-line argument: --labelslices.

mask_filea pathlike object or string representing an existing file

Filename of mask input volume. Maps to a command-line argument: --mask=%s.

num_partitionsan integer

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’ or ‘GIFTI’

FSL output type.

process2da boolean

Does all processing in 2D (slice at a time). Maps to a command-line argument: --slices. Mutually exclusive with inputs: labelprocess2d.

process3da boolean

Forces all processing to be full 3D. Maps to a command-line argument: --force3D. Mutually exclusive with inputs: labelprocess2d, process2d.

rawphase_filea pathlike object or string representing a file

Saving the raw phase output. Maps to a command-line argument: --rawphase=%s.

removerampsa boolean

Remove phase ramps during unwrapping. Maps to a command-line argument: --removeramps.

savemask_filea pathlike object or string representing a file

Saving the mask volume. Maps to a command-line argument: --savemask=%s.

startan integer

First image number to process (default 0). Maps to a command-line argument: --start=%d.

thresholda float

Intensity threshold for masking. Maps to a command-line argument: --thresh=%.10f.

unwrapped_phase_filea pathlike object or string representing a file

File containing unwrapepd phase. Maps to a command-line argument: --unwrap=%s.

unwrapped_phase_filea 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
anatomical.nii
>>> 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()
brightness_thresholda 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).

fwhma float

Fwhm of smoothing, in mm, gets converted using sqrt(8*log(2)). Maps to a command-line argument: %.10f (position: 3).

in_filea pathlike object or string representing an existing file

Filename of input timeseries. Maps to a command-line argument: %s (position: 1).

argsa string

Additional parameters to the command. Maps to a command-line argument: %s.

dimension3 or 2

Within-plane (2) or fully 3D (3). Maps to a command-line argument: %d (position: 4). (Nipype default value: 3)

environa 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_filea 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’ or ‘GIFTI’

FSL output type.

usansa 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_median1 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_filea 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()
in_filea pathlike object or string representing an existing file

Filename of input timeseries. Maps to a command-line argument: --in=%s (position: 0).

argsa string

Additional parameters to the command. Maps to a command-line argument: %s.

custom_ordera 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_timingsa 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.

environa 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_shifta float

Shift in fraction of TR, range 0:1 (default is 0.5 = no shift). Maps to a command-line argument: --tglobal.

index_dira boolean

Slice indexing from top to bottom. Maps to a command-line argument: --down.

interleaveda boolean

Use interleaved acquisition. Maps to a command-line argument: --odd.

out_filea 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’ or ‘GIFTI’

FSL output type.

slice_direction1 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_repetitiona float

Specify TR of data - default is 3s. Maps to a command-line argument: --repeat=%f.

slice_time_corrected_filea pathlike object or string representing an existing file

Slice time corrected file.