Home · Quickstart · User Guide and Examples · Interfaces Index · Developers · About · Nipy

# 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 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`.

> 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’

>   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 (int or long)

>   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 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()

> 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 unicode 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 (int or long)

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

> coarse_searchan 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_inita boolean

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

> dofan integer (int or long)

>   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 (int or long)

>   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’

>   FSL output type.

> padding_sizean integer (int or long)

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

> pediran 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_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 (int or long)

>   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 (int or long)

>   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 (int or long)

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

> sinc_widthan 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_qforma boolean

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

> verbosean integer (int or long)

>   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 unicode string

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

> centera 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`.

> 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’

>   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 (int or long)

>   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
>     >>> 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()

> 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 unicode string

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

> bias_iters1 <= a long integer <= 10

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

> bias_lowpass4 <= a long 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 <= a long 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 <= a long 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’

>   FSL output type.

> probability_mapsa boolean

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

> segment_iters1 <= a long 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 unicode 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 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_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’

>   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 unicode 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 (int or long)

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

> coarse_searchan 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_inita boolean

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

> dofan integer (int or long)

>   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 (int or long)

>   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’

>   FSL output type.

> padding_sizean integer (int or long)

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

> pediran 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_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 (int or long)

>   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 (int or long)

>   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 (int or long)

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

> sinc_widthan 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_qforma boolean

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

> verbosean integer (int or long)

>   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 unicode 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 (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_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 (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_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 (int or long)

>   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 (int or long)

>   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’

>   FSL output type.

> ref_fwhma 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_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 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_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 (int or long)

>   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 (int or long)

>   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 (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_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 unicode 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 (int or long)

>   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’

>   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 (int or long)

>   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 unicode string

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

> binsan 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`.

> dofan integer (int or long)

>   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

>   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_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’

>   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 (int or long)

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

> rotationan integer (int or long)

>   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 (int or long)

>   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 unicode string

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

> endan integer (int or long)

>   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 (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.

> 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 (int or long)

>   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 unicode 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’

>   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 unicode 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’

>   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.