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¶
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()
- Mandatory Inputs
in_file (a pathlike object or string representing an existing file) – Image to be warped. Maps to a command-line argument:
--in=%s
(position: 0).ref_file (a pathlike object or string representing an existing file) – Reference image. Maps to a command-line argument:
--ref=%s
(position: 1).- Optional Inputs
abswarp (a boolean) – Treat warp field as absolute: x’ = w(x). Maps to a command-line argument:
--abs
. Mutually exclusive with inputs:relwarp
.args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s
.datatype (‘char’ or ‘short’ or ‘int’ or ‘float’ or ‘double’) – Force output data type [char short int float double]. Maps to a command-line argument:
--datatype=%s
.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{}
)field_file (a pathlike object or string representing an existing file) – File containing warp field. Maps to a command-line argument:
--warp=%s
.interp (‘nn’ or ‘trilinear’ or ‘sinc’ or ‘spline’) – Interpolation method. Maps to a command-line argument:
--interp=%s
(position: -2).mask_file (a pathlike object or string representing an existing file) – Filename for mask image (in reference space). Maps to a command-line argument:
--mask=%s
.out_file (a pathlike object or string representing a file) – Output filename. Maps to a command-line argument:
--out=%s
(position: 2).output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’) – FSL output type.
postmat (a pathlike object or string representing an existing file) – Filename for post-transform (affine matrix). Maps to a command-line argument:
--postmat=%s
.premat (a pathlike object or string representing an existing file) – Filename for pre-transform (affine matrix). Maps to a command-line argument:
--premat=%s
.relwarp (a boolean) – Treat warp field as relative: x’ = x + w(x). Maps to a command-line argument:
--rel
(position: -1). Mutually exclusive with inputs:abswarp
.superlevel (‘a’ or an integer) – Level of intermediary supersampling, a for ‘automatic’ or integer level. Default = 2. Maps to a command-line argument:
--superlevel=%s
.supersample (a boolean) – Intermediary supersampling of output, default is off. Maps to a command-line argument:
--super
.- Outputs
out_file (a pathlike object or string representing an existing file) – Warped output file.
ApplyXFM¶
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()
- Mandatory Inputs
in_file (a pathlike object or string representing an existing file) – Input file. Maps to a command-line argument:
-in %s
(position: 0).reference (a pathlike object or string representing an existing file) – Reference file. Maps to a command-line argument:
-ref %s
(position: 1).- Optional Inputs
angle_rep (‘quaternion’ or ‘euler’) – Representation of rotation angles. Maps to a command-line argument:
-anglerep %s
.apply_isoxfm (a float) – As applyxfm but forces isotropic resampling. Maps to a command-line argument:
-applyisoxfm %f
. Mutually exclusive with inputs:apply_xfm
.apply_xfm (a boolean) – Apply transformation supplied by in_matrix_file or uses_qform to use the affine matrix stored in the reference header. Maps to a command-line argument:
-applyxfm
. (Nipype default value:True
)args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s
.bbrslope (a float) – Value of bbr slope. Maps to a command-line argument:
-bbrslope %f
.bbrtype (‘signed’ or ‘global_abs’ or ‘local_abs’) – Type of bbr cost function: signed [default], global_abs, local_abs. Maps to a command-line argument:
-bbrtype %s
.bgvalue (a float) – Use specified background value for points outside FOV. Maps to a command-line argument:
-setbackground %f
.bins (an integer) – Number of histogram bins. Maps to a command-line argument:
-bins %d
.coarse_search (an 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_init (a boolean) – Display initial matrix. Maps to a command-line argument:
-displayinit
.dof (an integer) – Number of transform degrees of freedom. Maps to a command-line argument:
-dof %d
.echospacing (a float) – Value of EPI echo spacing - units of seconds. Maps to a command-line argument:
-echospacing %f
.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{}
)fieldmap (a pathlike object or string representing a file) – Fieldmap image in rads/s - must be already registered to the reference image. Maps to a command-line argument:
-fieldmap %s
.fieldmapmask (a pathlike object or string representing a file) – Mask for fieldmap image. Maps to a command-line argument:
-fieldmapmask %s
.fine_search (an integer) – Fine search delta angle. Maps to a command-line argument:
-finesearch %d
.force_scaling (a boolean) – Force rescaling even for low-res images. Maps to a command-line argument:
-forcescaling
.in_matrix_file (a pathlike object or string representing a file) – Input 4x4 affine matrix. Maps to a command-line argument:
-init %s
.in_weight (a pathlike object or string representing an existing file) – File for input weighting volume. Maps to a command-line argument:
-inweight %s
.interp (‘trilinear’ or ‘nearestneighbour’ or ‘sinc’ or ‘spline’) – Final interpolation method used in reslicing. Maps to a command-line argument:
-interp %s
.min_sampling (a float) – Set minimum voxel dimension for sampling. Maps to a command-line argument:
-minsampling %f
.no_clamp (a boolean) – Do not use intensity clamping. Maps to a command-line argument:
-noclamp
.no_resample (a boolean) – Do not change input sampling. Maps to a command-line argument:
-noresample
.no_resample_blur (a boolean) – Do not use blurring on downsampling. Maps to a command-line argument:
-noresampblur
.no_search (a boolean) – Set all angular searches to ranges 0 to 0. Maps to a command-line argument:
-nosearch
.out_file (a pathlike object or string representing a file) – Registered output file. Maps to a command-line argument:
-out %s
(position: 2).out_log (a pathlike object or string representing a file) – Output log. Requires inputs:
save_log
.out_matrix_file (a pathlike object or string representing a file) – Output affine matrix in 4x4 asciii format. Maps to a command-line argument:
-omat %s
(position: 3).output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’) – FSL output type.
padding_size (an integer) – For applyxfm: interpolates outside image by size. Maps to a command-line argument:
-paddingsize %d
.pedir (an 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_weight (a pathlike object or string representing an existing file) – File for reference weighting volume. Maps to a command-line argument:
-refweight %s
.rigid2D (a boolean) – Use 2D rigid body mode - ignores dof. Maps to a command-line argument:
-2D
.save_log (a boolean) – Save to log file.
schedule (a pathlike object or string representing an existing file) – Replaces default schedule. Maps to a command-line argument:
-schedule %s
.searchr_x (a list of from 2 to 2 items which are an integer) – Search angles along x-axis, in degrees. Maps to a command-line argument:
-searchrx %s
.searchr_y (a list of from 2 to 2 items which are an integer) – Search angles along y-axis, in degrees. Maps to a command-line argument:
-searchry %s
.searchr_z (a list of from 2 to 2 items which are an integer) – Search angles along z-axis, in degrees. Maps to a command-line argument:
-searchrz %s
.sinc_width (an 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_qform (a boolean) – Initialize using sform or qform. Maps to a command-line argument:
-usesqform
.verbose (an integer) – Verbose mode, 0 is least. Maps to a command-line argument:
-verbose %d
.wm_seg (a pathlike object or string representing a file) – White matter segmentation volume needed by BBR cost function. Maps to a command-line argument:
-wmseg %s
.wmcoords (a pathlike object or string representing a file) – White matter boundary coordinates for BBR cost function. Maps to a command-line argument:
-wmcoords %s
.wmnorms (a pathlike object or string representing a file) – White matter boundary normals for BBR cost function. Maps to a command-line argument:
-wmnorms %s
.- Outputs
out_file (a pathlike object or string representing an existing file) – Path/name of registered file (if generated).
out_log (a pathlike object or string representing a file) – Path/name of output log (if generated).
out_matrix_file (a pathlike object or string representing an existing file) – Path/name of calculated affine transform (if generated).
BET¶
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()
- Mandatory Inputs
in_file (a pathlike object or string representing an existing file) – Input file to skull strip. Maps to a command-line argument:
%s
(position: 0).- Optional Inputs
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s
.center (a list of at most 3 items which are an integer) – Center of gravity in voxels. Maps to a command-line argument:
-c %s
.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{}
)frac (a float) – Fractional intensity threshold. Maps to a command-line argument:
-f %.2f
.functional (a boolean) – Apply to 4D fMRI data. Maps to a command-line argument:
-F
. Mutually exclusive with inputs:functional
,reduce_bias
,robust
,padding
,remove_eyes
,surfaces
,t2_guided
.mask (a boolean) – Create binary mask image. Maps to a command-line argument:
-m
.mesh (a boolean) – Generate a vtk mesh brain surface. Maps to a command-line argument:
-e
.no_output (a boolean) – Don’t generate segmented output. Maps to a command-line argument:
-n
.out_file (a pathlike object or string representing a file) – Name of output skull stripped image. Maps to a command-line argument:
%s
(position: 1).outline (a boolean) – Create surface outline image. Maps to a command-line argument:
-o
.output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’) – FSL output type.
padding (a boolean) – Improve BET if FOV is very small in Z (by temporarily padding end slices). Maps to a command-line argument:
-Z
. Mutually exclusive with inputs:functional
,reduce_bias
,robust
,padding
,remove_eyes
,surfaces
,t2_guided
.radius (an integer) – Head radius. Maps to a command-line argument:
-r %d
.reduce_bias (a boolean) – Bias field and neck cleanup. Maps to a command-line argument:
-B
. Mutually exclusive with inputs:functional
,reduce_bias
,robust
,padding
,remove_eyes
,surfaces
,t2_guided
.remove_eyes (a boolean) – Eye & optic nerve cleanup (can be useful in SIENA). Maps to a command-line argument:
-S
. Mutually exclusive with inputs:functional
,reduce_bias
,robust
,padding
,remove_eyes
,surfaces
,t2_guided
.robust (a boolean) – Robust brain centre estimation (iterates BET several times). Maps to a command-line argument:
-R
. Mutually exclusive with inputs:functional
,reduce_bias
,robust
,padding
,remove_eyes
,surfaces
,t2_guided
.skull (a boolean) – Create skull image. Maps to a command-line argument:
-s
.surfaces (a boolean) – Run bet2 and then betsurf to get additional skull and scalp surfaces (includes registrations). Maps to a command-line argument:
-A
. Mutually exclusive with inputs:functional
,reduce_bias
,robust
,padding
,remove_eyes
,surfaces
,t2_guided
.t2_guided (a pathlike object or string representing a file) – As with creating surfaces, when also feeding in non-brain-extracted T2 (includes registrations). Maps to a command-line argument:
-A2 %s
. Mutually exclusive with inputs:functional
,reduce_bias
,robust
,padding
,remove_eyes
,surfaces
,t2_guided
.threshold (a boolean) – Apply thresholding to segmented brain image and mask. Maps to a command-line argument:
-t
.vertical_gradient (a float) – Vertical gradient in fractional intensity threshold (-1, 1). Maps to a command-line argument:
-g %.2f
.- Outputs
inskull_mask_file (a pathlike object or string representing a file) – Path/name of inskull mask (if generated).
inskull_mesh_file (a pathlike object or string representing a file) – Path/name of inskull mesh outline (if generated).
mask_file (a pathlike object or string representing a file) – Path/name of binary brain mask (if generated).
meshfile (a pathlike object or string representing a file) – Path/name of vtk mesh file (if generated).
out_file (a pathlike object or string representing a file) – Path/name of skullstripped file (if generated).
outline_file (a pathlike object or string representing a file) – Path/name of outline file (if generated).
outskin_mask_file (a pathlike object or string representing a file) – Path/name of outskin mask (if generated).
outskin_mesh_file (a pathlike object or string representing a file) – Path/name of outskin mesh outline (if generated).
outskull_mask_file (a pathlike object or string representing a file) – Path/name of outskull mask (if generated).
outskull_mesh_file (a pathlike object or string representing a file) – Path/name of outskull mesh outline (if generated).
skull_file (a pathlike object or string representing a file) – Path/name of skull file (if generated).
skull_mask_file (a pathlike object or string representing a file) – Path/name of skull mask (if generated).
FAST¶
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()
- Mandatory Inputs
in_files (a list of items which are a pathlike object or string representing an existing file) – Image, or multi-channel set of images, to be segmented. Maps to a command-line argument:
%s
(position: -1).- Optional Inputs
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s
.bias_iters (1 <= an integer <= 10) – Number of main-loop iterations during bias-field removal. Maps to a command-line argument:
-I %d
.bias_lowpass (4 <= an integer <= 40) – Bias field smoothing extent (FWHM) in mm. Maps to a command-line argument:
-l %d
.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{}
)hyper (0.0 <= a floating point number <= 1.0) – Segmentation spatial smoothness. Maps to a command-line argument:
-H %.2f
.img_type (1 or 2 or 3) – Int specifying type of image: (1 = T1, 2 = T2, 3 = PD). Maps to a command-line argument:
-t %d
.init_seg_smooth (0.0001 <= a floating point number <= 0.1) – Initial segmentation spatial smoothness (during bias field estimation). Maps to a command-line argument:
-f %.3f
.init_transform (a pathlike object or string representing an existing file) – <standard2input.mat> initialise using priors. Maps to a command-line argument:
-a %s
.iters_afterbias (1 <= an integer <= 20) – Number of main-loop iterations after bias-field removal. Maps to a command-line argument:
-O %d
.manual_seg (a pathlike object or string representing an existing file) – Filename containing intensities. Maps to a command-line argument:
-s %s
.mixel_smooth (0.0 <= a floating point number <= 1.0) – Spatial smoothness for mixeltype. Maps to a command-line argument:
-R %.2f
.no_bias (a boolean) – Do not remove bias field. Maps to a command-line argument:
-N
.no_pve (a boolean) – Turn off PVE (partial volume estimation). Maps to a command-line argument:
--nopve
.number_classes (1 <= an integer <= 10) – Number of tissue-type classes. Maps to a command-line argument:
-n %d
.other_priors (a list of from 3 to 3 items which are a pathlike object or string representing a file) – Alternative prior images. Maps to a command-line argument:
-A %s
.out_basename (a pathlike object or string representing a file) – Base name of output files. Maps to a command-line argument:
-o %s
.output_biascorrected (a boolean) – Output restored image (bias-corrected image). Maps to a command-line argument:
-B
.output_biasfield (a boolean) – Output estimated bias field. Maps to a command-line argument:
-b
.output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’) – FSL output type.
probability_maps (a boolean) – Outputs individual probability maps. Maps to a command-line argument:
-p
.segment_iters (1 <= an integer <= 50) – Number of segmentation-initialisation iterations. Maps to a command-line argument:
-W %d
.segments (a boolean) – Outputs a separate binary image for each tissue type. Maps to a command-line argument:
-g
.use_priors (a boolean) – Use priors throughout. Maps to a command-line argument:
-P
.verbose (a boolean) – Switch on diagnostic messages. Maps to a command-line argument:
-v
.- Outputs
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¶
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()
- Mandatory Inputs
in_file (a pathlike object or string representing an existing file) – Input data file. Maps to a command-line argument:
-i %s
(position: -2).out_file (a pathlike object or string representing a file) – Output data file. Maps to a command-line argument:
-o %s
(position: -1). (Nipype default value:segmented
)- Optional Inputs
affine_file (a pathlike object or string representing an existing file) – Affine matrix to use (e.g. img2std.mat) (does not re-run registration). Maps to a command-line argument:
-a %s
(position: 6).args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s
.brain_extracted (a boolean) – Input structural image is already brain-extracted. Maps to a command-line argument:
-b
(position: 2).environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{}
)list_of_specific_structures (a list of at least 1 items which are a string) – Runs only on the specified structures (e.g. L_Hipp, R_HippL_Accu, R_Accu, L_Amyg, R_AmygL_Caud, R_Caud, L_Pall, R_PallL_Puta, R_Puta, L_Thal, R_Thal, BrStem. Maps to a command-line argument:
-s %s
(position: 5).method (‘auto’ or ‘fast’ or ‘none’) – Method must be one of auto, fast, none, or it can be entered using the ‘method_as_numerical_threshold’ input. Maps to a command-line argument:
-m %s
(position: 4). Mutually exclusive with inputs:method_as_numerical_threshold
. (Nipype default value:auto
)method_as_numerical_threshold (a float) – Specify a numerical threshold value or use the ‘method’ input to choose auto, fast, or none. Maps to a command-line argument:
-m %.4f
(position: 4).no_cleanup (a boolean) – Input structural image is already brain-extracted. Maps to a command-line argument:
-d
(position: 3).output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’) – FSL output type.
verbose (a boolean) – Use verbose logging. Maps to a command-line argument:
-v
(position: 1).- Outputs
bvars (a list of items which are a pathlike object or string representing an existing file) – Bvars for each subcortical region.
original_segmentations (a pathlike object or string representing an existing file) – 3D image file containing the segmented regions as integer values. Uses CMA labelling.
segmentation_file (a pathlike object or string representing an existing file) – 4D image file containing a single volume per segmented region.
vtk_surfaces (a list of items which are a pathlike object or string representing an existing file) – VTK format meshes for each subcortical region.
FLIRT¶
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()
- Mandatory Inputs
in_file (a pathlike object or string representing an existing file) – Input file. Maps to a command-line argument:
-in %s
(position: 0).reference (a pathlike object or string representing an existing file) – Reference file. Maps to a command-line argument:
-ref %s
(position: 1).- Optional Inputs
angle_rep (‘quaternion’ or ‘euler’) – Representation of rotation angles. Maps to a command-line argument:
-anglerep %s
.apply_isoxfm (a float) – As applyxfm but forces isotropic resampling. Maps to a command-line argument:
-applyisoxfm %f
. Mutually exclusive with inputs:apply_xfm
.apply_xfm (a boolean) – Apply transformation supplied by in_matrix_file or uses_qform to use the affine matrix stored in the reference header. Maps to a command-line argument:
-applyxfm
.args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s
.bbrslope (a float) – Value of bbr slope. Maps to a command-line argument:
-bbrslope %f
.bbrtype (‘signed’ or ‘global_abs’ or ‘local_abs’) – Type of bbr cost function: signed [default], global_abs, local_abs. Maps to a command-line argument:
-bbrtype %s
.bgvalue (a float) – Use specified background value for points outside FOV. Maps to a command-line argument:
-setbackground %f
.bins (an integer) – Number of histogram bins. Maps to a command-line argument:
-bins %d
.coarse_search (an 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_init (a boolean) – Display initial matrix. Maps to a command-line argument:
-displayinit
.dof (an integer) – Number of transform degrees of freedom. Maps to a command-line argument:
-dof %d
.echospacing (a float) – Value of EPI echo spacing - units of seconds. Maps to a command-line argument:
-echospacing %f
.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{}
)fieldmap (a pathlike object or string representing a file) – Fieldmap image in rads/s - must be already registered to the reference image. Maps to a command-line argument:
-fieldmap %s
.fieldmapmask (a pathlike object or string representing a file) – Mask for fieldmap image. Maps to a command-line argument:
-fieldmapmask %s
.fine_search (an integer) – Fine search delta angle. Maps to a command-line argument:
-finesearch %d
.force_scaling (a boolean) – Force rescaling even for low-res images. Maps to a command-line argument:
-forcescaling
.in_matrix_file (a pathlike object or string representing a file) – Input 4x4 affine matrix. Maps to a command-line argument:
-init %s
.in_weight (a pathlike object or string representing an existing file) – File for input weighting volume. Maps to a command-line argument:
-inweight %s
.interp (‘trilinear’ or ‘nearestneighbour’ or ‘sinc’ or ‘spline’) – Final interpolation method used in reslicing. Maps to a command-line argument:
-interp %s
.min_sampling (a float) – Set minimum voxel dimension for sampling. Maps to a command-line argument:
-minsampling %f
.no_clamp (a boolean) – Do not use intensity clamping. Maps to a command-line argument:
-noclamp
.no_resample (a boolean) – Do not change input sampling. Maps to a command-line argument:
-noresample
.no_resample_blur (a boolean) – Do not use blurring on downsampling. Maps to a command-line argument:
-noresampblur
.no_search (a boolean) – Set all angular searches to ranges 0 to 0. Maps to a command-line argument:
-nosearch
.out_file (a pathlike object or string representing a file) – Registered output file. Maps to a command-line argument:
-out %s
(position: 2).out_log (a pathlike object or string representing a file) – Output log. Requires inputs:
save_log
.out_matrix_file (a pathlike object or string representing a file) – Output affine matrix in 4x4 asciii format. Maps to a command-line argument:
-omat %s
(position: 3).output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’) – FSL output type.
padding_size (an integer) – For applyxfm: interpolates outside image by size. Maps to a command-line argument:
-paddingsize %d
.pedir (an 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_weight (a pathlike object or string representing an existing file) – File for reference weighting volume. Maps to a command-line argument:
-refweight %s
.rigid2D (a boolean) – Use 2D rigid body mode - ignores dof. Maps to a command-line argument:
-2D
.save_log (a boolean) – Save to log file.
schedule (a pathlike object or string representing an existing file) – Replaces default schedule. Maps to a command-line argument:
-schedule %s
.searchr_x (a list of from 2 to 2 items which are an integer) – Search angles along x-axis, in degrees. Maps to a command-line argument:
-searchrx %s
.searchr_y (a list of from 2 to 2 items which are an integer) – Search angles along y-axis, in degrees. Maps to a command-line argument:
-searchry %s
.searchr_z (a list of from 2 to 2 items which are an integer) – Search angles along z-axis, in degrees. Maps to a command-line argument:
-searchrz %s
.sinc_width (an 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_qform (a boolean) – Initialize using sform or qform. Maps to a command-line argument:
-usesqform
.verbose (an integer) – Verbose mode, 0 is least. Maps to a command-line argument:
-verbose %d
.wm_seg (a pathlike object or string representing a file) – White matter segmentation volume needed by BBR cost function. Maps to a command-line argument:
-wmseg %s
.wmcoords (a pathlike object or string representing a file) – White matter boundary coordinates for BBR cost function. Maps to a command-line argument:
-wmcoords %s
.wmnorms (a pathlike object or string representing a file) – White matter boundary normals for BBR cost function. Maps to a command-line argument:
-wmnorms %s
.- Outputs
out_file (a pathlike object or string representing an existing file) – Path/name of registered file (if generated).
out_log (a pathlike object or string representing a file) – Path/name of output log (if generated).
out_matrix_file (a pathlike object or string representing an existing file) – Path/name of calculated affine transform (if generated).
FLIRT.
aggregate_outputs
(runtime=None, needed_outputs=None)¶Collate expected outputs and apply output traits validation.
FNIRT¶
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'
- Mandatory Inputs
in_file (a pathlike object or string representing an existing file) – Name of input image. Maps to a command-line argument:
--in=%s
.ref_file (a pathlike object or string representing an existing file) – Name of reference image. Maps to a command-line argument:
--ref=%s
.- Optional Inputs
affine_file (a pathlike object or string representing an existing file) – Name of file containing affine transform. Maps to a command-line argument:
--aff=%s
.apply_inmask (a list of items which are 0 or 1) – List of iterations to use input mask on (1 to use, 0 to skip). Maps to a command-line argument:
--applyinmask=%s
. Mutually exclusive with inputs:skip_inmask
.apply_intensity_mapping (a list of items which are 0 or 1) – List of subsampling levels to apply intensity mapping for (0 to skip, 1 to apply). Maps to a command-line argument:
--estint=%s
. Mutually exclusive with inputs:skip_intensity_mapping
.apply_refmask (a list of items which are 0 or 1) – List of iterations to use reference mask on (1 to use, 0 to skip). Maps to a command-line argument:
--applyrefmask=%s
. Mutually exclusive with inputs:skip_refmask
.args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s
.bias_regularization_lambda (a float) – Weight of regularisation for bias-field, default 10000. Maps to a command-line argument:
--biaslambda=%f
.biasfield_resolution (a tuple of the form: (an integer, 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_ref (a boolean) – If true, ref image is used to calculate derivatives. Default false. Maps to a command-line argument:
--refderiv
.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{}
)field_file (a boolean or a pathlike object or string representing a file) – Name of output file with field or true. Maps to a command-line argument:
--fout=%s
.fieldcoeff_file (a boolean or a pathlike object or string representing a file) – Name of output file with field coefficients or true. Maps to a command-line argument:
--cout=%s
.hessian_precision (‘double’ or ‘float’) – Precision for representing Hessian, double or float. Default double. Maps to a command-line argument:
--numprec=%s
.in_fwhm (a list of items which are an integer) – FWHM (in mm) of gaussian smoothing kernel for input volume, default [6, 4, 2, 2]. Maps to a command-line argument:
--infwhm=%s
.in_intensitymap_file (a list of from 1 to 2 items which are a pathlike object or string representing an existing file) – Name of file/files containing initial intensity mapping usually generated by previous fnirt run. Maps to a command-line argument:
--intin=%s
.inmask_file (a pathlike object or string representing an existing file) – Name of file with mask in input image space. Maps to a command-line argument:
--inmask=%s
.inmask_val (a float) – Value to mask out in –in image. Default =0.0. Maps to a command-line argument:
--impinval=%f
.intensity_mapping_model (‘none’ or ‘global_linear’ or ‘global_non_linear’ or ‘local_linear’ or ‘global_non_linear_with_bias’ or ‘local_non_linear’) – Model for intensity-mapping. Maps to a command-line argument:
--intmod=%s
.intensity_mapping_order (an integer) – Order of poynomial for mapping intensities, default 5. Maps to a command-line argument:
--intorder=%d
.inwarp_file (a pathlike object or string representing an existing file) – Name of file containing initial non-linear warps. Maps to a command-line argument:
--inwarp=%s
.jacobian_file (a boolean or a pathlike object or string representing a file) – Name of file for writing out the Jacobian of the field (for diagnostic or VBM purposes). Maps to a command-line argument:
--jout=%s
.jacobian_range (a tuple of the form: (a float, a float)) – Allowed range of Jacobian determinants, default 0.01, 100.0. Maps to a command-line argument:
--jacrange=%f,%f
.log_file (a pathlike object or string representing a file) – Name of log-file. Maps to a command-line argument:
--logout=%s
.max_nonlin_iter (a list of items which are an integer) – Max # of non-linear iterations list, default [5, 5, 5, 5]. Maps to a command-line argument:
--miter=%s
.modulatedref_file (a boolean or a pathlike object or string representing a file) – Name of file for writing out intensity modulated –ref (for diagnostic purposes). Maps to a command-line argument:
--refout=%s
.out_intensitymap_file (a boolean or a pathlike object or string representing a file) – Name of files for writing information pertaining to intensity mapping. Maps to a command-line argument:
--intout=%s
.output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’) – FSL output type.
ref_fwhm (a list of items which are an integer) – FWHM (in mm) of gaussian smoothing kernel for ref volume, default [4, 2, 0, 0]. Maps to a command-line argument:
--reffwhm=%s
.refmask_file (a pathlike object or string representing an existing file) – Name of file with mask in reference space. Maps to a command-line argument:
--refmask=%s
.refmask_val (a float) – Value to mask out in –ref image. Default =0.0. Maps to a command-line argument:
--imprefval=%f
.regularization_lambda (a list of items which are a float) – Weight of regularisation, default depending on –ssqlambda and –regmod switches. See user documetation. Maps to a command-line argument:
--lambda=%s
.regularization_model (‘membrane_energy’ or ‘bending_energy’) – Model for regularisation of warp-field [membrane_energy bending_energy], default bending_energy. Maps to a command-line argument:
--regmod=%s
.skip_implicit_in_masking (a boolean) – Skip implicit masking based on value in –in image. Default = 0. Maps to a command-line argument:
--impinm=0
.skip_implicit_ref_masking (a boolean) – Skip implicit masking based on value in –ref image. Default = 0. Maps to a command-line argument:
--imprefm=0
.skip_inmask (a boolean) – Skip specified inmask if set, default false. Maps to a command-line argument:
--applyinmask=0
. Mutually exclusive with inputs:apply_inmask
.skip_intensity_mapping (a boolean) – Skip estimate intensity-mapping default false. Maps to a command-line argument:
--estint=0
. Mutually exclusive with inputs:apply_intensity_mapping
.skip_lambda_ssq (a boolean) – If true, lambda is not weighted by current ssq, default false. Maps to a command-line argument:
--ssqlambda=0
.skip_refmask (a boolean) – Skip specified refmask if set, default false. Maps to a command-line argument:
--applyrefmask=0
. Mutually exclusive with inputs:apply_refmask
.spline_order (an integer) – Order of spline, 2->Qadratic spline, 3->Cubic spline. Default=3. Maps to a command-line argument:
--splineorder=%d
.subsampling_scheme (a list of items which are an integer) – Sub-sampling scheme, list, default [4, 2, 1, 1]. Maps to a command-line argument:
--subsamp=%s
.warp_resolution (a tuple of the form: (an integer, 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_file (a pathlike object or string representing a file) – Name of output image. Maps to a command-line argument:
--iout=%s
.- Outputs
field_file (a pathlike object or string representing a file) – File with warp field.
fieldcoeff_file (a pathlike object or string representing an existing file) – File with field coefficients.
jacobian_file (a pathlike object or string representing a file) – File containing Jacobian of the field.
log_file (a pathlike object or string representing a file) – Name of log-file.
modulatedref_file (a pathlike object or string representing a file) – File containing intensity modulated –ref.
out_intensitymap_file (a list of from 2 to 2 items which are a pathlike object or string representing a file) – Files containing info pertaining to intensity mapping.
warped_file (a pathlike object or string representing an existing file) – Warped image.
FNIRT.
filemap
= {'field_file': 'field', 'fieldcoeff_file': 'fieldwarp', 'jacobian_file': 'field_jacobian', 'log_file': 'log.txt', 'modulatedref_file': 'modulated', 'out_intensitymap_file': 'intmap', 'warped_file': 'warped'}¶
- classmethod
FNIRT.
intensitymap_file_basename
(f)¶Removes valid intensitymap extensions from f, returning a basename that can refer to both intensitymap files.
FNIRT.
write_config
(configfile)¶Writes out currently set options to specified config file
XX TODO : need to figure out how the config file is written
- Parameters
configfile (/path/to/configfile)
FUGUE¶
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
improving registration with non-distorted images (e.g. structurals), or
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()
- Optional Inputs
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s
.asym_se_time (a float) – Set the fieldmap asymmetric spin echo time (sec). Maps to a command-line argument:
--asym=%.10f
.despike_2dfilter (a boolean) – Apply a 2D de-spiking filter. Maps to a command-line argument:
--despike
.despike_threshold (a float) – Specify the threshold for de-spiking (default=3.0). Maps to a command-line argument:
--despikethreshold=%s
.dwell_time (a float) – Set the EPI dwell time per phase-encode line - same as echo spacing - (sec). Maps to a command-line argument:
--dwell=%.10f
.dwell_to_asym_ratio (a float) – Set the dwell to asym time ratio. Maps to a command-line argument:
--dwelltoasym=%.10f
.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{}
)fmap_in_file (a pathlike object or string representing an existing file) – Filename for loading fieldmap (rad/s). Maps to a command-line argument:
--loadfmap=%s
.fmap_out_file (a pathlike object or string representing a file) – Filename for saving fieldmap (rad/s). Maps to a command-line argument:
--savefmap=%s
.forward_warping (a boolean) – Apply forward warping instead of unwarping. (Nipype default value:
False
)fourier_order (an integer) – Apply Fourier (sinusoidal) fitting of order N. Maps to a command-line argument:
--fourier=%d
.icorr (a boolean) – Apply intensity correction to unwarping (pixel shift method only). Maps to a command-line argument:
--icorr
. Requires inputs:shift_in_file
.icorr_only (a boolean) – Apply intensity correction only. Maps to a command-line argument:
--icorronly
. Requires inputs:unwarped_file
.in_file (a pathlike object or string representing an existing file) – Filename of input volume. Maps to a command-line argument:
--in=%s
.mask_file (a pathlike object or string representing an existing file) – Filename for loading valid mask. Maps to a command-line argument:
--mask=%s
.median_2dfilter (a boolean) – Apply 2D median filtering. Maps to a command-line argument:
--median
.no_extend (a boolean) – Do not apply rigid-body extrapolation to the fieldmap. Maps to a command-line argument:
--noextend
.no_gap_fill (a boolean) – Do not apply gap-filling measure to the fieldmap. Maps to a command-line argument:
--nofill
.nokspace (a boolean) – Do not use k-space forward warping. Maps to a command-line argument:
--nokspace
.output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’) – FSL output type.
pava (a boolean) – Apply monotonic enforcement via PAVA. Maps to a command-line argument:
--pava
.phase_conjugate (a boolean) – Apply phase conjugate method of unwarping. Maps to a command-line argument:
--phaseconj
.phasemap_in_file (a pathlike object or string representing an existing file) – Filename for input phase image. Maps to a command-line argument:
--phasemap=%s
.poly_order (an integer) – Apply polynomial fitting of order N. Maps to a command-line argument:
--poly=%d
.save_fmap (a boolean) – Write field map volume. Mutually exclusive with inputs:
save_unmasked_fmap
.save_shift (a boolean) – Write pixel shift volume. Mutually exclusive with inputs:
save_unmasked_shift
.save_unmasked_fmap (a boolean) – Saves the unmasked fieldmap when using –savefmap. Maps to a command-line argument:
--unmaskfmap
. Mutually exclusive with inputs:save_fmap
.save_unmasked_shift (a boolean) – Saves the unmasked shiftmap when using –saveshift. Maps to a command-line argument:
--unmaskshift
. Mutually exclusive with inputs:save_shift
.shift_in_file (a pathlike object or string representing an existing file) – Filename for reading pixel shift volume. Maps to a command-line argument:
--loadshift=%s
.shift_out_file (a pathlike object or string representing a file) – Filename for saving pixel shift volume. Maps to a command-line argument:
--saveshift=%s
.smooth2d (a float) – Apply 2D Gaussian smoothing of sigma N (in mm). Maps to a command-line argument:
--smooth2=%.2f
.smooth3d (a float) – Apply 3D Gaussian smoothing of sigma N (in mm). Maps to a command-line argument:
--smooth3=%.2f
.unwarp_direction (‘x’ or ‘y’ or ‘z’ or ‘x-‘ or ‘y-‘ or ‘z-‘) – Specifies direction of warping (default y). Maps to a command-line argument:
--unwarpdir=%s
.unwarped_file (a pathlike object or string representing a file) – Apply unwarping and save as filename. Maps to a command-line argument:
--unwarp=%s
. Mutually exclusive with inputs:warped_file
. Requires inputs:in_file
.warped_file (a pathlike object or string representing a file) – Apply forward warping and save as filename. Maps to a command-line argument:
--warp=%s
. Mutually exclusive with inputs:unwarped_file
. Requires inputs:in_file
.- Outputs
fmap_out_file (a pathlike object or string representing a file) – Fieldmap file.
shift_out_file (a pathlike object or string representing a file) – Voxel shift map file.
unwarped_file (a pathlike object or string representing a file) – Unwarped file.
warped_file (a pathlike object or string representing a file) – Forward warped file.
MCFLIRT¶
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()
- Mandatory Inputs
in_file (a pathlike object or string representing an existing file) – Timeseries to motion-correct. Maps to a command-line argument:
-in %s
(position: 0).- Optional Inputs
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s
.bins (an 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
.dof (an integer) – Degrees of freedom for the transformation. Maps to a command-line argument:
-dof %d
.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{}
)init (a pathlike object or string representing an existing file) – Inital transformation matrix. Maps to a command-line argument:
-init %s
.interpolation (‘spline’ or ‘nn’ or ‘sinc’) – Interpolation method for transformation. Maps to a command-line argument:
-%s_final
.mean_vol (a boolean) – Register to mean volume. Maps to a command-line argument:
-meanvol
.out_file (a pathlike object or string representing a file) – File to write. Maps to a command-line argument:
-out %s
.output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’) – FSL output type.
ref_file (a pathlike object or string representing an existing file) – Target image for motion correction. Maps to a command-line argument:
-reffile %s
.ref_vol (an integer) – Volume to align frames to. Maps to a command-line argument:
-refvol %d
.rotation (an integer) – Scaling factor for rotation tolerances. Maps to a command-line argument:
-rotation %d
.save_mats (a boolean) – Save transformation matrices. Maps to a command-line argument:
-mats
.save_plots (a boolean) – Save transformation parameters. Maps to a command-line argument:
-plots
.save_rms (a boolean) – Save rms displacement parameters. Maps to a command-line argument:
-rmsabs -rmsrel
.scaling (a float) – Scaling factor to use. Maps to a command-line argument:
-scaling %.2f
.smooth (a float) – Smoothing factor for the cost function. Maps to a command-line argument:
-smooth %.2f
.stages (an integer) – Stages (if 4, perform final search with sinc interpolation. Maps to a command-line argument:
-stages %d
.stats_imgs (a boolean) – Produce variance and std. dev. images. Maps to a command-line argument:
-stats
.use_contour (a boolean) – Run search on contour images. Maps to a command-line argument:
-edge
.use_gradient (a boolean) – Run search on gradient images. Maps to a command-line argument:
-gdt
.- Outputs
mat_file (a list of items which are a pathlike object or string representing an existing file) – Transformation matrices.
mean_img (a pathlike object or string representing an existing file) – Mean timeseries image (if mean_vol=True).
out_file (a pathlike object or string representing an existing file) – Motion-corrected timeseries.
par_file (a pathlike object or string representing an existing file) – Text-file with motion parameters.
rms_files (a list of items which are a pathlike object or string representing an existing file) – Absolute and relative displacement parameters.
std_img (a pathlike object or string representing an existing file) – Standard deviation image.
variance_img (a pathlike object or string representing an existing file) – Variance image.
PRELUDE¶
Bases: FSLCommand
Wrapped executable:
prelude
.FSL prelude wrapper for phase unwrapping
Examples
Please insert examples for use of this command
- Mandatory Inputs
complex_phase_file (a pathlike object or string representing an existing file) – Complex phase input volume. Maps to a command-line argument:
--complex=%s
. Mutually exclusive with inputs:magnitude_file
,phase_file
.magnitude_file (a pathlike object or string representing an existing file) – File containing magnitude image. Maps to a command-line argument:
--abs=%s
. Mutually exclusive with inputs:complex_phase_file
.phase_file (a pathlike object or string representing an existing file) – Raw phase file. Maps to a command-line argument:
--phase=%s
. Mutually exclusive with inputs:complex_phase_file
.- Optional Inputs
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s
.end (an integer) – Final image number to process (default Inf). Maps to a command-line argument:
--end=%d
.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{}
)label_file (a pathlike object or string representing a file) – Saving the area labels output. Maps to a command-line argument:
--labels=%s
.labelprocess2d (a boolean) – Does label processing in 2D (slice at a time). Maps to a command-line argument:
--labelslices
.mask_file (a pathlike object or string representing an existing file) – Filename of mask input volume. Maps to a command-line argument:
--mask=%s
.num_partitions (an integer) – Number of phase partitions to use. Maps to a command-line argument:
--numphasesplit=%d
.output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’) – FSL output type.
process2d (a boolean) – Does all processing in 2D (slice at a time). Maps to a command-line argument:
--slices
. Mutually exclusive with inputs:labelprocess2d
.process3d (a boolean) – Forces all processing to be full 3D. Maps to a command-line argument:
--force3D
. Mutually exclusive with inputs:labelprocess2d
,process2d
.rawphase_file (a pathlike object or string representing a file) – Saving the raw phase output. Maps to a command-line argument:
--rawphase=%s
.removeramps (a boolean) – Remove phase ramps during unwrapping. Maps to a command-line argument:
--removeramps
.savemask_file (a pathlike object or string representing a file) – Saving the mask volume. Maps to a command-line argument:
--savemask=%s
.start (an integer) – First image number to process (default 0). Maps to a command-line argument:
--start=%d
.threshold (a float) – Intensity threshold for masking. Maps to a command-line argument:
--thresh=%.10f
.unwrapped_phase_file (a pathlike object or string representing a file) – File containing unwrapepd phase. Maps to a command-line argument:
--unwrap=%s
.- Outputs
unwrapped_phase_file (a pathlike object or string representing an existing file) – Unwrapped phase file.
SUSAN¶
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()
- Mandatory Inputs
brightness_threshold (a float) – Brightness threshold and should be greater than noise level and less than contrast of edges to be preserved. Maps to a command-line argument:
%.10f
(position: 2).fwhm (a float) – Fwhm of smoothing, in mm, gets converted using sqrt(8*log(2)). Maps to a command-line argument:
%.10f
(position: 3).in_file (a pathlike object or string representing an existing file) – Filename of input timeseries. Maps to a command-line argument:
%s
(position: 1).- Optional Inputs
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s
.dimension (3 or 2) – Within-plane (2) or fully 3D (3). Maps to a command-line argument:
%d
(position: 4). (Nipype default value:3
)environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{}
)out_file (a pathlike object or string representing a file) – Output file name. Maps to a command-line argument:
%s
(position: -1).output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’) – FSL output type.
usans (a list of at most 2 items which are a tuple of the form: (a pathlike object or string representing an existing file, a float)) – Determines whether the smoothing area (USAN) is to be found from secondary images (0, 1 or 2). A negative value for any brightness threshold will auto-set the threshold at 10% of the robust range. (Nipype default value:
[]
)use_median (1 or 0) – Whether to use a local median filter in the cases where single-point noise is detected. Maps to a command-line argument:
%d
(position: 5). (Nipype default value:1
)- Outputs
smoothed_file (a pathlike object or string representing an existing file) – Smoothed output file.
SliceTimer¶
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()
- Mandatory Inputs
in_file (a pathlike object or string representing an existing file) – Filename of input timeseries. Maps to a command-line argument:
--in=%s
(position: 0).- Optional Inputs
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s
.custom_order (a pathlike object or string representing an existing file) – Filename of single-column custom interleave order file (first slice is referred to as 1 not 0). Maps to a command-line argument:
--ocustom=%s
.custom_timings (a pathlike object or string representing an existing file) – Slice timings, in fractions of TR, range 0:1 (default is 0.5 = no shift). Maps to a command-line argument:
--tcustom=%s
.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{}
)global_shift (a float) – Shift in fraction of TR, range 0:1 (default is 0.5 = no shift). Maps to a command-line argument:
--tglobal
.index_dir (a boolean) – Slice indexing from top to bottom. Maps to a command-line argument:
--down
.interleaved (a boolean) – Use interleaved acquisition. Maps to a command-line argument:
--odd
.out_file (a pathlike object or string representing a file) – Filename of output timeseries. Maps to a command-line argument:
--out=%s
.output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’) – FSL output type.
slice_direction (1 or 2 or 3) – Direction of slice acquisition (x=1, y=2, z=3) - default is z. Maps to a command-line argument:
--direction=%d
.time_repetition (a float) – Specify TR of data - default is 3s. Maps to a command-line argument:
--repeat=%f
.- Outputs
slice_time_corrected_file (a pathlike object or string representing an existing file) – Slice time corrected file.