nipype.interfaces.fsl.epi module¶
The fsl module provides classes for interfacing with the FSL command line tools. This was written to work with FSL version 5.0.4.
ApplyTOPUP¶
Bases: FSLCommand
Wrapped executable:
applytopup
.Interface for FSL topup, a tool for estimating and correcting susceptibility induced distortions. General reference and use example.
Examples
>>> from nipype.interfaces.fsl import ApplyTOPUP >>> applytopup = ApplyTOPUP() >>> applytopup.inputs.in_files = ["epi.nii", "epi_rev.nii"] >>> applytopup.inputs.encoding_file = "topup_encoding.txt" >>> applytopup.inputs.in_topup_fieldcoef = "topup_fieldcoef.nii.gz" >>> applytopup.inputs.in_topup_movpar = "topup_movpar.txt" >>> applytopup.inputs.output_type = "NIFTI_GZ" >>> applytopup.cmdline 'applytopup --datain=topup_encoding.txt --imain=epi.nii,epi_rev.nii --inindex=1,2 --topup=topup --out=epi_corrected.nii.gz' >>> res = applytopup.run()
- encoding_filea pathlike object or string representing an existing file
Name of text file with PE directions/times. Maps to a command-line argument:
--datain=%s
.- in_filesa list of items which are a pathlike object or string representing an existing file
Name of file with images. Maps to a command-line argument:
--imain=%s
.
- argsa string
Additional parameters to the command. Maps to a command-line argument:
%s
.- datatype‘char’ or ‘short’ or ‘int’ or ‘float’ or ‘double’
Force output data type. Maps to a command-line argument:
-d=%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:
{}
)- in_indexa list of items which are an integer
Comma separated list of indices corresponding to –datain. Maps to a command-line argument:
--inindex=%s
.- in_topup_fieldcoefa pathlike object or string representing an existing file
Topup file containing the field coefficients. Maps to a command-line argument:
--topup=%s
. Requires inputs:in_topup_movpar
.- in_topup_movpara pathlike object or string representing an existing file
Topup movpar.txt file. Requires inputs:
in_topup_fieldcoef
.- interp‘trilinear’ or ‘spline’
Interpolation method. Maps to a command-line argument:
--interp=%s
.- method‘jac’ or ‘lsr’
Use jacobian modulation (jac) or least-squares resampling (lsr). Maps to a command-line argument:
--method=%s
.- out_correcteda pathlike object or string representing a file
Output (warped) image. Maps to a command-line argument:
--out=%s
.- output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’ or ‘GIFTI’
FSL output type.
- out_correcteda pathlike object or string representing an existing file
Name of 4D image file with unwarped images.
EPIDeWarp¶
Bases: FSLCommand
Wrapped executable:
epidewarp.fsl
.Wraps the unwarping script epidewarp.fsl.
Warning
deprecated in FSL, please use
niflow.nipype1.workflows.dmri.preprocess.epi.sdc_fmb()
instead.Examples
>>> from nipype.interfaces.fsl import EPIDeWarp >>> dewarp = EPIDeWarp() >>> dewarp.inputs.epi_file = "functional.nii" >>> dewarp.inputs.mag_file = "magnitude.nii" >>> dewarp.inputs.dph_file = "phase.nii" >>> dewarp.inputs.output_type = "NIFTI_GZ" >>> dewarp.cmdline 'epidewarp.fsl --mag magnitude.nii --dph phase.nii --epi functional.nii --esp 0.58 --exfdw .../exfdw.nii.gz --nocleanup --sigma 2 --tediff 2.46 --tmpdir .../temp --vsm .../vsm.nii.gz' >>> res = dewarp.run()
- dph_filea pathlike object or string representing an existing file
Phase file assumed to be scaled from 0 to 4095. Maps to a command-line argument:
--dph %s
.- mag_filea pathlike object or string representing an existing file
Magnitude file. Maps to a command-line argument:
--mag %s
(position: 0).
- argsa string
Additional parameters to the command. Maps to a command-line argument:
%s
.- cleanupa boolean
Cleanup. Maps to a command-line argument:
--cleanup
.- 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:
{}
)- epi_filea pathlike object or string representing an existing file
EPI volume to unwarp. Maps to a command-line argument:
--epi %s
.- epidwa string
Dewarped epi volume. Maps to a command-line argument:
--epidw %s
.- espa float
EPI echo spacing. Maps to a command-line argument:
--esp %s
. (Nipype default value:0.58
)- exf_filea pathlike object or string representing an existing file
Example func volume (or use epi). Maps to a command-line argument:
--exf %s
.- exfdwa string
Dewarped example func volume. Maps to a command-line argument:
--exfdw %s
.- nocleanupa boolean
No cleanup. Maps to a command-line argument:
--nocleanup
. (Nipype default value:True
)- output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’ or ‘GIFTI’
FSL output type.
- sigmaan integer
2D spatial gaussing smoothing stdev (default = 2mm). Maps to a command-line argument:
--sigma %s
. (Nipype default value:2
)- tediffa float
Difference in B0 field map TEs. Maps to a command-line argument:
--tediff %s
. (Nipype default value:2.46
)- tmpdira string
Tmpdir. Maps to a command-line argument:
--tmpdir %s
.- vsma string
Voxel shift map. Maps to a command-line argument:
--vsm %s
.
- exf_maska pathlike object or string representing a file
Mask from example functional volume.
- exfdwa pathlike object or string representing a file
Dewarped functional volume example.
- unwarped_filea pathlike object or string representing a file
Unwarped epi file.
- vsm_filea pathlike object or string representing a file
Voxel shift map.
Eddy¶
Bases: FSLCommand
Wrapped executable:
eddy_openmp
.Interface for FSL eddy, a tool for estimating and correcting eddy currents induced distortions. User guide and more info regarding acqp file.
Examples
>>> from nipype.interfaces.fsl import EddyRunning eddy on a CPU using OpenMP: >>> eddy = Eddy() >>> eddy.inputs.in_file = ‘epi.nii’ >>> eddy.inputs.in_mask = ‘epi_mask.nii’ >>> eddy.inputs.in_index = ‘epi_index.txt’ >>> eddy.inputs.in_acqp = ‘epi_acqp.txt’ >>> eddy.inputs.in_bvec = ‘bvecs.scheme’ >>> eddy.inputs.in_bval = ‘bvals.scheme’ >>> eddy.cmdline # doctest: +ELLIPSIS ‘eddy_openmp –flm=quadratic –ff=10.0 –acqp=epi_acqp.txt –bvals=bvals.scheme –bvecs=bvecs.scheme –imain=epi.nii –index=epi_index.txt –mask=epi_mask.nii –interp=spline –resamp=jac –niter=5 –nvoxhp=1000 –out=…/eddy_corrected –slm=none’
Running eddy on an Nvidia GPU using cuda: >>> eddy.inputs.use_cuda = True >>> eddy.cmdline # doctest: +ELLIPSIS ‘eddy_cuda –flm=quadratic –ff=10.0 –acqp=epi_acqp.txt –bvals=bvals.scheme –bvecs=bvecs.scheme –imain=epi.nii –index=epi_index.txt –mask=epi_mask.nii –interp=spline –resamp=jac –niter=5 –nvoxhp=1000 –out=…/eddy_corrected –slm=none’
Running eddy with slice-to-volume motion correction: >>> eddy.inputs.mporder = 6 >>> eddy.inputs.slice2vol_niter = 5 >>> eddy.inputs.slice2vol_lambda = 1 >>> eddy.inputs.slice2vol_interp = ‘trilinear’ >>> eddy.inputs.slice_order = ‘epi_slspec.txt’ >>> eddy.cmdline # doctest: +ELLIPSIS ‘eddy_cuda –flm=quadratic –ff=10.0 –acqp=epi_acqp.txt –bvals=bvals.scheme –bvecs=bvecs.scheme –imain=epi.nii –index=epi_index.txt –mask=epi_mask.nii –interp=spline –resamp=jac –mporder=6 –niter=5 –nvoxhp=1000 –out=…/eddy_corrected –s2v_interp=trilinear –s2v_lambda=1 –s2v_niter=5 –slspec=epi_slspec.txt –slm=none’ >>> res = eddy.run() # doctest: +SKIP
- in_acqpa pathlike object or string representing an existing file
File containing acquisition parameters. Maps to a command-line argument:
--acqp=%s
.- in_bvala pathlike object or string representing an existing file
File containing the b-values for all volumes in –imain. Maps to a command-line argument:
--bvals=%s
.- in_bveca pathlike object or string representing an existing file
File containing the b-vectors for all volumes in –imain. Maps to a command-line argument:
--bvecs=%s
.- in_filea pathlike object or string representing an existing file
File containing all the images to estimate distortions for. Maps to a command-line argument:
--imain=%s
.- in_indexa pathlike object or string representing an existing file
File containing indices for all volumes in –imain into –acqp and –topup. Maps to a command-line argument:
--index=%s
.- in_maska pathlike object or string representing an existing file
Mask to indicate brain. Maps to a command-line argument:
--mask=%s
.
- argsa string
Additional parameters to the command. Maps to a command-line argument:
%s
.- cnr_mapsa boolean
Output CNR-Maps. Maps to a command-line argument:
--cnr_maps
.- dont_peasa boolean
Do NOT perform a post-eddy alignment of shells. Maps to a command-line argument:
--dont_peas
.- dont_sep_offs_movea boolean
Do NOT attempt to separate field offset from subject movement. Maps to a command-line argument:
--dont_sep_offs_move
.- 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:
{}
)- estimate_move_by_susceptibilitya boolean
Estimate how susceptibility field changes with subject movement. Maps to a command-line argument:
--estimate_move_by_susceptibility
.- fepa boolean
Fill empty planes in x- or y-directions. Maps to a command-line argument:
--fep
.- fielda pathlike object or string representing an existing file
Non-topup derived fieldmap scaled in Hz. Maps to a command-line argument:
--field=%s
.- field_mata pathlike object or string representing an existing file
Matrix specifying the relative positions of the fieldmap, –field, and the first volume of the input file, –imain. Maps to a command-line argument:
--field_mat=%s
.- flm‘quadratic’ or ‘linear’ or ‘cubic’
First level EC model. Maps to a command-line argument:
--flm=%s
. (Nipype default value:quadratic
)- fudge_factora float
Fudge factor for hyperparameter error variance. Maps to a command-line argument:
--ff=%s
. (Nipype default value:10.0
)- fwhma float
FWHM for conditioning filter when estimating the parameters. Maps to a command-line argument:
--fwhm=%s
.- in_topup_fieldcoefa pathlike object or string representing an existing file
Topup results file containing the field coefficients. Maps to a command-line argument:
--topup=%s
. Requires inputs:in_topup_movpar
.- in_topup_movpara pathlike object or string representing an existing file
Topup results file containing the movement parameters (movpar.txt). Requires inputs:
in_topup_fieldcoef
.- initranda boolean
Resets rand for when selecting voxels. Maps to a command-line argument:
--initrand
.- interp‘spline’ or ‘trilinear’
Interpolation model for estimation step. Maps to a command-line argument:
--interp=%s
. (Nipype default value:spline
)- is_shelleda boolean
Override internal check to ensure that date are acquired on a set of b-value shells. Maps to a command-line argument:
--data_is_shelled
.- jsona string or os.PathLike object referring to an existing file
Name of .json text file with information about slice timing. Maps to a command-line argument:
--json=%s
. Mutually exclusive with inputs:slice_order
. Requires inputs:mporder
.- mbs_kspan integer
Knot-spacing for MBS field estimation. Maps to a command-line argument:
--mbs_ksp=%smm
. Requires inputs:estimate_move_by_susceptibility
.- mbs_lambdaan integer
Weighting of regularisation for MBS estimation. Maps to a command-line argument:
--mbs_lambda=%s
. Requires inputs:estimate_move_by_susceptibility
.- mbs_niteran integer
Number of iterations for MBS estimation. Maps to a command-line argument:
--mbs_niter=%s
. Requires inputs:estimate_move_by_susceptibility
.- method‘jac’ or ‘lsr’
Final resampling method (jacobian/least squares). Maps to a command-line argument:
--resamp=%s
. (Nipype default value:jac
)- mporderan integer
Order of slice-to-vol movement model. Maps to a command-line argument:
--mporder=%s
. Requires inputs:use_cuda
.- multiband_factoran integer
Multi-band factor. Maps to a command-line argument:
--mb=%s
.- multiband_offset0 or 1 or -1
Multi-band offset (-1 if bottom slice removed, 1 if top slice removed. Maps to a command-line argument:
--mb_offs=%d
. Requires inputs:multiband_factor
.- niteran integer
Number of iterations. Maps to a command-line argument:
--niter=%s
. (Nipype default value:5
)- num_threadsan integer
Number of openmp threads to use. (Nipype default value:
1
)- nvoxhpan integer
# of voxels used to estimate the hyperparameters. Maps to a command-line argument:
--nvoxhp=%s
. (Nipype default value:1000
)- out_basea string
Basename for output image. Maps to a command-line argument:
--out=%s
. (Nipype default value:eddy_corrected
)- outlier_nstdan integer
Number of std off to qualify as outlier. Maps to a command-line argument:
--ol_nstd
. Requires inputs:repol
.- outlier_nvoxan integer
Min # of voxels in a slice for inclusion in outlier detection. Maps to a command-line argument:
--ol_nvox
. Requires inputs:repol
.- outlier_posa boolean
Consider both positive and negative outliers if set. Maps to a command-line argument:
--ol_pos
. Requires inputs:repol
.- outlier_sqra boolean
Consider outliers among sums-of-squared differences if set. Maps to a command-line argument:
--ol_sqr
. Requires inputs:repol
.- outlier_type‘sw’ or ‘gw’ or ‘both’
Type of outliers, slicewise (sw), groupwise (gw) or both (both). Maps to a command-line argument:
--ol_type
. Requires inputs:repol
.- output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’ or ‘GIFTI’
FSL output type.
- repola boolean
Detect and replace outlier slices. Maps to a command-line argument:
--repol
.- residualsa boolean
Output Residuals. Maps to a command-line argument:
--residuals
.- sessiona pathlike object or string representing an existing file
File containing session indices for all volumes in –imain. Maps to a command-line argument:
--session=%s
.- slice2vol_interp‘trilinear’ or ‘spline’
Slice-to-vol interpolation model for estimation step. Maps to a command-line argument:
--s2v_interp=%s
. Requires inputs:mporder
.- slice2vol_lambdaan integer
Regularisation weight for slice-to-vol movement (reasonable range 1-10). Maps to a command-line argument:
--s2v_lambda=%d
. Requires inputs:mporder
.- slice2vol_niteran integer
Number of iterations for slice-to-vol. Maps to a command-line argument:
--s2v_niter=%d
. Requires inputs:mporder
.- slice_ordera string or os.PathLike object referring to an existing file
Name of text file completely specifying slice/group acquisition. Maps to a command-line argument:
--slspec=%s
. Mutually exclusive with inputs:json
. Requires inputs:mporder
.- slm‘none’ or ‘linear’ or ‘quadratic’
Second level EC model. Maps to a command-line argument:
--slm=%s
. (Nipype default value:none
)- use_cudaa boolean
Run eddy using cuda gpu.
- out_cnr_mapsa pathlike object or string representing an existing file
Path/name of file with the cnr_maps.
- out_correcteda pathlike object or string representing an existing file
4D image file containing all the corrected volumes.
- out_movement_over_timea pathlike object or string representing an existing file
Text file containing translations (mm) and rotations (radians) for each excitation.
- out_movement_rmsa pathlike object or string representing an existing file
Summary of the ‘total movement’ in each volume.
- out_outlier_freea pathlike object or string representing an existing file
4D image file not corrected for susceptibility or eddy-current distortions or subject movement but with outlier slices replaced.
- out_outlier_mapa pathlike object or string representing an existing file
Matrix where rows represent volumes and columns represent slices. “0” indicates that scan-slice is not an outlier and “1” indicates that it is.
- out_outlier_n_sqr_stdev_mapa pathlike object or string representing an existing file
Matrix where rows represent volumes and columns represent slices. Values indicate number of standard deivations off the square root of the mean squared difference between observation and prediction is.
- out_outlier_n_stdev_mapa pathlike object or string representing an existing file
Matrix where rows represent volumes and columns represent slices. Values indicate number of standard deviations off the mean difference between observation and prediction is.
- out_outlier_reporta pathlike object or string representing an existing file
Text file with a plain language report on what outlier slices eddy has found.
- out_parametera pathlike object or string representing an existing file
Text file with parameters defining the field and movement for each scan.
- out_residualsa pathlike object or string representing an existing file
Path/name of file with the residuals.
- out_restricted_movement_rmsa pathlike object or string representing an existing file
Summary of the ‘total movement’ in each volume disregarding translation in the PE direction.
- out_rotated_bvecsa pathlike object or string representing an existing file
File containing rotated b-values for all volumes.
- out_shell_alignment_parametersa pathlike object or string representing an existing file
Text file containing rigid body movement parameters between the different shells as estimated by a post-hoc mutual information based registration.
- out_shell_pe_translation_parametersa pathlike object or string representing an existing file
Text file containing translation along the PE-direction between the different shells as estimated by a post-hoc mutual information based registration.
EddyCorrect¶
Bases: FSLCommand
Wrapped executable:
eddy_correct
.Warning
Deprecated in FSL. Please use
nipype.interfaces.fsl.epi.Eddy
insteadExample
>>> from nipype.interfaces.fsl import EddyCorrect >>> eddyc = EddyCorrect(in_file='diffusion.nii', ... out_file="diffusion_edc.nii", ref_num=0) >>> eddyc.cmdline 'eddy_correct diffusion.nii diffusion_edc.nii 0'
- in_filea pathlike object or string representing an existing file
4D input file. Maps to a command-line argument:
%s
(position: 0).- ref_numan integer
Reference number. Maps to a command-line argument:
%d
(position: 2). (Nipype default value:0
)
- argsa string
Additional parameters to the command. Maps to a command-line argument:
%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:
{}
)- out_filea pathlike object or string representing a file
4D output file. Maps to a command-line argument:
%s
(position: 1).- output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’ or ‘GIFTI’
FSL output type.
- eddy_correcteda pathlike object or string representing an existing file
Path/name of 4D eddy corrected output file.
EddyQuad¶
Bases: FSLCommand
Wrapped executable:
eddy_quad
.Interface for FSL eddy_quad, a tool for generating single subject reports and storing the quality assessment indices for each subject. User guide
Examples
>>> from nipype.interfaces.fsl import EddyQuad >>> quad = EddyQuad() >>> quad.inputs.base_name = 'eddy_corrected' >>> quad.inputs.idx_file = 'epi_index.txt' >>> quad.inputs.param_file = 'epi_acqp.txt' >>> quad.inputs.mask_file = 'epi_mask.nii' >>> quad.inputs.bval_file = 'bvals.scheme' >>> quad.inputs.bvec_file = 'bvecs.scheme' >>> quad.inputs.output_dir = 'eddy_corrected.qc' >>> quad.inputs.field = 'fieldmap_phase_fslprepared.nii' >>> quad.inputs.verbose = True >>> quad.cmdline 'eddy_quad eddy_corrected --bvals bvals.scheme --bvecs bvecs.scheme --field fieldmap_phase_fslprepared.nii --eddyIdx epi_index.txt --mask epi_mask.nii --output-dir eddy_corrected.qc --eddyParams epi_acqp.txt --verbose' >>> res = quad.run()
- bval_filea pathlike object or string representing an existing file
B-values file. Maps to a command-line argument:
--bvals %s
.- idx_filea pathlike object or string representing an existing file
File containing indices for all volumes into acquisition parameters. Maps to a command-line argument:
--eddyIdx %s
.- mask_filea pathlike object or string representing an existing file
Binary mask file. Maps to a command-line argument:
--mask %s
.- param_filea pathlike object or string representing an existing file
File containing acquisition parameters. Maps to a command-line argument:
--eddyParams %s
.
- argsa string
Additional parameters to the command. Maps to a command-line argument:
%s
.- base_namea string
Basename (including path) for EDDY output files, i.e., corrected images and QC files. Maps to a command-line argument:
%s
(position: 0). (Nipype default value:eddy_corrected
)- bvec_filea pathlike object or string representing an existing file
B-vectors file - only used when <base_name>.eddy_residuals file is present. Maps to a command-line argument:
--bvecs %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:
{}
)- fielda pathlike object or string representing an existing file
TOPUP estimated field (in Hz). Maps to a command-line argument:
--field %s
.- output_dira string
Output directory - default = ‘<base_name>.qc’. Maps to a command-line argument:
--output-dir %s
.- output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’ or ‘GIFTI’
FSL output type.
- slice_speca pathlike object or string representing an existing file
Text file specifying slice/group acquisition. Maps to a command-line argument:
--slspec %s
.- verbosea boolean
Display debug messages. Maps to a command-line argument:
--verbose
.
- avg_b0_pe_pnga list of items which are a pathlike object or string representing an existing file
Image showing mid-sagittal, -coronal and -axial slices of each averaged pe-direction b0 volume. Generated when using the -f option.
- avg_b_pnga list of items which are a pathlike object or string representing an existing file
Image showing mid-sagittal, -coronal and -axial slices of each averaged b-shell volume.
- clean_volumesa pathlike object or string representing an existing file
Text file containing a list of clean volumes, based on the eddy squared residuals. To generate a version of the pre-processed dataset without outlier volumes, use: fslselectvols -i <eddy_corrected_data> -o eddy_corrected_data_clean –vols=vols_no_outliers.txt.
- cnr_pnga list of items which are a pathlike object or string representing an existing file
Image showing mid-sagittal, -coronal and -axial slices of each b-shell CNR volume. Generated when CNR maps are available.
- qc_jsona pathlike object or string representing an existing file
Single subject database containing quality metrics and data info.
- qc_pdfa pathlike object or string representing an existing file
Single subject QC report.
- residualsa pathlike object or string representing an existing file
Text file containing the volume-wise mask-averaged squared residuals. Generated when residual maps are available.
- vdm_pnga pathlike object or string representing an existing file
Image showing mid-sagittal, -coronal and -axial slices of the voxel displacement map. Generated when using the -f option.
EpiReg¶
Bases: FSLCommand
Wrapped executable:
epi_reg
.Runs FSL epi_reg script for simultaneous coregistration and fieldmap unwarping.
Examples
>>> from nipype.interfaces.fsl import EpiReg >>> epireg = EpiReg() >>> epireg.inputs.epi='epi.nii' >>> epireg.inputs.t1_head='T1.nii' >>> epireg.inputs.t1_brain='T1_brain.nii' >>> epireg.inputs.out_base='epi2struct' >>> epireg.inputs.fmap='fieldmap_phase_fslprepared.nii' >>> epireg.inputs.fmapmag='fieldmap_mag.nii' >>> epireg.inputs.fmapmagbrain='fieldmap_mag_brain.nii' >>> epireg.inputs.echospacing=0.00067 >>> epireg.inputs.pedir='y' >>> epireg.cmdline 'epi_reg --echospacing=0.000670 --fmap=fieldmap_phase_fslprepared.nii --fmapmag=fieldmap_mag.nii --fmapmagbrain=fieldmap_mag_brain.nii --noclean --pedir=y --epi=epi.nii --t1=T1.nii --t1brain=T1_brain.nii --out=epi2struct' >>> epireg.run()
- epia pathlike object or string representing an existing file
EPI image. Maps to a command-line argument:
--epi=%s
(position: -4).- t1_braina pathlike object or string representing an existing file
Brain extracted T1 image. Maps to a command-line argument:
--t1brain=%s
(position: -2).- t1_heada pathlike object or string representing an existing file
Wholehead T1 image. Maps to a command-line argument:
--t1=%s
(position: -3).
- argsa string
Additional parameters to the command. Maps to a command-line argument:
%s
.- echospacinga float
Effective EPI echo spacing (sometimes called dwell time) - in 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:
{}
)- fmapa pathlike object or string representing an existing file
Fieldmap image (in rad/s). Maps to a command-line argument:
--fmap=%s
.- fmapmaga pathlike object or string representing an existing file
Fieldmap magnitude image - wholehead. Maps to a command-line argument:
--fmapmag=%s
.- fmapmagbraina pathlike object or string representing an existing file
Fieldmap magnitude image - brain extracted. Maps to a command-line argument:
--fmapmagbrain=%s
.- no_cleana boolean
Do not clean up intermediate files. Maps to a command-line argument:
--noclean
. (Nipype default value:True
)- no_fmaprega boolean
Do not perform registration of fmap to T1 (use if fmap already registered). Maps to a command-line argument:
--nofmapreg
.- out_basea string
Output base name. Maps to a command-line argument:
--out=%s
(position: -1). (Nipype default value:epi2struct
)- output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’ or ‘GIFTI’
FSL output type.
- pedir‘x’ or ‘y’ or ‘z’ or ‘-x’ or ‘-y’ or ‘-z’
Phase encoding direction, dir = x/y/z/-x/-y/-z. Maps to a command-line argument:
--pedir=%s
.- weight_imagea pathlike object or string representing an existing file
Weighting image (in T1 space). Maps to a command-line argument:
--weight=%s
.- wmsega pathlike object or string representing an existing file
White matter segmentation of T1 image, has to be named like the t1brain and end on _wmseg. Maps to a command-line argument:
--wmseg=%s
.
- epi2str_inva pathlike object or string representing an existing file
Rigid structural-to-epi transform.
- epi2str_mata pathlike object or string representing an existing file
Rigid epi-to-structural transform.
- fmap2epi_mata pathlike object or string representing an existing file
Rigid fieldmap-to-epi transform.
- fmap2str_mata pathlike object or string representing an existing file
Rigid fieldmap-to-structural transform.
- fmap_epia pathlike object or string representing an existing file
Fieldmap in epi space.
- fmap_stra pathlike object or string representing an existing file
Fieldmap in structural space.
- fmapmag_stra pathlike object or string representing an existing file
Fieldmap magnitude image in structural space.
- fullwarpa pathlike object or string representing an existing file
Warpfield to unwarp epi and transform into structural space.
- out_1vola pathlike object or string representing an existing file
Unwarped and coregistered single volume.
- out_filea pathlike object or string representing an existing file
Unwarped and coregistered epi input.
- sega pathlike object or string representing an existing file
White matter, gray matter, csf segmentation.
- shiftmapa pathlike object or string representing an existing file
Shiftmap in epi space.
- wmedgea pathlike object or string representing an existing file
White matter edges for visualization.
- wmsega pathlike object or string representing an existing file
White matter segmentation used in flirt bbr.
PrepareFieldmap¶
Bases: FSLCommand
Wrapped executable:
fsl_prepare_fieldmap
.Interface for the fsl_prepare_fieldmap script (FSL 5.0)
Prepares a fieldmap suitable for FEAT from SIEMENS data - saves output in rad/s format (e.g.
`fsl_prepare_fieldmap SIEMENS images_3_gre_field_mapping images_4_gre_field_mapping fmap_rads 2.65`
).Examples
>>> from nipype.interfaces.fsl import PrepareFieldmap >>> prepare = PrepareFieldmap() >>> prepare.inputs.in_phase = "phase.nii" >>> prepare.inputs.in_magnitude = "magnitude.nii" >>> prepare.inputs.output_type = "NIFTI_GZ" >>> prepare.cmdline 'fsl_prepare_fieldmap SIEMENS phase.nii magnitude.nii .../phase_fslprepared.nii.gz 2.460000' >>> res = prepare.run()
- delta_TEa float
Echo time difference of the fieldmap sequence in ms. (usually 2.46ms in Siemens). Maps to a command-line argument:
%f
(position: -2). (Nipype default value:2.46
)- in_magnitudea pathlike object or string representing an existing file
Magnitude difference map, brain extracted. Maps to a command-line argument:
%s
(position: 3).- in_phasea pathlike object or string representing an existing file
Phase difference map, in SIEMENS format range from 0-4096 or 0-8192). Maps to a command-line argument:
%s
(position: 2).
- argsa string
Additional parameters to the command. Maps to a command-line argument:
%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:
{}
)- nochecka boolean
Do not perform sanity checks for image size/range/dimensions. Maps to a command-line argument:
--nocheck
(position: -1). (Nipype default value:False
)- out_fieldmapa pathlike object or string representing a file
Output name for prepared fieldmap. Maps to a command-line argument:
%s
(position: 4).- output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’ or ‘GIFTI’
FSL output type.
- scannera string
Must be SIEMENS. Maps to a command-line argument:
%s
(position: 1). (Nipype default value:SIEMENS
)
- out_fieldmapa pathlike object or string representing an existing file
Output name for prepared fieldmap.
SigLoss¶
Bases: FSLCommand
Wrapped executable:
sigloss
.Estimates signal loss from a field map (in rad/s)
Examples
>>> from nipype.interfaces.fsl import SigLoss >>> sigloss = SigLoss() >>> sigloss.inputs.in_file = "phase.nii" >>> sigloss.inputs.echo_time = 0.03 >>> sigloss.inputs.output_type = "NIFTI_GZ" >>> sigloss.cmdline 'sigloss --te=0.030000 -i phase.nii -s .../phase_sigloss.nii.gz' >>> res = sigloss.run()
- in_filea pathlike object or string representing an existing file
B0 fieldmap file. Maps to a command-line argument:
-i %s
.
- argsa string
Additional parameters to the command. Maps to a command-line argument:
%s
.- echo_timea float
Echo time in seconds. Maps to a command-line argument:
--te=%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:
{}
)- mask_filea pathlike object or string representing an existing file
Brain mask file. Maps to a command-line argument:
-m %s
.- out_filea pathlike object or string representing a file
Output signal loss estimate file. Maps to a command-line argument:
-s %s
.- output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’ or ‘GIFTI’
FSL output type.
- slice_direction‘x’ or ‘y’ or ‘z’
Slicing direction. Maps to a command-line argument:
-d %s
.
- out_filea pathlike object or string representing an existing file
Signal loss estimate file.
TOPUP¶
Bases: FSLCommand
Wrapped executable:
topup
.Interface for FSL topup, a tool for estimating and correcting susceptibility induced distortions. See FSL documentation for reference, usage examples, and exemplary config files.
Examples
>>> from nipype.interfaces.fsl import TOPUP >>> topup = TOPUP() >>> topup.inputs.in_file = "b0_b0rev.nii" >>> topup.inputs.encoding_file = "topup_encoding.txt" >>> topup.inputs.output_type = "NIFTI_GZ" >>> topup.cmdline 'topup --config=b02b0.cnf --datain=topup_encoding.txt --imain=b0_b0rev.nii --out=b0_b0rev_base --iout=b0_b0rev_corrected.nii.gz --fout=b0_b0rev_field.nii.gz --jacout=jac --logout=b0_b0rev_topup.log --rbmout=xfm --dfout=warpfield' >>> res = topup.run()
- encoding_directiona list of items which are ‘y’ or ‘x’ or ‘z’ or ‘x-’ or ‘y-’ or ‘z-’
Encoding direction for automatic generation of encoding_file. Maps to a command-line argument:
--datain=%s
. Mutually exclusive with inputs:encoding_file
. Requires inputs:readout_times
.- encoding_filea pathlike object or string representing an existing file
Name of text file with PE directions/times. Maps to a command-line argument:
--datain=%s
. Mutually exclusive with inputs:encoding_direction
.- in_filea pathlike object or string representing an existing file
Name of 4D file with images. Maps to a command-line argument:
--imain=%s
.- readout_timesa list of items which are a float
Readout times (dwell times by # phase-encode steps minus 1). Mutually exclusive with inputs:
encoding_file
. Requires inputs:encoding_direction
.
- argsa string
Additional parameters to the command. Maps to a command-line argument:
%s
.- configa string
Name of config file specifying command line arguments. Maps to a command-line argument:
--config=%s
. (Nipype default value:b02b0.cnf
)- 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:
{}
)- estmov1 or 0
Estimate movements if set. Maps to a command-line argument:
--estmov=%d
.- fwhma float
FWHM (in mm) of gaussian smoothing kernel. Maps to a command-line argument:
--fwhm=%f
.- interp‘spline’ or ‘linear’
Image interpolation model, linear or spline. Maps to a command-line argument:
--interp=%s
.- max_iteran integer
Max # of non-linear iterations. Maps to a command-line argument:
--miter=%d
.- minmet0 or 1
Minimisation method 0=Levenberg-Marquardt, 1=Scaled Conjugate Gradient. Maps to a command-line argument:
--minmet=%d
.- numprec‘double’ or ‘float’
Precision for representing Hessian, double or float. Maps to a command-line argument:
--numprec=%s
.- out_basea pathlike object or string representing a file
Base-name of output files (spline coefficients (Hz) and movement parameters). Maps to a command-line argument:
--out=%s
.- out_correcteda pathlike object or string representing a file
Name of 4D image file with unwarped images. Maps to a command-line argument:
--iout=%s
.- out_fielda pathlike object or string representing a file
Name of image file with field (Hz). Maps to a command-line argument:
--fout=%s
.- out_jac_prefixa string
Prefix for the warpfield images. Maps to a command-line argument:
--jacout=%s
. (Nipype default value:jac
)- out_logfilea pathlike object or string representing a file
Name of log-file. Maps to a command-line argument:
--logout=%s
.- out_mat_prefixa string
Prefix for the realignment matrices. Maps to a command-line argument:
--rbmout=%s
. (Nipype default value:xfm
)- out_warp_prefixa string
Prefix for the warpfield images (in mm). Maps to a command-line argument:
--dfout=%s
. (Nipype default value:warpfield
)- output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’ or ‘GIFTI’
FSL output type.
- reg_lambdaa float
Weight of regularisation, default depending on –ssqlambda and –regmod switches. Maps to a command-line argument:
--lambda=%0.f
.- regmod‘bending_energy’ or ‘membrane_energy’
Regularisation term implementation. Defaults to bending_energy. Note that the two functions have vastly different scales. The membrane energy is based on the first derivatives and the bending energy on the second derivatives. The second derivatives will typically be much smaller than the first derivatives, so input lambda will have to be larger for bending_energy to yield approximately the same level of regularisation. Maps to a command-line argument:
--regmod=%s
.- regrid1 or 0
If set (=1), the calculations are done in a different grid. Maps to a command-line argument:
--regrid=%d
.- scale0 or 1
If set (=1), the images are individually scaled to a common mean. Maps to a command-line argument:
--scale=%d
.- splineorderan integer
Order of spline, 2->Qadratic spline, 3->Cubic spline. Maps to a command-line argument:
--splineorder=%d
.- ssqlambda1 or 0
Weight lambda by the current value of the ssd. If used (=1), the effective weight of regularisation term becomes higher for the initial iterations, therefore initial steps are a little smoother than they would without weighting. This reduces the risk of finding a local minimum. Maps to a command-line argument:
--ssqlambda=%d
.- subsampan integer
Sub-sampling scheme. Maps to a command-line argument:
--subsamp=%d
.- warp_resa float
(approximate) resolution (in mm) of warp basis for the different sub-sampling levels. Maps to a command-line argument:
--warpres=%f
.
- out_correcteda pathlike object or string representing a file
Name of 4D image file with unwarped images.
- out_enc_filea pathlike object or string representing a file
Encoding directions file output for applytopup.
- out_fielda pathlike object or string representing a file
Name of image file with field (Hz).
- out_fieldcoefa pathlike object or string representing an existing file
File containing the field coefficients.
- out_jacsa list of items which are a pathlike object or string representing an existing file
Jacobian images.
- out_logfilea pathlike object or string representing a file
Name of log-file.
- out_matsa list of items which are a pathlike object or string representing an existing file
Realignment matrices.
- out_movpara pathlike object or string representing an existing file
Movpar.txt output file.
- out_warpsa list of items which are a pathlike object or string representing an existing file
Warpfield images.