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interfaces.fsl.epi

ApplyTOPUP

Link to code

Wraps command 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_index = [ 1,2 ]
>>> applytopup.inputs.in_topup = "my_topup_results"
>>> applytopup.cmdline 
'applytopup --datain=topup_encoding.txt --imain=epi.nii,epi_rev.nii --inindex=1,2 --topup=my_topup_results --out=.../nipypeatu'
>>> res = applytopup.run() 

Inputs:

[Mandatory]
encoding_file: (an existing file name)
        name of text file with PE directions/times
in_files: (an existing file name)
        name of 4D file with images
in_index: (a list of items which are any value)
        comma separated list of indicies into --datain of the input image
        (to be corrected)
in_topup: (a file name)
        basename of field/movements (from topup)
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
        Control terminal output: `stream` - displays to terminal
        immediately, `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored

[Optional]
args: (a string)
        Additional parameters to the command
datatype: ('char' or 'short' or 'int' or 'float' or 'double')
        force output data type
encoding_file: (an existing file name)
        name of text file with PE directions/times
environ: (a dictionary with keys which are a value of type 'str' and
         with values which are a value of type 'str', nipype default value:
         {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the
        interface fails to run
in_files: (an existing file name)
        name of 4D file with images
in_index: (a list of items which are any value)
        comma separated list of indicies into --datain of the input image
        (to be corrected)
in_topup: (a file name)
        basename of field/movements (from topup)
interp: ('trilinear' or 'spline')
        interpolation method
method: ('jac' or 'lsr')
        use jacobian modulation (jac) or least-squares resampling (lsr)
out_base: (a file name)
        basename for output (warped) image
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
         'NIFTI')
        FSL output type
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
        Control terminal output: `stream` - displays to terminal
        immediately, `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored

Outputs:

out_corrected: (an existing file name)
        name of 4D image file with unwarped images

EPIDeWarp

Link to code

Wraps command epidewarp.fsl

Wraps fieldmap unwarping script from Freesurfer’s epidewarp.fsl_

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() 

References

_epidewarp.fsl: http://surfer.nmr.mgh.harvard.edu/fswiki/epidewarp.fsl

Inputs:

[Mandatory]
dph_file: (an existing file name)
        Phase file assumed to be scaled from 0 to 4095
mag_file: (an existing file name)
        Magnitude file
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
        Control terminal output: `stream` - displays to terminal
        immediately, `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored

[Optional]
args: (a string)
        Additional parameters to the command
cleanup: (a boolean)
        cleanup
dph_file: (an existing file name)
        Phase file assumed to be scaled from 0 to 4095
environ: (a dictionary with keys which are a value of type 'str' and
         with values which are a value of type 'str', nipype default value:
         {})
        Environment variables
epi_file: (an existing file name)
        EPI volume to unwarp
epidw: (a string)
        dewarped epi volume
esp: (a float, nipype default value: 0.58)
        EPI echo spacing
exf_file: (an existing file name)
        example func volume (or use epi)
exfdw: (a string)
        dewarped example func volume
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the
        interface fails to run
mag_file: (an existing file name)
        Magnitude file
nocleanup: (a boolean, nipype default value: True)
        no cleanup
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
         'NIFTI')
        FSL output type
sigma: (an integer, nipype default value: 2)
        2D spatial gaussing smoothing stdev (default = 2mm)
tediff: (a float, nipype default value: 2.46)
        difference in B0 field map TEs
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
        Control terminal output: `stream` - displays to terminal
        immediately, `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored
tmpdir: (a string)
        tmpdir
vsm: (a string)
        voxel shift map

Outputs:

exf_mask: (a file name)
        Mask from example functional volume
exfdw: (a file name)
        dewarped functional volume example
unwarped_file: (a file name)
        unwarped epi file
vsm_file: (a file name)
        voxel shift map

Eddy

Link to code

Wraps command eddy

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 Eddy
>>> 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 
'eddy --acqp=epi_acqp.txt --bvals=bvals.scheme --bvecs=bvecs.scheme --imain=epi.nii --index=epi_index.txt --mask=epi_mask.nii --out=.../eddy_corrected'
>>> res = eddy.run() 

Inputs:

[Mandatory]
in_acqp: (an existing file name)
        File containing acquisition parameters
in_bval: (an existing file name)
        File containing the b-values for all volumes in --imain
in_bvec: (an existing file name)
        File containing the b-vectors for all volumes in --imain
in_file: (an existing file name)
        File containing all the images to estimate distortions for
in_index: (an existing file name)
        File containing indices for all volumes in --imain into --acqp and
        --topup
in_mask: (an existing file name)
        Mask to indicate brain
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
        Control terminal output: `stream` - displays to terminal
        immediately, `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored

[Optional]
args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and
         with values which are a value of type 'str', nipype default value:
         {})
        Environment variables
flm: ('linear' or 'quadratic' or 'cubic')
        First level EC model
fwhm: (a float)
        FWHM for conditioning filter when estimating the parameters
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the
        interface fails to run
in_acqp: (an existing file name)
        File containing acquisition parameters
in_bval: (an existing file name)
        File containing the b-values for all volumes in --imain
in_bvec: (an existing file name)
        File containing the b-vectors for all volumes in --imain
in_file: (an existing file name)
        File containing all the images to estimate distortions for
in_index: (an existing file name)
        File containing indices for all volumes in --imain into --acqp and
        --topup
in_mask: (an existing file name)
        Mask to indicate brain
in_topup: (an existing file name)
        Base name for output files from topup
method: ('jac' or 'lsr')
        Final resampling method (jacobian/least squeares)
niter: (an integer)
        Number of iterations
out_base: (a file name)
        basename for output (warped) image
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
         'NIFTI')
        FSL output type
repol: (a boolean)
        Detect and replace outlier slices
session: (an existing file name)
        File containing session indices for all volumes in --imain
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
        Control terminal output: `stream` - displays to terminal
        immediately, `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored

Outputs:

out_corrected: (an existing file name)
        4D image file containing all the corrected volumes
out_parameter: (an existing file name)
        text file with parameters definining the field and movement for each
        scan

EddyCorrect

Link to code

Wraps command eddy_correct

Deprecated! Please use create_eddy_correct_pipeline instead

Example

>>> 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'

Inputs:

[Mandatory]
in_file: (an existing file name)
        4D input file
ref_num: (an integer)
        reference number
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
        Control terminal output: `stream` - displays to terminal
        immediately, `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored

[Optional]
args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and
         with values which are a value of type 'str', nipype default value:
         {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the
        interface fails to run
in_file: (an existing file name)
        4D input file
out_file: (a file name)
        4D output file
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
         'NIFTI')
        FSL output type
ref_num: (an integer)
        reference number
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
        Control terminal output: `stream` - displays to terminal
        immediately, `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored

Outputs:

eddy_corrected: (an existing file name)
        path/name of 4D eddy corrected output file

PrepareFieldmap

Link to code

Wraps command 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() 

Inputs:

[Mandatory]
delta_TE: (a float, nipype default value: 2.46)
        echo time difference of the fielmap sequence in ms. (usually 2.46ms
        in Siemens)
in_magnitude: (an existing file name)
        Magnitude difference map, brain extracted
in_phase: (an existing file name)
        Phase difference map, in SIEMENS format range from 0-4096 or 0-8192
        ~
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
        Control terminal output: `stream` - displays to terminal
        immediately, `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored

[Optional]
args: (a string)
        Additional parameters to the command
delta_TE: (a float, nipype default value: 2.46)
        echo time difference of the fielmap sequence in ms. (usually 2.46ms
        in Siemens)
environ: (a dictionary with keys which are a value of type 'str' and
         with values which are a value of type 'str', nipype default value:
         {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the
        interface fails to run
in_magnitude: (an existing file name)
        Magnitude difference map, brain extracted
in_phase: (an existing file name)
        Phase difference map, in SIEMENS format range from 0-4096 or 0-8192
        ~
nocheck: (a boolean, nipype default value: False)
        do not perform sanity checks for image size/range/dimensions
out_fieldmap: (a file name)
        output name for prepared fieldmap
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
         'NIFTI')
        FSL output type
scanner: (a string, nipype default value: SIEMENS)
        must be SIEMENS
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
        Control terminal output: `stream` - displays to terminal
        immediately, `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored

Outputs:

out_fieldmap: (an existing file name)
        output name for prepared fieldmap

SigLoss

Link to code

Wraps command 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() 

Inputs:

[Mandatory]
in_file: (an existing file name)
        b0 fieldmap file
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
        Control terminal output: `stream` - displays to terminal
        immediately, `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored

[Optional]
args: (a string)
        Additional parameters to the command
echo_time: (a float)
        echo time in seconds
environ: (a dictionary with keys which are a value of type 'str' and
         with values which are a value of type 'str', nipype default value:
         {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the
        interface fails to run
in_file: (an existing file name)
        b0 fieldmap file
mask_file: (an existing file name)
        brain mask file
out_file: (a file name)
        output signal loss estimate file
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
         'NIFTI')
        FSL output type
slice_direction: ('x' or 'y' or 'z')
        slicing direction
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
        Control terminal output: `stream` - displays to terminal
        immediately, `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored

Outputs:

out_file: (an existing file name)
        signal loss estimate file

TOPUP

Link to code

Wraps command topup

Interface for FSL topup, a tool for estimating and correcting susceptibility induced distortions Reference: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TOPUP Example: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/ExampleTopupFollowedByApplytopup

topup –imain=<some 4D image> –datain=<text file> –config=<text file with parameters> –coutname=my_field

Examples

>>> from nipype.interfaces.fsl import TOPUP
>>> topup = TOPUP()
>>> topup.inputs.in_file = "b0_b0rev.nii"
>>> topup.inputs.encoding_file = "topup_encoding.txt"
>>> topup.cmdline 
'topup --config=b02b0.cnf --datain=topup_encoding.txt --imain=b0_b0rev.nii --out=.../nipypetu'
>>> res = topup.run() 

Inputs:

[Mandatory]
in_file: (an existing file name)
        name of 4D file with images
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
        Control terminal output: `stream` - displays to terminal
        immediately, `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored

[Optional]
args: (a string)
        Additional parameters to the command
config: (a string, nipype default value: b02b0.cnf)
        Name of config file specifying command line arguments
encoding_direction: ('y' or 'x' or 'z' or 'x-' or 'y-' or 'z-')
        encoding direction for automatic generation of encoding_file
encoding_file: (an existing file name)
        name of text file with PE directions/times
environ: (a dictionary with keys which are a value of type 'str' and
         with values which are a value of type 'str', nipype default value:
         {})
        Environment variables
estmov: (1 or 0)
        estimate movements if set
fwhm: (a float)
        FWHM (in mm) of gaussian smoothing kernel
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the
        interface fails to run
in_file: (an existing file name)
        name of 4D file with images
interp: ('spline' or 'linear')
        Image interpolation model, linear or spline.
max_iter: (an integer)
        max # of non-linear iterations
minmet: (0 or 1)
        Minimisation method 0=Levenberg-Marquardt, 1=Scaled Conjugate
        Gradient
numprec: ('double' or 'float')
        Precision for representing Hessian, double or float.
out_base: (a file name)
        base-name of output files (spline coefficients (Hz) and movement
        parameters)
out_corrected: (a file name)
        name of 4D image file with unwarped images
out_field: (a file name)
        name of image file with field (Hz)
out_logfile: (a file name)
        name of log-file
output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
         'NIFTI')
        FSL output type
readout_times: (a list of items which are a float)
        readout times (dwell times by # phase-encode steps minus 1)
regrid: (1 or 0)
        If set (=1), the calculations are done in a different grid
scale: (0 or 1)
        If set (=1), the images are individually scaled to a common mean
splineorder: (an integer)
        order of spline, 2->Qadratic spline, 3->Cubic spline
subsamp: (an integer)
        sub-sampling scheme, default 1
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
        Control terminal output: `stream` - displays to terminal
        immediately, `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored
warp_res: (a float)
        (approximate) resolution (in mm) of warp basis for the different
        sub-sampling levels

Outputs:

out_corrected: (a file name)
        name of 4D image file with unwarped images
out_enc_file: (a file name)
        encoding directions file output for applytopup
out_field: (a file name)
        name of image file with field (Hz)
out_fieldcoef: (an existing file name)
        file containing the field coefficients
out_logfile: (a file name)
        name of log-file
out_movpar: (an existing file name)
        movpar.txt output file
out_topup: (a file name)
        basename for the <out_base>_fieldcoef.nii.gz and
        <out_base>_movpar.txt files