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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_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()

Inputs:

    [Mandatory]
    encoding_file: (an existing file name)
            name of text file with PE directions/times
            flag: --datain=%s
    in_files: (an existing file name)
            name of 4D file with images
            flag: --imain=%s
    in_index: (a list of items which are an integer)
            comma separated list of indicies into --datain of the input image
            (to be corrected)
            flag: --inindex=%s
    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
            flag: %s
    datatype: ('char' or 'short' or 'int' or 'float' or 'double')
            force output data type
            flag: -d=%s
    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_topup_fieldcoef: (an existing file name)
            topup file containing the field coefficients
            flag: --topup=%s
            requires: in_topup_movpar
    in_topup_movpar: (an existing file name)
            topup movpar.txt file
            requires: in_topup_fieldcoef
    interp: ('trilinear' or 'spline')
            interpolation method
            flag: --interp=%s
    method: ('jac' or 'lsr')
            use jacobian modulation (jac) or least-squares resampling (lsr)
            flag: --method=%s
    out_corrected: (a file name)
            output (warped) image
            flag: --out=%s
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
             'NIFTI')
            FSL output type

Outputs:

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

## EPIDeWarp

Link to code

Wraps command epidewarp.fsl

Wraps the unwarping script epidewarp.fsl.

Warning

deprecated in FSL, please use `nipype.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()

Inputs:

    [Mandatory]
    dph_file: (an existing file name)
            Phase file assumed to be scaled from 0 to 4095
            flag: --dph %s
    mag_file: (an existing file name)
            Magnitude file
            flag: --mag %s, position: 0
    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
            flag: %s
    cleanup: (a boolean)
            cleanup
            flag: --cleanup
    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
            flag: --epi %s
    epidw: (a string)
            dewarped epi volume
            flag: --epidw %s
    esp: (a float, nipype default value: 0.58)
            EPI echo spacing
            flag: --esp %s
    exf_file: (an existing file name)
            example func volume (or use epi)
            flag: --exf %s
    exfdw: (a string)
            dewarped example func volume
            flag: --exfdw %s
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    nocleanup: (a boolean, nipype default value: True)
            no cleanup
            flag: --nocleanup
    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)
            flag: --sigma %s
    tediff: (a float, nipype default value: 2.46)
            difference in B0 field map TEs
            flag: --tediff %s
    tmpdir: (a string)
            tmpdir
            flag: --tmpdir %s
    vsm: (a string)
            voxel shift map
            flag: --vsm %s

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
            flag: --acqp=%s
    in_bval: (an existing file name)
            File containing the b-values for all volumes in --imain
            flag: --bvals=%s
    in_bvec: (an existing file name)
            File containing the b-vectors for all volumes in --imain
            flag: --bvecs=%s
    in_file: (an existing file name)
            File containing all the images to estimate distortions for
            flag: --imain=%s
    in_index: (an existing file name)
            File containing indices for all volumes in --imain into --acqp and
            --topup
            flag: --index=%s
    in_mask: (an existing file name)
            Mask to indicate brain
            flag: --mask=%s
    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
            flag: %s
    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
            flag: --flm=%s
    fwhm: (a float)
            FWHM for conditioning filter when estimating the parameters
            flag: --fwhm=%s
    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_topup_fieldcoef: (an existing file name)
            topup file containing the field coefficients
            flag: --topup=%s
            requires: in_topup_movpar
    in_topup_movpar: (an existing file name)
            topup movpar.txt file
            requires: in_topup_fieldcoef
    method: ('jac' or 'lsr')
            Final resampling method (jacobian/least squares)
            flag: --resamp=%s
    niter: (an integer)
            Number of iterations
            flag: --niter=%s
    num_threads: (an integer, nipype default value: 1)
            Number of openmp threads to use
    out_base: (a unicode string, nipype default value: eddy_corrected)
            basename for output (warped) image
            flag: --out=%s
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
             'NIFTI')
            FSL output type
    repol: (a boolean)
            Detect and replace outlier slices
            flag: --repol
    session: (an existing file name)
            File containing session indices for all volumes in --imain
            flag: --session=%s

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

Warning

Deprecated in FSL. Please use `nipype.interfaces.fsl.epi.Eddy` 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
            flag: %s, position: 0
    ref_num: (an integer, nipype default value: 0)
            reference number
            flag: %d, position: 2
    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
            flag: %s
    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
    out_file: (a file name)
            4D output file
            flag: %s, position: 1
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
             'NIFTI')
            FSL output type

Outputs:

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

## EpiReg

Link to code

Wraps command 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 --pedir=y --epi=epi.nii --t1=T1.nii --t1brain=T1_brain.nii --out=epi2struct'
    >>> epireg.run()

Inputs:

    [Mandatory]
    epi: (an existing file name)
            EPI image
            flag: --epi=%s, position: -4
    t1_brain: (an existing file name)
            brain extracted T1 image
            flag: --t1brain=%s, position: -2
    t1_head: (an existing file name)
            wholehead T1 image
            flag: --t1=%s, position: -3
    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
            flag: %s
    echospacing: (a float)
            Effective EPI echo spacing (sometimes called dwell time) - in
            seconds
            flag: --echospacing=%f
    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
    fmap: (an existing file name)
            fieldmap image (in rad/s)
            flag: --fmap=%s
    fmapmag: (an existing file name)
            fieldmap magnitude image - wholehead
            flag: --fmapmag=%s
    fmapmagbrain: (an existing file name)
            fieldmap magnitude image - brain extracted
            flag: --fmapmagbrain=%s
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    no_clean: (a boolean)
            do not clean up intermediate files
            flag: --noclean
    no_fmapreg: (a boolean)
            do not perform registration of fmap to T1 (use if fmap already
            registered)
            flag: --nofmapreg
    out_base: (a string)
            output base name
            flag: --out=%s, position: -1
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
             'NIFTI')
            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
            flag: --pedir=%s
    weight_image: (an existing file name)
            weighting image (in T1 space)
            flag: --weight=%s
    wmseg: (an existing file name)
            white matter segmentation of T1 image, has to be named like the
            t1brain and end on _wmseg
            flag: --wmseg=%s

Outputs:

    epi2str_inv: (an existing file name)
            rigid structural-to-epi transform
    epi2str_mat: (an existing file name)
            rigid epi-to-structural transform
    fmap2epi_mat: (an existing file name)
            rigid fieldmap-to-epi transform
    fmap2str_mat: (an existing file name)
            rigid fieldmap-to-structural transform
    fmap_epi: (an existing file name)
            fieldmap in epi space
    fmap_str: (an existing file name)
            fieldmap in structural space
    fmapmag_str: (an existing file name)
            fieldmap magnitude image in structural space
    fullwarp: (an existing file name)
            warpfield to unwarp epi and transform into structural space
    out_1vol: (an existing file name)
            unwarped and coregistered single volume
    out_file: (an existing file name)
            unwarped and coregistered epi input
    shiftmap: (an existing file name)
            shiftmap in epi space
    wmedge: (an existing file name)
            white matter edges for visualization
    wmseg: (an existing file name)
            white matter segmentation used in flirt bbr

## 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 fieldmap sequence in ms. (usually 2.46ms
            in Siemens)
            flag: %f, position: -2
    in_magnitude: (an existing file name)
            Magnitude difference map, brain extracted
            flag: %s, position: 3
    in_phase: (an existing file name)
            Phase difference map, in SIEMENS format range from 0-4096 or 0-8192)
            flag: %s, position: 2
    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
            flag: %s
    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
    nocheck: (a boolean, nipype default value: False)
            do not perform sanity checks for image size/range/dimensions
            flag: --nocheck, position: -1
    out_fieldmap: (a file name)
            output name for prepared fieldmap
            flag: %s, position: 4
    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
            flag: %s, position: 1

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
            flag: -i %s
    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
            flag: %s
    echo_time: (a float)
            echo time in seconds
            flag: --te=%f
    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
    mask_file: (an existing file name)
            brain mask file
            flag: -m %s
    out_file: (a file name)
            output signal loss estimate file
            flag: -s %s
    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
            flag: -d %s

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. See FSL documentation for reference, usage examples, and `exemplary config files <https://github.com/ahheckel/FSL-scripts/blob/master/rsc/fsl/fsl4/topup/b02b0.cnf`_.

### 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 --logout=b0_b0rev_topup.log'
    >>> res = topup.run()

Inputs:

    [Mandatory]
    encoding_direction: (a list of items which are 'y' or 'x' or 'z' or
             'x-' or 'y-' or 'z-')
            encoding direction for automatic generation of encoding_file
            flag: --datain=%s
            mutually_exclusive: encoding_file
            requires: readout_times
    encoding_file: (an existing file name)
            name of text file with PE directions/times
            flag: --datain=%s
            mutually_exclusive: encoding_direction
    in_file: (an existing file name)
            name of 4D file with images
            flag: --imain=%s
    readout_times: (a float)
            readout times (dwell times by # phase-encode steps minus 1)
            mutually_exclusive: encoding_file
            requires: encoding_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

    [Optional]
    args: (a string)
            Additional parameters to the command
            flag: %s
    config: (a string, nipype default value: b02b0.cnf)
            Name of config file specifying command line arguments
            flag: --config=%s
    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
            flag: --estmov=%d
    fwhm: (a float)
            FWHM (in mm) of gaussian smoothing kernel
            flag: --fwhm=%f
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    interp: ('spline' or 'linear')
            Image interpolation model, linear or spline.
            flag: --interp=%s
    max_iter: (an integer)
            max # of non-linear iterations
            flag: --miter=%d
    minmet: (0 or 1)
            Minimisation method 0=Levenberg-Marquardt, 1=Scaled Conjugate
            Gradient
            flag: --minmet=%d
    numprec: ('double' or 'float')
            Precision for representing Hessian, double or float.
            flag: --numprec=%s
    out_base: (a file name)
            base-name of output files (spline coefficients (Hz) and movement
            parameters)
            flag: --out=%s
    out_corrected: (a file name)
            name of 4D image file with unwarped images
            flag: --iout=%s
    out_field: (a file name)
            name of image file with field (Hz)
            flag: --fout=%s
    out_logfile: (a file name)
            name of log-file
            flag: --logout=%s
    output_type: ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or
             'NIFTI')
            FSL output type
    reg_lambda: (a float)
            lambda weighting value of the regularisation term
            flag: --miter=%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.
            flag: --regmod=%s
    regrid: (1 or 0)
            If set (=1), the calculations are done in a different grid
            flag: --regrid=%d
    scale: (0 or 1)
            If set (=1), the images are individually scaled to a common mean
            flag: --scale=%d
    splineorder: (an integer)
            order of spline, 2->Qadratic spline, 3->Cubic spline
            flag: --splineorder=%d
    ssqlambda: (1 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.
            flag: --ssqlambda=%d
    subsamp: (an integer)
            sub-sampling scheme
            flag: --subsamp=%d
    warp_res: (a float)
            (approximate) resolution (in mm) of warp basis for the different
            sub-sampling levels.
            flag: --warpres=%f

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