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# interfaces.minc.minc

## Average

Link to code

Wraps command mincaverage

Average a number of MINC files.

### Examples

    >>> from nipype.interfaces.minc import Average
    >>> from nipype.interfaces.minc.testdata import nonempty_minc_data

    >>> files = [nonempty_minc_data(i) for i in range(3)]
    >>> average = Average(input_files=files, output_file='/tmp/tmp.mnc')
    >>> average.run()

Inputs:

    [Mandatory]
    filelist: (a file name)
            Specify the name of a file containing input file names.
            flag: -filelist %s
            mutually_exclusive: input_files, filelist
    input_files: (a list of items which are a file name)
            input file(s)
            flag: %s, position: -2
            mutually_exclusive: input_files, filelist

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    avgdim: (a unicode string)
            Specify a dimension along which we wish to average.
            flag: -avgdim %s
    binarize: (a boolean)
            Binarize the volume by looking for values in a given range.
            flag: -binarize
    binrange: (a tuple of the form: (a float, a float))
            Specify a range for binarization. Default value: 1.79769e+308
            -1.79769e+308.
            flag: -binrange %s %s
    binvalue: (a float)
            Specify a target value (+/- 0.5) forbinarization. Default value:
            -1.79769e+308
            flag: -binvalue %s
    check_dimensions: (a boolean)
            Check that dimension info matches across files (default).
            flag: -check_dimensions
            mutually_exclusive: check_dimensions, no_check_dimensions
    clobber: (a boolean, nipype default value: True)
            Overwrite existing file.
            flag: -clobber
    copy_header: (a boolean)
            Copy all of the header from the first file (default for one file).
            flag: -copy_header
            mutually_exclusive: copy_header, no_copy_header
    debug: (a boolean)
            Print out debugging messages.
            flag: -debug
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    format_byte: (a boolean)
            Write out byte data.
            flag: -byte
            mutually_exclusive: format_filetype, format_byte, format_short,
             format_int, format_long, format_float, format_double,
             format_signed, format_unsigned
    format_double: (a boolean)
            Write out double-precision floating-point data.
            flag: -double
            mutually_exclusive: format_filetype, format_byte, format_short,
             format_int, format_long, format_float, format_double,
             format_signed, format_unsigned
    format_filetype: (a boolean)
            Use data type of first file (default).
            flag: -filetype
            mutually_exclusive: format_filetype, format_byte, format_short,
             format_int, format_long, format_float, format_double,
             format_signed, format_unsigned
    format_float: (a boolean)
            Write out single-precision floating-point data.
            flag: -float
            mutually_exclusive: format_filetype, format_byte, format_short,
             format_int, format_long, format_float, format_double,
             format_signed, format_unsigned
    format_int: (a boolean)
            Write out 32-bit integer data.
            flag: -int
            mutually_exclusive: format_filetype, format_byte, format_short,
             format_int, format_long, format_float, format_double,
             format_signed, format_unsigned
    format_long: (a boolean)
            Superseded by -int.
            flag: -long
            mutually_exclusive: format_filetype, format_byte, format_short,
             format_int, format_long, format_float, format_double,
             format_signed, format_unsigned
    format_short: (a boolean)
            Write out short integer data.
            flag: -short
            mutually_exclusive: format_filetype, format_byte, format_short,
             format_int, format_long, format_float, format_double,
             format_signed, format_unsigned
    format_signed: (a boolean)
            Write signed integer data.
            flag: -signed
            mutually_exclusive: format_filetype, format_byte, format_short,
             format_int, format_long, format_float, format_double,
             format_signed, format_unsigned
    format_unsigned: (a boolean)
            Write unsigned integer data (default).
            flag: -unsigned
            mutually_exclusive: format_filetype, format_byte, format_short,
             format_int, format_long, format_float, format_double,
             format_signed, format_unsigned
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    max_buffer_size_in_kb: (an integer >= 0)
            Specify the maximum size of the internal buffers (in kbytes).
            flag: -max_buffer_size_in_kb %d
    no_check_dimensions: (a boolean)
            Do not check dimension info.
            flag: -nocheck_dimensions
            mutually_exclusive: check_dimensions, no_check_dimensions
    no_copy_header: (a boolean)
            Do not copy all of the header from the first file (default for many
            files)).
            flag: -nocopy_header
            mutually_exclusive: copy_header, no_copy_header
    nonormalize: (a boolean)
            Do not normalize data sets (default).
            flag: -nonormalize
            mutually_exclusive: normalize, nonormalize
    normalize: (a boolean)
            Normalize data sets for mean intensity.
            flag: -normalize
            mutually_exclusive: normalize, nonormalize
    output_file: (a file name)
            output file
            flag: %s, position: -1
    quiet: (a boolean)
            Do not print out log messages.
            flag: -quiet
            mutually_exclusive: verbose, quiet
    sdfile: (a file name)
            Specify an output sd file (default=none).
            flag: -sdfile %s
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    two: (a boolean)
            Create a MINC 2 output file.
            flag: -2
    verbose: (a boolean)
            Print out log messages (default).
            flag: -verbose
            mutually_exclusive: verbose, quiet
    voxel_range: (a tuple of the form: (an integer (int or long), an
             integer (int or long)))
            Valid range for output data.
            flag: -range %d %d
    weights: (a list of items which are a unicode string)
            Specify weights for averaging ("<w1>,<w2>,...").
            flag: -weights %s
    width_weighted: (a boolean)
            Weight by dimension widths when -avgdim is used.
            flag: -width_weighted
            requires: avgdim

Outputs:

    output_file: (an existing file name)
            output file

## BBox

Link to code

Wraps command mincbbox

Determine a bounding box of image.

### Examples

    >>> from nipype.interfaces.minc import BBox
    >>> from nipype.interfaces.minc.testdata import nonempty_minc_data

    >>> file0 = nonempty_minc_data(0)
    >>> bbox = BBox(input_file=file0)
    >>> bbox.run()

Inputs:

    [Mandatory]
    input_file: (an existing file name)
            input file
            flag: %s, position: -2

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    format_minccrop: (a boolean)
            Output format for minccrop: (-xlim x1 x2 -ylim y1 y2 -zlim z1 z2
            flag: -minccrop
    format_mincresample: (a boolean)
            Output format for mincresample: (-step x y z -start x y z -nelements
            x y z
            flag: -mincresample
    format_mincreshape: (a boolean)
            Output format for mincreshape: (-start x,y,z -count dx,dy,dz
            flag: -mincreshape
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    one_line: (a boolean)
            Output on one line (default): start_x y z width_x y z
            flag: -one_line
            mutually_exclusive: one_line, two_lines
    out_file: (a file name)
            flag: > %s, position: -1
    output_file: (a file name)
            output file containing bounding box corners
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    threshold: (an integer (int or long))
            VIO_Real value threshold for bounding box. Default value: 0.
            flag: -threshold
    two_lines: (a boolean)
            Output on two lines: start_x y z
             width_x y z
            flag: -two_lines
            mutually_exclusive: one_line, two_lines

Outputs:

    output_file: (an existing file name)
            output file containing bounding box corners

## Beast

Link to code

Wraps command mincbeast

Extract brain image using BEaST (Brain Extraction using non-local Segmentation Technique).

### Examples

    >>> from nipype.interfaces.minc import Beast
    >>> from nipype.interfaces.minc.testdata import nonempty_minc_data

    >>> file0 = nonempty_minc_data(0)
    >>> beast = Beast(input_file=file0)
    >>> beast .run()

Inputs:

    [Mandatory]
    input_file: (a file name)
            input file
            flag: %s, position: -2
    library_dir: (a directory name)
            library directory
            flag: %s, position: -3

    [Optional]
    abspath: (a boolean, nipype default value: True)
            File paths in the library are absolute (default is relative to
            library root).
            flag: -abspath
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    clobber: (a boolean, nipype default value: True)
            Overwrite existing file.
            flag: -clobber
    confidence_level_alpha: (a float)
            Specify confidence level Alpha. Default value: 0.5
            flag: -alpha %s
    configuration_file: (a file name)
            Specify configuration file.
            flag: -configuration %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    fill_holes: (a boolean)
            Fill holes in the binary output.
            flag: -fill
    flip_images: (a boolean)
            Flip images around the mid-sagittal plane to increase patch count.
            flag: -flip
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    load_moments: (a boolean)
            Do not calculate moments instead use precalculatedlibrary moments.
            (for optimization purposes)
            flag: -load_moments
    median_filter: (a boolean)
            Apply a median filter on the probability map.
            flag: -median
    nlm_filter: (a boolean)
            Apply an NLM filter on the probability map (experimental).
            flag: -nlm_filter
    number_selected_images: (an integer (int or long))
            Specify number of selected images. Default value: 20
            flag: -selection_num %s
    output_file: (a file name)
            output file
            flag: %s, position: -1
    patch_size: (an integer (int or long))
            Specify patch size for single scale approach. Default value: 1.
            flag: -patch_size %s
    probability_map: (a boolean)
            Output the probability map instead of crisp mask.
            flag: -probability
    same_resolution: (a boolean)
            Output final mask with the same resolution as input file.
            flag: -same_resolution
    search_area: (an integer (int or long))
            Specify size of search area for single scale approach. Default
            value: 2.
            flag: -search_area %s
    smoothness_factor_beta: (a float)
            Specify smoothness factor Beta. Default value: 0.25
            flag: -beta %s
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    threshold_patch_selection: (a float)
            Specify threshold for patch selection. Default value: 0.95
            flag: -threshold %s
    voxel_size: (an integer (int or long))
            Specify voxel size for calculations (4, 2, or 1).Default value: 4.
            Assumes no multiscale. Use configurationfile for multiscale.
            flag: -voxel_size %s

Outputs:

    output_file: (an existing file name)
            output mask file

## BestLinReg

Link to code

Wraps command bestlinreg

Hierachial linear fitting between two files.

The bestlinreg script is part of the EZminc package:

https://github.com/BIC-MNI/EZminc/blob/master/scripts/bestlinreg.pl

### Examples

    >>> from nipype.interfaces.minc import BestLinReg
    >>> from nipype.interfaces.minc.testdata import nonempty_minc_data

    >>> input_file = nonempty_minc_data(0)
    >>> target_file = nonempty_minc_data(1)
    >>> linreg = BestLinReg(source=input_file, target=target_file)
    >>> linreg.run()

Inputs:

    [Mandatory]
    source: (an existing file name)
            source Minc file
            flag: %s, position: -4
    target: (an existing file name)
            target Minc file
            flag: %s, position: -3

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    clobber: (a boolean, nipype default value: True)
            Overwrite existing file.
            flag: -clobber
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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
    output_mnc: (a file name)
            output mnc file
            flag: %s, position: -1
    output_xfm: (a file name)
            output xfm file
            flag: %s, position: -2
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    verbose: (a boolean)
            Print out log messages. Default: False.
            flag: -verbose

Outputs:

    output_mnc: (an existing file name)
            output mnc file
    output_xfm: (an existing file name)
            output xfm file

## BigAverage

Link to code

Wraps command mincbigaverage

Average 1000’s of MINC files in linear time.

mincbigaverage is designed to discretise the problem of averaging either a large number of input files or averaging a smaller number of large files. (>1GB each). There is also some code included to perform “robust” averaging in which only the most common features are kept via down-weighting outliers beyond a standard deviation.

One advantage of mincbigaverage is that it avoids issues around the number of possible open files in HDF/netCDF. In short if you have more than 100 files open at once while averaging things will slow down significantly.

mincbigaverage does this via a iterative approach to averaging files and is a direct drop in replacement for mincaverage. That said not all the arguments of mincaverage are supported in mincbigaverage but they should be.

This tool is part of the minc-widgets package:

https://github.com/BIC-MNI/minc-widgets/blob/master/mincbigaverage/mincbigaverage

### Examples

    >>> from nipype.interfaces.minc import BigAverage
    >>> from nipype.interfaces.minc.testdata import nonempty_minc_data

    >>> files = [nonempty_minc_data(i) for i in range(3)]
    >>> average = BigAverage(input_files=files, output_float=True, robust=True)
    >>> average.run()

Inputs:

    [Mandatory]
    input_files: (a list of items which are a file name)
            input file(s)
            flag: %s, position: -2

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    clobber: (a boolean, nipype default value: True)
            Overwrite existing file.
            flag: --clobber
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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
    output_file: (a file name)
            output file
            flag: %s, position: -1
    output_float: (a boolean)
            Output files with float precision.
            flag: --float
    robust: (a boolean)
            Perform robust averaging, features that are outside 1
            standarddeviation from the mean are downweighted. Works well for
            noisydata with artifacts. see the --tmpdir option if you have alarge
            number of input files.
            flag: -robust
    sd_file: (a file name)
            Place standard deviation image in specified file.
            flag: --sdfile %s
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    tmpdir: (a directory name)
            temporary files directory
            flag: -tmpdir %s
    verbose: (a boolean)
            Print out log messages. Default: False.
            flag: --verbose

Outputs:

    output_file: (an existing file name)
            output file
    sd_file: (an existing file name)
            standard deviation image

## Blob

Link to code

Wraps command mincblob

Calculate blobs from minc deformation grids.

### Examples

    >>> from nipype.interfaces.minc import Blob
    >>> from nipype.interfaces.minc.testdata import minc2Dfile

    >>> blob = Blob(input_file=minc2Dfile, output_file='/tmp/tmp.mnc', trace=True)
    >>> blob.run()

Inputs:

    [Mandatory]
    input_file: (an existing file name)
            input file to blob
            flag: %s, position: -2

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    determinant: (a boolean)
            compute the determinant (exact growth and shrinkage) -- SLOW
            flag: -determinant
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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
    magnitude: (a boolean)
            compute the magnitude of the displacement vector
            flag: -magnitude
    output_file: (a file name)
            output file
            flag: %s, position: -1
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    trace: (a boolean)
            compute the trace (approximate growth and shrinkage) -- FAST
            flag: -trace
    translation: (a boolean)
            compute translation (structure displacement)
            flag: -translation

Outputs:

    output_file: (an existing file name)
            output file

## Blur

Link to code

Wraps command mincblur

Convolve an input volume with a Gaussian blurring kernel of user-defined width. Optionally, the first partial derivatives and the gradient magnitude volume can be calculated.

### Examples

    >>> from nipype.interfaces.minc import Blur
    >>> from nipype.interfaces.minc.testdata import minc3Dfile

(1) Blur an input volume with a 6mm fwhm isotropic Gaussian blurring kernel:

    >>> blur = Blur(input_file=minc3Dfile, fwhm=6, output_file_base='/tmp/out_6')
    >>> blur.run()

mincblur will create /tmp/out_6_blur.mnc.

2. Calculate the blurred and gradient magnitude data:

    >>> blur = Blur(input_file=minc3Dfile, fwhm=6, gradient=True, output_file_base='/tmp/out_6')
    >>> blur.run()

will create /tmp/out_6_blur.mnc and /tmp/out_6_dxyz.mnc.

(3) Calculate the blurred data, the partial derivative volumes and the gradient magnitude for the same data:

    >>> blur = Blur(input_file=minc3Dfile, fwhm=6, partial=True, output_file_base='/tmp/out_6')
    >>> blur.run()

will create /tmp/out_6_blur.mnc, /tmp/out_6_dx.mnc, /tmp/out_6_dy.mnc, /tmp/out_6_dz.mnc and /tmp/out_6_dxyz.mnc.

Inputs:

    [Mandatory]
    fwhm: (a float)
            Full-width-half-maximum of gaussian kernel. Default value: 0.
            flag: -fwhm %s
            mutually_exclusive: fwhm, fwhm3d, standard_dev
    fwhm3d: (a tuple of the form: (a float, a float, a float))
            Full-width-half-maximum of gaussian kernel.Default value:
            -1.79769e+308 -1.79769e+308 -1.79769e+308.
            flag: -3dfwhm %s %s %s
            mutually_exclusive: fwhm, fwhm3d, standard_dev
    input_file: (an existing file name)
            input file
            flag: %s, position: -2
    standard_dev: (a float)
            Standard deviation of gaussian kernel. Default value: 0.
            flag: -standarddev %s
            mutually_exclusive: fwhm, fwhm3d, standard_dev

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    clobber: (a boolean, nipype default value: True)
            Overwrite existing file.
            flag: -clobber
    dimensions: (1 or 2 or 3)
            Number of dimensions to blur (either 1,2 or 3). Default value: 3.
            flag: -dimensions %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    gaussian: (a boolean)
            Use a gaussian smoothing kernel (default).
            flag: -gaussian
            mutually_exclusive: gaussian, rect
    gradient: (a boolean)
            Create the gradient magnitude volume as well.
            flag: -gradient
    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_apodize: (a boolean)
            Do not apodize the data before blurring.
            flag: -no_apodize
    output_file_base: (a file name)
            output file base
            flag: %s, position: -1
    partial: (a boolean)
            Create the partial derivative and gradient magnitude volumes as
            well.
            flag: -partial
    rect: (a boolean)
            Use a rect (box) smoothing kernel.
            flag: -rect
            mutually_exclusive: gaussian, rect
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    gradient_dxyz: (a file name)
            Gradient dxyz.
    output_file: (an existing file name)
            Blurred output file.
    partial_dx: (a file name)
            Partial gradient dx.
    partial_dxyz: (a file name)
            Partial gradient dxyz.
    partial_dy: (a file name)
            Partial gradient dy.
    partial_dz: (a file name)
            Partial gradient dz.

## Calc

Link to code

Wraps command minccalc

Compute an expression using MINC files as input.

### Examples

    >>> from nipype.interfaces.minc import Calc
    >>> from nipype.interfaces.minc.testdata import nonempty_minc_data

    >>> file0 = nonempty_minc_data(0)
    >>> file1 = nonempty_minc_data(1)
    >>> calc = Calc(input_files=[file0, file1], output_file='/tmp/calc.mnc', expression='A[0] + A[1]') # add files together
    >>> calc.run()

Inputs:

    [Mandatory]
    expfile: (a file name)
            Name of file containing expression.
            flag: -expfile %s
            mutually_exclusive: expression, expfile
    expression: (a unicode string)
            Expression to use in calculations.
            flag: -expression '%s'
            mutually_exclusive: expression, expfile
    filelist: (a file name)
            Specify the name of a file containing input file names.
            flag: -filelist %s
            mutually_exclusive: input_files, filelist
    input_files: (a list of items which are a file name)
            input file(s) for calculation
            flag: %s, position: -2

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    check_dimensions: (a boolean)
            Check that files have matching dimensions (default).
            flag: -check_dimensions
            mutually_exclusive: check_dimensions, no_check_dimensions
    clobber: (a boolean, nipype default value: True)
            Overwrite existing file.
            flag: -clobber
    copy_header: (a boolean)
            Copy all of the header from the first file.
            flag: -copy_header
            mutually_exclusive: copy_header, no_copy_header
    debug: (a boolean)
            Print out debugging messages.
            flag: -debug
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    eval_width: (an integer (int or long))
            Number of voxels to evaluate simultaneously.
            flag: -eval_width %s
    format_byte: (a boolean)
            Write out byte data.
            flag: -byte
            mutually_exclusive: format_filetype, format_byte, format_short,
             format_int, format_long, format_float, format_double,
             format_signed, format_unsigned
    format_double: (a boolean)
            Write out double-precision floating-point data.
            flag: -double
            mutually_exclusive: format_filetype, format_byte, format_short,
             format_int, format_long, format_float, format_double,
             format_signed, format_unsigned
    format_filetype: (a boolean)
            Use data type of first file (default).
            flag: -filetype
            mutually_exclusive: format_filetype, format_byte, format_short,
             format_int, format_long, format_float, format_double,
             format_signed, format_unsigned
    format_float: (a boolean)
            Write out single-precision floating-point data.
            flag: -float
            mutually_exclusive: format_filetype, format_byte, format_short,
             format_int, format_long, format_float, format_double,
             format_signed, format_unsigned
    format_int: (a boolean)
            Write out 32-bit integer data.
            flag: -int
            mutually_exclusive: format_filetype, format_byte, format_short,
             format_int, format_long, format_float, format_double,
             format_signed, format_unsigned
    format_long: (a boolean)
            Superseded by -int.
            flag: -long
            mutually_exclusive: format_filetype, format_byte, format_short,
             format_int, format_long, format_float, format_double,
             format_signed, format_unsigned
    format_short: (a boolean)
            Write out short integer data.
            flag: -short
            mutually_exclusive: format_filetype, format_byte, format_short,
             format_int, format_long, format_float, format_double,
             format_signed, format_unsigned
    format_signed: (a boolean)
            Write signed integer data.
            flag: -signed
            mutually_exclusive: format_filetype, format_byte, format_short,
             format_int, format_long, format_float, format_double,
             format_signed, format_unsigned
    format_unsigned: (a boolean)
            Write unsigned integer data (default).
            flag: -unsigned
            mutually_exclusive: format_filetype, format_byte, format_short,
             format_int, format_long, format_float, format_double,
             format_signed, format_unsigned
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    ignore_nan: (a boolean)
            Ignore invalid data (NaN) for accumulations.
            flag: -ignore_nan
    max_buffer_size_in_kb: (an integer >= 0)
            Specify the maximum size of the internal buffers (in kbytes).
            flag: -max_buffer_size_in_kb %d
    no_check_dimensions: (a boolean)
            Do not check that files have matching dimensions.
            flag: -nocheck_dimensions
            mutually_exclusive: check_dimensions, no_check_dimensions
    no_copy_header: (a boolean)
            Do not copy all of the header from the first file.
            flag: -nocopy_header
            mutually_exclusive: copy_header, no_copy_header
    outfiles: (a list of items which are a tuple of the form: (a unicode
             string, a file name))
    output_file: (a file name)
            output file
            flag: %s, position: -1
    output_illegal: (a boolean)
            Value to write out when an illegal operation is done. Default value:
            1.79769e+308
            flag: -illegal_value
            mutually_exclusive: output_nan, output_zero, output_illegal_value
    output_nan: (a boolean)
            Output NaN when an illegal operation is done (default).
            flag: -nan
            mutually_exclusive: output_nan, output_zero, output_illegal_value
    output_zero: (a boolean)
            Output zero when an illegal operation is done.
            flag: -zero
            mutually_exclusive: output_nan, output_zero, output_illegal_value
    propagate_nan: (a boolean)
            Invalid data in any file at a voxel produces a NaN (default).
            flag: -propagate_nan
    quiet: (a boolean)
            Do not print out log messages.
            flag: -quiet
            mutually_exclusive: verbose, quiet
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    two: (a boolean)
            Create a MINC 2 output file.
            flag: -2
    verbose: (a boolean)
            Print out log messages (default).
            flag: -verbose
            mutually_exclusive: verbose, quiet
    voxel_range: (a tuple of the form: (an integer (int or long), an
             integer (int or long)))
            Valid range for output data.
            flag: -range %d %d

Outputs:

    output_file: (an existing file name)
            output file

## Convert

Link to code

Wraps command mincconvert

convert between MINC 1 to MINC 2 format.

### Examples

    >>> from nipype.interfaces.minc import Convert
    >>> from nipype.interfaces.minc.testdata import minc2Dfile
    >>> c = Convert(input_file=minc2Dfile, output_file='/tmp/out.mnc', two=True) # Convert to MINC2 format.
    >>> c.run()

Inputs:

    [Mandatory]
    input_file: (an existing file name)
            input file for converting
            flag: %s, position: -2

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    chunk: (an integer >= 0)
            Set the target block size for chunking (0 default, >1 block size).
            flag: -chunk %d
    clobber: (a boolean, nipype default value: True)
            Overwrite existing file.
            flag: -clobber
    compression: (0 or 1 or 2 or 3 or 4 or 5 or 6 or 7 or 8 or 9)
            Set the compression level, from 0 (disabled) to 9 (maximum).
            flag: -compress %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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
    output_file: (a file name)
            output file
            flag: %s, position: -1
    template: (a boolean)
            Create a template file. The dimensions, variables, andattributes of
            the input file are preserved but all data it set to zero.
            flag: -template
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    two: (a boolean)
            Create a MINC 2 output file.
            flag: -2

Outputs:

    output_file: (an existing file name)
            output file

## Copy

Link to code

Wraps command minccopy

Copy image values from one MINC file to another. Both the input and output files must exist, and the images in both files must have an equal number dimensions and equal dimension lengths.

NOTE: This program is intended primarily for use with scripts such as mincedit. It does not follow the typical design rules of most MINC command-line tools and therefore should be used only with caution.

Inputs:

    [Mandatory]
    input_file: (an existing file name)
            input file to copy
            flag: %s, position: -2

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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
    output_file: (a file name)
            output file
            flag: %s, position: -1
    pixel_values: (a boolean)
            Copy pixel values as is.
            flag: -pixel_values
            mutually_exclusive: pixel_values, real_values
    real_values: (a boolean)
            Copy real pixel intensities (default).
            flag: -real_values
            mutually_exclusive: pixel_values, real_values
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    output_file: (an existing file name)
            output file

## Dump

Link to code

Wraps command mincdump

Dump a MINC file. Typically used in conjunction with mincgen (see Gen).

### Examples

    >>> from nipype.interfaces.minc import Dump
    >>> from nipype.interfaces.minc.testdata import minc2Dfile

    >>> dump = Dump(input_file=minc2Dfile)
    >>> dump.run()

    >>> dump = Dump(input_file=minc2Dfile, output_file='/tmp/out.txt', precision=(3, 4))
    >>> dump.run()

Inputs:

    [Mandatory]
    input_file: (an existing file name)
            input file
            flag: %s, position: -2

    [Optional]
    annotations_brief: (u'c' or u'f')
            Brief annotations for C or Fortran indices in data.
            flag: -b %s
            mutually_exclusive: annotations_brief, annotations_full
    annotations_full: (u'c' or u'f')
            Full annotations for C or Fortran indices in data.
            flag: -f %s
            mutually_exclusive: annotations_brief, annotations_full
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    coordinate_data: (a boolean)
            Coordinate variable data and header information.
            flag: -c
            mutually_exclusive: coordinate_data, header_data
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    header_data: (a boolean)
            Header information only, no data.
            flag: -h
            mutually_exclusive: coordinate_data, header_data
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    line_length: (an integer >= 0)
            Line length maximum in data section (default 80).
            flag: -l %d
    netcdf_name: (a unicode string)
            Name for netCDF (default derived from file name).
            flag: -n %s
    out_file: (a file name)
            flag: > %s, position: -1
    output_file: (a file name)
            output file
    precision: (an integer (int or long) or a tuple of the form: (an
             integer (int or long), an integer (int or long)))
            Display floating-point values with less precision
            flag: %s
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    variables: (a list of items which are a unicode string)
            Output data for specified variables only.
            flag: -v %s

Outputs:

    output_file: (an existing file name)
            output file

## Extract

Link to code

Wraps command mincextract

Dump a hyperslab of MINC file data.

### Examples

    >>> from nipype.interfaces.minc import Extract
    >>> from nipype.interfaces.minc.testdata import minc2Dfile

    >>> extract = Extract(input_file=minc2Dfile)
    >>> extract.run()

    >>> extract = Extract(input_file=minc2Dfile, start=[3, 10, 5], count=[4, 4, 4]) # extract a 4x4x4 slab at offset [3, 10, 5]
    >>> extract.run()

Inputs:

    [Mandatory]
    input_file: (an existing file name)
            input file
            flag: %s, position: -2

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    count: (a list of items which are an integer (int or long))
            Specifies edge lengths of hyperslab to read.
            flag: -count %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    flip_any_direction: (a boolean)
            Do not flip images (Default).
            flag: -any_direction
            mutually_exclusive: flip_positive_direction,
             flip_negative_direction, flip_any_direction
    flip_negative_direction: (a boolean)
            Flip images to always have negative direction.
            flag: -negative_direction
            mutually_exclusive: flip_positive_direction,
             flip_negative_direction, flip_any_direction
    flip_positive_direction: (a boolean)
            Flip images to always have positive direction.
            flag: -positive_direction
            mutually_exclusive: flip_positive_direction,
             flip_negative_direction, flip_any_direction
    flip_x_any: (a boolean)
            Don't flip images along x-axis (default).
            flag: -xanydirection
            mutually_exclusive: flip_x_positive, flip_x_negative, flip_x_any
    flip_x_negative: (a boolean)
            Flip images to give negative xspace:step value (right-to-left).
            flag: -xdirection
            mutually_exclusive: flip_x_positive, flip_x_negative, flip_x_any
    flip_x_positive: (a boolean)
            Flip images to give positive xspace:step value (left-to-right).
            flag: +xdirection
            mutually_exclusive: flip_x_positive, flip_x_negative, flip_x_any
    flip_y_any: (a boolean)
            Don't flip images along y-axis (default).
            flag: -yanydirection
            mutually_exclusive: flip_y_positive, flip_y_negative, flip_y_any
    flip_y_negative: (a boolean)
            Flip images to give negative yspace:step value (ant-to-post).
            flag: -ydirection
            mutually_exclusive: flip_y_positive, flip_y_negative, flip_y_any
    flip_y_positive: (a boolean)
            Flip images to give positive yspace:step value (post-to-ant).
            flag: +ydirection
            mutually_exclusive: flip_y_positive, flip_y_negative, flip_y_any
    flip_z_any: (a boolean)
            Don't flip images along z-axis (default).
            flag: -zanydirection
            mutually_exclusive: flip_z_positive, flip_z_negative, flip_z_any
    flip_z_negative: (a boolean)
            Flip images to give negative zspace:step value (sup-to-inf).
            flag: -zdirection
            mutually_exclusive: flip_z_positive, flip_z_negative, flip_z_any
    flip_z_positive: (a boolean)
            Flip images to give positive zspace:step value (inf-to-sup).
            flag: +zdirection
            mutually_exclusive: flip_z_positive, flip_z_negative, flip_z_any
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    image_maximum: (a float)
            Specify the maximum real image value for normalization.Default
            value: 1.79769e+308.
            flag: -image_maximum %s
    image_minimum: (a float)
            Specify the minimum real image value for normalization.Default
            value: 1.79769e+308.
            flag: -image_minimum %s
    image_range: (a tuple of the form: (a float, a float))
            Specify the range of real image values for normalization.
            flag: -image_range %s %s
    nonormalize: (a boolean)
            Turn off pixel normalization.
            flag: -nonormalize
            mutually_exclusive: normalize, nonormalize
    normalize: (a boolean)
            Normalize integer pixel values to file max and min.
            flag: -normalize
            mutually_exclusive: normalize, nonormalize
    out_file: (a file name)
            flag: > %s, position: -1
    output_file: (a file name)
            output file
    start: (a list of items which are an integer (int or long))
            Specifies corner of hyperslab (C conventions for indices).
            flag: -start %s
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    write_ascii: (a boolean)
            Write out data as ascii strings (default).
            flag: -ascii
            mutually_exclusive: write_ascii, write_ascii, write_byte,
             write_short, write_int, write_long, write_float, write_double,
             write_signed, write_unsigned
    write_byte: (a boolean)
            Write out data as bytes.
            flag: -byte
            mutually_exclusive: write_ascii, write_ascii, write_byte,
             write_short, write_int, write_long, write_float, write_double,
             write_signed, write_unsigned
    write_double: (a boolean)
            Write out data as double precision floating-point values.
            flag: -double
            mutually_exclusive: write_ascii, write_ascii, write_byte,
             write_short, write_int, write_long, write_float, write_double,
             write_signed, write_unsigned
    write_float: (a boolean)
            Write out data as single precision floating-point values.
            flag: -float
            mutually_exclusive: write_ascii, write_ascii, write_byte,
             write_short, write_int, write_long, write_float, write_double,
             write_signed, write_unsigned
    write_int: (a boolean)
            Write out data as 32-bit integers.
            flag: -int
            mutually_exclusive: write_ascii, write_ascii, write_byte,
             write_short, write_int, write_long, write_float, write_double,
             write_signed, write_unsigned
    write_long: (a boolean)
            Superseded by write_int.
            flag: -long
            mutually_exclusive: write_ascii, write_ascii, write_byte,
             write_short, write_int, write_long, write_float, write_double,
             write_signed, write_unsigned
    write_range: (a tuple of the form: (a float, a float))
            Specify the range of output values
            Default value: 1.79769e+308 1.79769e+308.
            flag: -range %s %s
    write_short: (a boolean)
            Write out data as short integers.
            flag: -short
            mutually_exclusive: write_ascii, write_ascii, write_byte,
             write_short, write_int, write_long, write_float, write_double,
             write_signed, write_unsigned
    write_signed: (a boolean)
            Write out signed data.
            flag: -signed
            mutually_exclusive: write_signed, write_unsigned
    write_unsigned: (a boolean)
            Write out unsigned data.
            flag: -unsigned
            mutually_exclusive: write_signed, write_unsigned

Outputs:

    output_file: (an existing file name)
            output file in raw/text format

## Gennlxfm

Link to code

Wraps command gennlxfm

Generate nonlinear xfms. Currently only identity xfms are supported!

This tool is part of minc-widgets:

https://github.com/BIC-MNI/minc-widgets/blob/master/gennlxfm/gennlxfm

### Examples

    >>> from nipype.interfaces.minc import Gennlxfm
    >>> from nipype.interfaces.minc.testdata import minc2Dfile
    >>> gennlxfm = Gennlxfm(step=1, like=minc2Dfile)
    >>> gennlxfm.run()

Inputs:

    [Mandatory]

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    clobber: (a boolean, nipype default value: True)
            Overwrite existing file.
            flag: -clobber
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    ident: (a boolean)
            Generate an identity xfm. Default: False.
            flag: -ident
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    like: (an existing file name)
            Generate a nlxfm like this file.
            flag: -like %s
    output_file: (a file name)
            output file
            flag: %s, position: -1
    step: (an integer (int or long))
            Output ident xfm step [default: 1].
            flag: -step %s
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    verbose: (a boolean)
            Print out log messages. Default: False.
            flag: -verbose

Outputs:

    output_file: (an existing file name)
            output file
    output_grid: (an existing file name)
            output grid

## Math

Link to code

Wraps command mincmath

Various mathematical operations supplied by mincmath.

### Examples

    >>> from nipype.interfaces.minc import Math
    >>> from nipype.interfaces.minc.testdata import minc2Dfile

Scale: volume*3.0 + 2:

    >>> scale = Math(input_files=[minc2Dfile], scale=(3.0, 2))
    >>> scale.run()

Test if >= 1.5:

    >>> gt = Math(input_files=[minc2Dfile], test_gt=1.5)
    >>> gt.run()

Inputs:

    [Mandatory]
    filelist: (a file name)
            Specify the name of a file containing input file names.
            flag: -filelist %s
            mutually_exclusive: input_files, filelist
    input_files: (a list of items which are a file name)
            input file(s) for calculation
            flag: %s, position: -2
            mutually_exclusive: input_files, filelist

    [Optional]
    abs: (a boolean)
            Take absolute value of a volume.
            flag: -abs
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    calc_add: (a boolean or a float)
            Add N volumes or volume + constant.
            flag: -add
    calc_and: (a boolean)
            Calculate vol1 && vol2 (&& ...).
            flag: -and
    calc_div: (a boolean or a float)
            Divide 2 volumes or volume / constant.
            flag: -div
    calc_mul: (a boolean or a float)
            Multiply N volumes or volume * constant.
            flag: -mult
    calc_not: (a boolean)
            Calculate !vol1.
            flag: -not
    calc_or: (a boolean)
            Calculate vol1 || vol2 (|| ...).
            flag: -or
    calc_sub: (a boolean or a float)
            Subtract 2 volumes or volume - constant.
            flag: -sub
    check_dimensions: (a boolean)
            Check that dimension info matches across files (default).
            flag: -check_dimensions
            mutually_exclusive: check_dimensions, no_check_dimensions
    clamp: (a tuple of the form: (a float, a float))
            Clamp a volume to lie between two values.
            flag: -clamp -const2 %s %s
    clobber: (a boolean, nipype default value: True)
            Overwrite existing file.
            flag: -clobber
    copy_header: (a boolean)
            Copy all of the header from the first file (default for one file).
            flag: -copy_header
            mutually_exclusive: copy_header, no_copy_header
    count_valid: (a boolean)
            Count the number of valid values in N volumes.
            flag: -count_valid
    dimension: (a unicode string)
            Specify a dimension along which we wish to perform a calculation.
            flag: -dimension %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    exp: (a tuple of the form: (a float, a float))
            Calculate c2*exp(c1*x). Both constants must be specified.
            flag: -exp -const2 %s %s
    format_byte: (a boolean)
            Write out byte data.
            flag: -byte
            mutually_exclusive: format_filetype, format_byte, format_short,
             format_int, format_long, format_float, format_double,
             format_signed, format_unsigned
    format_double: (a boolean)
            Write out double-precision floating-point data.
            flag: -double
            mutually_exclusive: format_filetype, format_byte, format_short,
             format_int, format_long, format_float, format_double,
             format_signed, format_unsigned
    format_filetype: (a boolean)
            Use data type of first file (default).
            flag: -filetype
            mutually_exclusive: format_filetype, format_byte, format_short,
             format_int, format_long, format_float, format_double,
             format_signed, format_unsigned
    format_float: (a boolean)
            Write out single-precision floating-point data.
            flag: -float
            mutually_exclusive: format_filetype, format_byte, format_short,
             format_int, format_long, format_float, format_double,
             format_signed, format_unsigned
    format_int: (a boolean)
            Write out 32-bit integer data.
            flag: -int
            mutually_exclusive: format_filetype, format_byte, format_short,
             format_int, format_long, format_float, format_double,
             format_signed, format_unsigned
    format_long: (a boolean)
            Superseded by -int.
            flag: -long
            mutually_exclusive: format_filetype, format_byte, format_short,
             format_int, format_long, format_float, format_double,
             format_signed, format_unsigned
    format_short: (a boolean)
            Write out short integer data.
            flag: -short
            mutually_exclusive: format_filetype, format_byte, format_short,
             format_int, format_long, format_float, format_double,
             format_signed, format_unsigned
    format_signed: (a boolean)
            Write signed integer data.
            flag: -signed
            mutually_exclusive: format_filetype, format_byte, format_short,
             format_int, format_long, format_float, format_double,
             format_signed, format_unsigned
    format_unsigned: (a boolean)
            Write unsigned integer data (default).
            flag: -unsigned
            mutually_exclusive: format_filetype, format_byte, format_short,
             format_int, format_long, format_float, format_double,
             format_signed, format_unsigned
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    ignore_nan: (a boolean)
            Ignore invalid data (NaN) for accumulations.
            flag: -ignore_nan
    invert: (a float)
            Calculate 1/c.
            flag: -invert -const %s
    isnan: (a boolean)
            Test for NaN values in vol1.
            flag: -isnan
    log: (a tuple of the form: (a float, a float))
            Calculate log(x/c2)/c1. The constants c1 and c2 default to 1.
            flag: -log -const2 %s %s
    max_buffer_size_in_kb: (an integer >= 0)
            Specify the maximum size of the internal buffers (in kbytes).
            flag: -max_buffer_size_in_kb %d
    maximum: (a boolean)
            Find maximum of N volumes.
            flag: -maximum
    minimum: (a boolean)
            Find minimum of N volumes.
            flag: -minimum
    nisnan: (a boolean)
            Negation of -isnan.
            flag: -nisnan
    no_check_dimensions: (a boolean)
            Do not check dimension info.
            flag: -nocheck_dimensions
            mutually_exclusive: check_dimensions, no_check_dimensions
    no_copy_header: (a boolean)
            Do not copy all of the header from the first file (default for many
            files)).
            flag: -nocopy_header
            mutually_exclusive: copy_header, no_copy_header
    nsegment: (a tuple of the form: (a float, a float))
            Opposite of -segment: within range = 0, outside range = 1.
            flag: -nsegment -const2 %s %s
    output_file: (a file name)
            output file
            flag: %s, position: -1
    output_illegal: (a boolean)
            Value to write out when an illegal operationis done. Default value:
            1.79769e+308
            flag: -illegal_value
            mutually_exclusive: output_nan, output_zero, output_illegal_value
    output_nan: (a boolean)
            Output NaN when an illegal operation is done (default).
            flag: -nan
            mutually_exclusive: output_nan, output_zero, output_illegal_value
    output_zero: (a boolean)
            Output zero when an illegal operation is done.
            flag: -zero
            mutually_exclusive: output_nan, output_zero, output_illegal_value
    percentdiff: (a float)
            Percent difference between 2 volumes, thresholded (const def=0.0).
            flag: -percentdiff
    propagate_nan: (a boolean)
            Invalid data in any file at a voxel produces a NaN (default).
            flag: -propagate_nan
    scale: (a tuple of the form: (a float, a float))
            Scale a volume: volume * c1 + c2.
            flag: -scale -const2 %s %s
    segment: (a tuple of the form: (a float, a float))
            Segment a volume using range of -const2: within range = 1, outside
            range = 0.
            flag: -segment -const2 %s %s
    sqrt: (a boolean)
            Take square root of a volume.
            flag: -sqrt
    square: (a boolean)
            Take square of a volume.
            flag: -square
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    test_eq: (a boolean or a float)
            Test for integer vol1 == vol2 or vol1 == constant.
            flag: -eq
    test_ge: (a boolean or a float)
            Test for vol1 >= vol2 or vol1 >= const.
            flag: -ge
    test_gt: (a boolean or a float)
            Test for vol1 > vol2 or vol1 > constant.
            flag: -gt
    test_le: (a boolean or a float)
            Test for vol1 <= vol2 or vol1 <= const.
            flag: -le
    test_lt: (a boolean or a float)
            Test for vol1 < vol2 or vol1 < constant.
            flag: -lt
    test_ne: (a boolean or a float)
            Test for integer vol1 != vol2 or vol1 != const.
            flag: -ne
    two: (a boolean)
            Create a MINC 2 output file.
            flag: -2
    voxel_range: (a tuple of the form: (an integer (int or long), an
             integer (int or long)))
            Valid range for output data.
            flag: -range %d %d

Outputs:

    output_file: (an existing file name)
            output file

## NlpFit

Link to code

Wraps command nlpfit

Hierarchial non-linear fitting with bluring.

This tool is part of the minc-widgets package:

https://github.com/BIC-MNI/minc-widgets/blob/master/nlpfit/nlpfit

### Examples

    >>> from nipype.interfaces.minc import NlpFit
    >>> from nipype.interfaces.minc.testdata import nonempty_minc_data, nlp_config
    >>> from nipype.testing import example_data

    >>> source = nonempty_minc_data(0)
    >>> target = nonempty_minc_data(1)
    >>> source_mask = nonempty_minc_data(2)
    >>> config = nlp_config
    >>> initial = example_data('minc_initial.xfm')
    >>> nlpfit = NlpFit(config_file=config, init_xfm=initial, source_mask=source_mask, source=source, target=target)
    >>> nlpfit.run()

Inputs:

    [Mandatory]
    config_file: (an existing file name)
            File containing the fitting configuration use.
            flag: -config_file %s
    init_xfm: (an existing file name)
            Initial transformation (default identity).
            flag: -init_xfm %s
    source: (an existing file name)
            source Minc file
            flag: %s, position: -3
    source_mask: (an existing file name)
            Source mask to use during fitting.
            flag: -source_mask %s
    target: (an existing file name)
            target Minc file
            flag: %s, position: -2

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    clobber: (a boolean, nipype default value: True)
            Overwrite existing file.
            flag: -clobber
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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
    input_grid_files: (a list of items which are a file name)
            input grid file(s)
    output_xfm: (a file name)
            output xfm file
            flag: %s, position: -1
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    verbose: (a boolean)
            Print out log messages. Default: False.
            flag: -verbose

Outputs:

    output_grid: (an existing file name)
            output grid file
    output_xfm: (an existing file name)
            output xfm file

## Norm

Link to code

Wraps command mincnorm

Normalise a file between a max and minimum (possibly)
  using two histogram pct’s.

### Examples

    >>> from nipype.interfaces.minc import Norm
    >>> from nipype.interfaces.minc.testdata import minc2Dfile
    >>> n = Norm(input_file=minc2Dfile, output_file='/tmp/out.mnc') # Normalise the file.
    >>> n.run()

Inputs:

    [Mandatory]
    input_file: (an existing file name)
            input file to normalise
            flag: %s, position: -2

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    clamp: (a boolean, nipype default value: True)
            Force the ouput range between limits [default].
            flag: -clamp
    clobber: (a boolean, nipype default value: True)
            Overwrite existing file.
            flag: -clobber
    cutoff: (0.0 <= a floating point number <= 100.0)
            Cutoff value to use to calculate thresholds by a histogram PcT in %.
            [default: 0.01]
            flag: -cutoff %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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
    lower: (a float)
            Lower real value to use.
            flag: -lower %s
    mask: (a file name)
            Calculate the image normalisation within a mask.
            flag: -mask %s
    out_ceil: (a float)
            Output files minimum [default: 100]
            flag: -out_ceil %s
    out_floor: (a float)
            Output files maximum [default: 0]
            flag: -out_floor %s
    output_file: (a file name)
            output file
            flag: %s, position: -1
    output_threshold_mask: (a file name)
            File in which to store the threshold mask.
            flag: -threshold_mask %s
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    threshold: (a boolean)
            Threshold the image (set values below threshold_perc to -out_floor).
            flag: -threshold
    threshold_blur: (a float)
            Blur FWHM for intensity edges then thresholding [default: 2].
            flag: -threshold_blur %s
    threshold_bmt: (a boolean)
            Use the resulting image BiModalT as the threshold.
            flag: -threshold_bmt
    threshold_perc: (0.0 <= a floating point number <= 100.0)
            Threshold percentage (0.1 == lower 10% of intensity range) [default:
            0.1].
            flag: -threshold_perc %s
    upper: (a float)
            Upper real value to use.
            flag: -upper %s

Outputs:

    output_file: (an existing file name)
            output file
    output_threshold_mask: (a file name)
            threshold mask file

## Pik

Link to code

Wraps command mincpik

Generate images from minc files.

Mincpik uses Imagemagick to generate images from Minc files.

### Examples

    >>> from nipype.interfaces.minc import Pik
    >>> from nipype.interfaces.minc.testdata import nonempty_minc_data

    >>> file0 = nonempty_minc_data(0)
    >>> pik = Pik(input_file=file0, title='foo')
    >>> pik .run()

Inputs:

    [Mandatory]
    input_file: (an existing file name)
            input file
            flag: %s, position: -2

    [Optional]
    annotated_bar: (a boolean)
            create an annotated bar to match the image (use height of the output
            image)
            flag: --anot_bar
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    auto_range: (a boolean)
            Automatically determine image range using a 5 and 95% PcT.
            (histogram)
            flag: --auto_range
            mutually_exclusive: image_range, auto_range
    clobber: (a boolean, nipype default value: True)
            Overwrite existing file.
            flag: -clobber
    depth: (8 or 16)
            Bitdepth for resulting image 8 or 16 (MSB machines only!)
            flag: --depth %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    horizontal_triplanar_view: (a boolean)
            Create a horizontal triplanar view.
            flag: --horizontal
            mutually_exclusive: vertical_triplanar_view,
             horizontal_triplanar_view
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    image_range: (a tuple of the form: (a float, a float))
            Range of image values to use for pixel intensity.
            flag: --image_range %s %s
            mutually_exclusive: image_range, auto_range
    jpg: (a boolean)
            Output a jpg file.
            mutually_exclusive: jpg, png
    lookup: (a unicode string)
            Arguments to pass to minclookup
            flag: --lookup %s
    minc_range: (a tuple of the form: (a float, a float))
            Valid range of values for MINC file.
            flag: --range %s %s
    output_file: (a file name)
            output file
            flag: %s, position: -1
    png: (a boolean)
            Output a png file (default).
            mutually_exclusive: jpg, png
    sagittal_offset: (an integer (int or long))
            Offset the sagittal slice from the centre.
            flag: --sagittal_offset %s
    sagittal_offset_perc: (0 <= an integer <= 100)
            Offset the sagittal slice by a percentage from the centre.
            flag: --sagittal_offset_perc %d
    scale: (an integer (int or long))
            Scaling factor for resulting image. By default images areoutput at
            twice their original resolution.
            flag: --scale %s
    slice_x: (a boolean)
            Get a sagittal (x) slice.
            flag: -x
            mutually_exclusive: slice_z, slice_y, slice_x
    slice_y: (a boolean)
            Get a coronal (y) slice.
            flag: -y
            mutually_exclusive: slice_z, slice_y, slice_x
    slice_z: (a boolean)
            Get an axial/transverse (z) slice.
            flag: -z
            mutually_exclusive: slice_z, slice_y, slice_x
    start: (an integer (int or long))
            Slice number to get. (note this is in voxel co-ordinates).
            flag: --slice %s
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    tile_size: (an integer (int or long))
            Pixel size for each image in a triplanar.
            flag: --tilesize %s
    title: (a boolean or a unicode string)
            flag: %s
    title_size: (an integer (int or long))
            Font point size for the title.
            flag: --title_size %s
            requires: title
    triplanar: (a boolean)
            Create a triplanar view of the input file.
            flag: --triplanar
    vertical_triplanar_view: (a boolean)
            Create a vertical triplanar view (Default).
            flag: --vertical
            mutually_exclusive: vertical_triplanar_view,
             horizontal_triplanar_view
    width: (an integer (int or long))
            Autoscale the resulting image to have a fixed image width (in
            pixels).
            flag: --width %s

Outputs:

    output_file: (an existing file name)
            output image

## Resample

Link to code

Wraps command mincresample

Resample a minc file.’

### Examples

    >>> from nipype.interfaces.minc import Resample
    >>> from nipype.interfaces.minc.testdata import minc2Dfile
    >>> r = Resample(input_file=minc2Dfile, output_file='/tmp/out.mnc') # Resample the file.
    >>> r.run()

Inputs:

    [Mandatory]
    input_file: (an existing file name)
            input file for resampling
            flag: %s, position: -2

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    clobber: (a boolean, nipype default value: True)
            Overwrite existing file.
            flag: -clobber
    coronal_slices: (a boolean)
            Write out coronal slices
            flag: -coronal
            mutually_exclusive: transverse, sagittal, coronal
    dircos: (a tuple of the form: (a float, a float, a float))
            Direction cosines along each dimension (X, Y, Z). Default
            value:1.79769e+308 1.79769e+308 1.79769e+308 1.79769e+308 ...
            1.79769e+308 1.79769e+308 1.79769e+308 1.79769e+308 1.79769e+308.
            flag: -dircos %s %s %s
            mutually_exclusive: nelements, nelements_x_y_or_z
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    fill: (a boolean)
            Use a fill value for points outside of input volume.
            flag: -fill
            mutually_exclusive: nofill, fill
    fill_value: (a float)
            Specify a fill value for points outside of input volume.Default
            value: 1.79769e+308.
            flag: -fillvalue %s
            requires: fill
    format_byte: (a boolean)
            Write out byte data.
            flag: -byte
            mutually_exclusive: format_byte, format_short, format_int,
             format_long, format_float, format_double, format_signed,
             format_unsigned
    format_double: (a boolean)
            Write out double-precision floating-point data.
            flag: -double
            mutually_exclusive: format_byte, format_short, format_int,
             format_long, format_float, format_double, format_signed,
             format_unsigned
    format_float: (a boolean)
            Write out single-precision floating-point data.
            flag: -float
            mutually_exclusive: format_byte, format_short, format_int,
             format_long, format_float, format_double, format_signed,
             format_unsigned
    format_int: (a boolean)
            Write out 32-bit integer data.
            flag: -int
            mutually_exclusive: format_byte, format_short, format_int,
             format_long, format_float, format_double, format_signed,
             format_unsigned
    format_long: (a boolean)
            Superseded by -int.
            flag: -long
            mutually_exclusive: format_byte, format_short, format_int,
             format_long, format_float, format_double, format_signed,
             format_unsigned
    format_short: (a boolean)
            Write out short integer data.
            flag: -short
            mutually_exclusive: format_byte, format_short, format_int,
             format_long, format_float, format_double, format_signed,
             format_unsigned
    format_signed: (a boolean)
            Write signed integer data.
            flag: -signed
            mutually_exclusive: format_byte, format_short, format_int,
             format_long, format_float, format_double, format_signed,
             format_unsigned
    format_unsigned: (a boolean)
            Write unsigned integer data (default).
            flag: -unsigned
            mutually_exclusive: format_byte, format_short, format_int,
             format_long, format_float, format_double, format_signed,
             format_unsigned
    half_width_sinc_window: (5 or 1 or 2 or 3 or 4 or 6 or 7 or 8 or 9 or
             10)
            Set half-width of sinc window (1-10). Default value: 5.
            flag: -width %s
            requires: sinc_interpolation
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    input_grid_files: (a list of items which are a file name)
            input grid file(s)
    invert_transformation: (a boolean)
            Invert the transformation before using it.
            flag: -invert_transformation
    keep_real_range: (a boolean)
            Keep the real scale of the input volume.
            flag: -keep_real_range
            mutually_exclusive: keep_real_range, nokeep_real_range
    like: (a file name)
            Specifies a model file for the resampling.
            flag: -like %s
    nearest_neighbour_interpolation: (a boolean)
            Do nearest neighbour interpolation.
            flag: -nearest_neighbour
            mutually_exclusive: trilinear_interpolation, tricubic_interpolation,
             nearest_neighbour_interpolation, sinc_interpolation
    nelements: (a tuple of the form: (an integer (int or long), an
             integer (int or long), an integer (int or long)))
            Number of elements along each dimension (X, Y, Z).
            flag: -nelements %s %s %s
            mutually_exclusive: nelements, nelements_x_y_or_z
    no_fill: (a boolean)
            Use value zero for points outside of input volume.
            flag: -nofill
            mutually_exclusive: nofill, fill
    no_input_sampling: (a boolean)
            Use the input sampling without transforming (old behaviour).
            flag: -use_input_sampling
            mutually_exclusive: vio_transform, no_input_sampling
    nokeep_real_range: (a boolean)
            Do not keep the real scale of the data (default).
            flag: -nokeep_real_range
            mutually_exclusive: keep_real_range, nokeep_real_range
    origin: (a tuple of the form: (a float, a float, a float))
            Origin of first pixel in 3D space.Default value: 1.79769e+308
            1.79769e+308 1.79769e+308.
            flag: -origin %s %s %s
    output_file: (a file name)
            output file
            flag: %s, position: -1
    output_range: (a tuple of the form: (a float, a float))
            Valid range for output data. Default value: -1.79769e+308
            -1.79769e+308.
            flag: -range %s %s
    sagittal_slices: (a boolean)
            Write out sagittal slices
            flag: -sagittal
            mutually_exclusive: transverse, sagittal, coronal
    sinc_interpolation: (a boolean)
            Do windowed sinc interpolation.
            flag: -sinc
            mutually_exclusive: trilinear_interpolation, tricubic_interpolation,
             nearest_neighbour_interpolation, sinc_interpolation
    sinc_window_hamming: (a boolean)
            Set sinc window type to Hamming.
            flag: -hamming
            mutually_exclusive: sinc_window_hanning, sinc_window_hamming
            requires: sinc_interpolation
    sinc_window_hanning: (a boolean)
            Set sinc window type to Hanning.
            flag: -hanning
            mutually_exclusive: sinc_window_hanning, sinc_window_hamming
            requires: sinc_interpolation
    spacetype: (a unicode string)
            Set the spacetype attribute to a specified string.
            flag: -spacetype %s
    standard_sampling: (a boolean)
            Set the sampling to standard values (step, start and dircos).
            flag: -standard_sampling
    start: (a tuple of the form: (a float, a float, a float))
            Start point along each dimension (X, Y, Z).Default value:
            1.79769e+308 1.79769e+308 1.79769e+308.
            flag: -start %s %s %s
            mutually_exclusive: nelements, nelements_x_y_or_z
    step: (a tuple of the form: (an integer (int or long), an integer
             (int or long), an integer (int or long)))
            Step size along each dimension (X, Y, Z). Default value: (0, 0, 0).
            flag: -step %s %s %s
            mutually_exclusive: nelements, nelements_x_y_or_z
    talairach: (a boolean)
            Output is in Talairach space.
            flag: -talairach
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    transformation: (a file name)
            File giving world transformation. (Default = identity).
            flag: -transformation %s
    transverse_slices: (a boolean)
            Write out transverse slices.
            flag: -transverse
            mutually_exclusive: transverse, sagittal, coronal
    tricubic_interpolation: (a boolean)
            Do tricubic interpolation.
            flag: -tricubic
            mutually_exclusive: trilinear_interpolation, tricubic_interpolation,
             nearest_neighbour_interpolation, sinc_interpolation
    trilinear_interpolation: (a boolean)
            Do trilinear interpolation.
            flag: -trilinear
            mutually_exclusive: trilinear_interpolation, tricubic_interpolation,
             nearest_neighbour_interpolation, sinc_interpolation
    two: (a boolean)
            Create a MINC 2 output file.
            flag: -2
    units: (a unicode string)
            Specify the units of the output sampling.
            flag: -units %s
    vio_transform: (a boolean)
            VIO_Transform the input sampling with the transform (default).
            flag: -tfm_input_sampling
            mutually_exclusive: vio_transform, no_input_sampling
    xdircos: (a float)
            Direction cosines along the X dimension.Default value: 1.79769e+308
            1.79769e+308 1.79769e+308.
            flag: -xdircos %s
            mutually_exclusive: dircos, dircos_x_y_or_z
            requires: ydircos, zdircos
    xnelements: (an integer (int or long))
            Number of elements along the X dimension.
            flag: -xnelements %s
            mutually_exclusive: nelements, nelements_x_y_or_z
            requires: ynelements, znelements
    xstart: (a float)
            Start point along the X dimension. Default value: 1.79769e+308.
            flag: -xstart %s
            mutually_exclusive: start, start_x_y_or_z
            requires: ystart, zstart
    xstep: (an integer (int or long))
            Step size along the X dimension. Default value: 0.
            flag: -xstep %s
            mutually_exclusive: step, step_x_y_or_z
            requires: ystep, zstep
    ydircos: (a float)
            Direction cosines along the Y dimension.Default value: 1.79769e+308
            1.79769e+308 1.79769e+308.
            flag: -ydircos %s
            mutually_exclusive: dircos, dircos_x_y_or_z
            requires: xdircos, zdircos
    ynelements: (an integer (int or long))
            Number of elements along the Y dimension.
            flag: -ynelements %s
            mutually_exclusive: nelements, nelements_x_y_or_z
            requires: xnelements, znelements
    ystart: (a float)
            Start point along the Y dimension. Default value: 1.79769e+308.
            flag: -ystart %s
            mutually_exclusive: start, start_x_y_or_z
            requires: xstart, zstart
    ystep: (an integer (int or long))
            Step size along the Y dimension. Default value: 0.
            flag: -ystep %s
            mutually_exclusive: step, step_x_y_or_z
            requires: xstep, zstep
    zdircos: (a float)
            Direction cosines along the Z dimension.Default value: 1.79769e+308
            1.79769e+308 1.79769e+308.
            flag: -zdircos %s
            mutually_exclusive: dircos, dircos_x_y_or_z
            requires: xdircos, ydircos
    znelements: (an integer (int or long))
            Number of elements along the Z dimension.
            flag: -znelements %s
            mutually_exclusive: nelements, nelements_x_y_or_z
            requires: xnelements, ynelements
    zstart: (a float)
            Start point along the Z dimension. Default value: 1.79769e+308.
            flag: -zstart %s
            mutually_exclusive: start, start_x_y_or_z
            requires: xstart, ystart
    zstep: (an integer (int or long))
            Step size along the Z dimension. Default value: 0.
            flag: -zstep %s
            mutually_exclusive: step, step_x_y_or_z
            requires: xstep, ystep

Outputs:

    output_file: (an existing file name)
            output file

## Reshape

Link to code

Wraps command mincreshape

Cut a hyperslab out of a minc file, with dimension reordering.

This is also useful for rewriting with a different format, for example converting to short (see example below).

### Examples

    >>> from nipype.interfaces.minc import Reshape
    >>> from nipype.interfaces.minc.testdata import nonempty_minc_data

    >>> input_file = nonempty_minc_data(0)
    >>> reshape_to_short = Reshape(input_file=input_file, write_short=True)
    >>> reshape_to_short.run()

Inputs:

    [Mandatory]
    input_file: (a file name)
            input file
            flag: %s, position: -2

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    clobber: (a boolean, nipype default value: True)
            Overwrite existing file.
            flag: -clobber
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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
    output_file: (a file name)
            output file
            flag: %s, position: -1
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    verbose: (a boolean)
            Print out log messages. Default: False.
            flag: -verbose
    write_short: (a boolean)
            Convert to short integer data.
            flag: -short

Outputs:

    output_file: (an existing file name)
            output file

## ToEcat

Link to code

Wraps command minctoecat

Convert a 2D image, a 3D volumes or a 4D dynamic volumes written in MINC file format to a 2D, 3D or 4D Ecat7 file.

### Examples

    >>> from nipype.interfaces.minc import ToEcat
    >>> from nipype.interfaces.minc.testdata import minc2Dfile

    >>> c = ToEcat(input_file=minc2Dfile)
    >>> c.run()

    >>> c = ToEcat(input_file=minc2Dfile, voxels_as_integers=True)
    >>> c.run()

Inputs:

    [Mandatory]
    input_file: (an existing file name)
            input file to convert
            flag: %s, position: -2

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    ignore_acquisition_variable: (a boolean)
            Ignore informations from the minc acquisition variable.
            flag: -ignore_acquisition_variable
    ignore_ecat_acquisition_variable: (a boolean)
            Ignore informations from the minc ecat_acquisition variable.
            flag: -ignore_ecat_acquisition_variable
    ignore_ecat_main: (a boolean)
            Ignore informations from the minc ecat-main variable.
            flag: -ignore_ecat_main
    ignore_ecat_subheader_variable: (a boolean)
            Ignore informations from the minc ecat-subhdr variable.
            flag: -ignore_ecat_subheader_variable
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    ignore_patient_variable: (a boolean)
            Ignore informations from the minc patient variable.
            flag: -ignore_patient_variable
    ignore_study_variable: (a boolean)
            Ignore informations from the minc study variable.
            flag: -ignore_study_variable
    no_decay_corr_fctr: (a boolean)
            Do not compute the decay correction factors
            flag: -no_decay_corr_fctr
    output_file: (a file name)
            output file
            flag: %s, position: -1
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    voxels_as_integers: (a boolean)
            Voxel values are treated as integers, scale andcalibration factors
            are set to unity
            flag: -label

Outputs:

    output_file: (an existing file name)
            output file

## ToRaw

Link to code

Wraps command minctoraw

Dump a chunk of MINC file data. This program is largely superceded by mincextract (see Extract).

### Examples

    >>> from nipype.interfaces.minc import ToRaw
    >>> from nipype.interfaces.minc.testdata import minc2Dfile

    >>> toraw = ToRaw(input_file=minc2Dfile)
    >>> toraw.run()

    >>> toraw = ToRaw(input_file=minc2Dfile, write_range=(0, 100))
    >>> toraw.run()

Inputs:

    [Mandatory]
    input_file: (an existing file name)
            input file
            flag: %s, position: -2

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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
    nonormalize: (a boolean)
            Turn off pixel normalization.
            flag: -nonormalize
            mutually_exclusive: normalize, nonormalize
    normalize: (a boolean)
            Normalize integer pixel values to file max and min.
            flag: -normalize
            mutually_exclusive: normalize, nonormalize
    out_file: (a file name)
            flag: > %s, position: -1
    output_file: (a file name)
            output file
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    write_byte: (a boolean)
            Write out data as bytes.
            flag: -byte
            mutually_exclusive: write_byte, write_short, write_int, write_long,
             write_float, write_double
    write_double: (a boolean)
            Write out data as double precision floating-point values.
            flag: -double
            mutually_exclusive: write_byte, write_short, write_int, write_long,
             write_float, write_double
    write_float: (a boolean)
            Write out data as single precision floating-point values.
            flag: -float
            mutually_exclusive: write_byte, write_short, write_int, write_long,
             write_float, write_double
    write_int: (a boolean)
            Write out data as 32-bit integers.
            flag: -int
            mutually_exclusive: write_byte, write_short, write_int, write_long,
             write_float, write_double
    write_long: (a boolean)
            Superseded by write_int.
            flag: -long
            mutually_exclusive: write_byte, write_short, write_int, write_long,
             write_float, write_double
    write_range: (a tuple of the form: (a float, a float))
            Specify the range of output values.Default value: 1.79769e+308
            1.79769e+308.
            flag: -range %s %s
    write_short: (a boolean)
            Write out data as short integers.
            flag: -short
            mutually_exclusive: write_byte, write_short, write_int, write_long,
             write_float, write_double
    write_signed: (a boolean)
            Write out signed data.
            flag: -signed
            mutually_exclusive: write_signed, write_unsigned
    write_unsigned: (a boolean)
            Write out unsigned data.
            flag: -unsigned
            mutually_exclusive: write_signed, write_unsigned

Outputs:

    output_file: (an existing file name)
            output file in raw format

## VolSymm

Link to code

Wraps command volsymm

Make a volume symmetric about an axis either linearly and/or nonlinearly. This is done by registering a volume to a flipped image of itself.

This tool is part of the minc-widgets package:

https://github.com/BIC-MNI/minc-widgets/blob/master/volsymm/volsymm

### Examples

    >>> from nipype.interfaces.minc import VolSymm
    >>> from nipype.interfaces.minc.testdata import nonempty_minc_data

    >>> input_file = nonempty_minc_data(0)
    >>> volsymm = VolSymm(input_file=input_file)
    >>> volsymm.run()

Inputs:

    [Mandatory]
    input_file: (a file name)
            input file
            flag: %s, position: -3

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    clobber: (a boolean, nipype default value: True)
            Overwrite existing file.
            flag: -clobber
    config_file: (an existing file name)
            File containing the fitting configuration (nlpfit -help for info).
            flag: -config_file %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    fit_linear: (a boolean)
            Fit using a linear xfm.
            flag: -linear
    fit_nonlinear: (a boolean)
            Fit using a non-linear xfm.
            flag: -nonlinear
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    input_grid_files: (a list of items which are a file name)
            input grid file(s)
    nofit: (a boolean)
            Use the input transformation instead of generating one.
            flag: -nofit
    output_file: (a file name)
            output file
            flag: %s, position: -1
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    trans_file: (a file name)
            output xfm trans file
            flag: %s, position: -2
    verbose: (a boolean)
            Print out log messages. Default: False.
            flag: -verbose
    x: (a boolean)
            Flip volume in x-plane (default).
            flag: -x
    y: (a boolean)
            Flip volume in y-plane.
            flag: -y
    z: (a boolean)
            Flip volume in z-plane.
            flag: -z

Outputs:

    output_file: (an existing file name)
            output file
    output_grid: (an existing file name)
            output grid file
    trans_file: (an existing file name)
            xfm trans file

## Volcentre

Link to code

Wraps command volcentre

Centre a MINC image’s sampling about a point, typically (0,0,0).

### Example

    >>> from nipype.interfaces.minc import Volcentre
    >>> from nipype.interfaces.minc.testdata import minc2Dfile
    >>> vc = Volcentre(input_file=minc2Dfile)
    >>> vc.run()

Inputs:

    [Mandatory]
    input_file: (an existing file name)
            input file to centre
            flag: %s, position: -2

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    centre: (a tuple of the form: (a float, a float, a float))
            Centre to use (x,y,z) [default: 0 0 0].
            flag: -centre %s %s %s
    clobber: (a boolean, nipype default value: True)
            Overwrite existing file.
            flag: -clobber
    com: (a boolean)
            Use the CoM of the volume for the new centre (via mincstats).
            Default: False
            flag: -com
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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
    output_file: (a file name)
            output file
            flag: %s, position: -1
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    verbose: (a boolean)
            Print out log messages. Default: False.
            flag: -verbose
    zero_dircos: (a boolean)
            Set the direction cosines to identity [default].
            flag: -zero_dircos

Outputs:

    output_file: (an existing file name)
            output file

## Voliso

Link to code

Wraps command voliso

Changes the steps and starts in order that the output volume has isotropic sampling.

### Examples

    >>> from nipype.interfaces.minc import Voliso
    >>> from nipype.interfaces.minc.testdata import minc2Dfile
    >>> viso = Voliso(input_file=minc2Dfile, minstep=0.1, avgstep=True)
    >>> viso.run()

Inputs:

    [Mandatory]
    input_file: (an existing file name)
            input file to convert to isotropic sampling
            flag: %s, position: -2

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    avgstep: (a boolean)
            Calculate the maximum step from the average steps of the input
            volume.
            flag: --avgstep
    clobber: (a boolean, nipype default value: True)
            Overwrite existing file.
            flag: --clobber
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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
    maxstep: (a float)
            The target maximum step desired in the output volume.
            flag: --maxstep %s
    minstep: (a float)
            The target minimum step desired in the output volume.
            flag: --minstep %s
    output_file: (a file name)
            output file
            flag: %s, position: -1
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    verbose: (a boolean)
            Print out log messages. Default: False.
            flag: --verbose

Outputs:

    output_file: (an existing file name)
            output file

## Volpad

Link to code

Wraps command volpad

Centre a MINC image’s sampling about a point, typically (0,0,0).

### Examples

    >>> from nipype.interfaces.minc import Volpad
    >>> from nipype.interfaces.minc.testdata import minc2Dfile
    >>> vp = Volpad(input_file=minc2Dfile, smooth=True, smooth_distance=4)
    >>> vp.run()

Inputs:

    [Mandatory]
    input_file: (an existing file name)
            input file to centre
            flag: %s, position: -2

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    auto: (a boolean)
            Automatically determine padding distances (uses -distance as max).
            Default: False.
            flag: -auto
    auto_freq: (a float)
            Frequency of voxels over bimodalt threshold to stop at [default:
            500].
            flag: -auto_freq %s
    clobber: (a boolean, nipype default value: True)
            Overwrite existing file.
            flag: -clobber
    distance: (an integer (int or long))
            Padding distance (in voxels) [default: 4].
            flag: -distance %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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
    output_file: (a file name)
            output file
            flag: %s, position: -1
    smooth: (a boolean)
            Smooth (blur) edges before padding. Default: False.
            flag: -smooth
    smooth_distance: (an integer (int or long))
            Smoothing distance (in voxels) [default: 4].
            flag: -smooth_distance %s
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    verbose: (a boolean)
            Print out log messages. Default: False.
            flag: -verbose

Outputs:

    output_file: (an existing file name)
            output file

## XfmAvg

Link to code

Wraps command xfmavg

Average a number of xfm transforms using matrix logs and exponents. The program xfmavg calls Octave for numerical work.

This tool is part of the minc-widgets package:

https://github.com/BIC-MNI/minc-widgets/tree/master/xfmavg

### Examples

    >>> from nipype.interfaces.minc import XfmAvg
    >>> from nipype.interfaces.minc.testdata import nonempty_minc_data, nlp_config
    >>> from nipype.testing import example_data

    >>> xfm1 = example_data('minc_initial.xfm')
    >>> xfm2 = example_data('minc_initial.xfm')  # cheating for doctest
    >>> xfmavg = XfmAvg(input_files=[xfm1, xfm2])
    >>> xfmavg.run()

Inputs:

    [Mandatory]
    input_files: (a list of items which are a file name)
            input file(s)
            flag: %s, position: -2

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    avg_linear: (a boolean)
            average the linear part [default].
            flag: -avg_linear
    avg_nonlinear: (a boolean)
            average the non-linear part [default].
            flag: -avg_nonlinear
    clobber: (a boolean, nipype default value: True)
            Overwrite existing file.
            flag: -clobber
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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
    ignore_linear: (a boolean)
            opposite of -avg_linear.
            flag: -ignore_linear
    ignore_nonlinear: (a boolean)
            opposite of -avg_nonlinear.
            flag: -ignore_nonline
    input_grid_files: (a list of items which are a file name)
            input grid file(s)
    output_file: (a file name)
            output file
            flag: %s, position: -1
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    verbose: (a boolean)
            Print out log messages. Default: False.
            flag: -verbose

Outputs:

    output_file: (an existing file name)
            output file
    output_grid: (an existing file name)
            output grid file

## XfmConcat

Link to code

Wraps command xfmconcat

Concatenate transforms together. The output transformation is equivalent to applying input1.xfm, then input2.xfm, …, in that order.

### Examples

    >>> from nipype.interfaces.minc import XfmConcat
    >>> from nipype.interfaces.minc.testdata import minc2Dfile
    >>> conc = XfmConcat(input_files=['input1.xfm', 'input1.xfm'])
    >>> conc.run()

Inputs:

    [Mandatory]
    input_files: (a list of items which are a file name)
            input file(s)
            flag: %s, position: -2

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    clobber: (a boolean, nipype default value: True)
            Overwrite existing file.
            flag: -clobber
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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
    input_grid_files: (a list of items which are a file name)
            input grid file(s)
    output_file: (a file name)
            output file
            flag: %s, position: -1
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    verbose: (a boolean)
            Print out log messages. Default: False.
            flag: -verbose

Outputs:

    output_file: (an existing file name)
            output file
    output_grids: (a list of items which are an existing file name)
            output grids

## XfmInvert

Link to code

Wraps command xfminvert

Invert an xfm transform file.

### Examples

    >>> from nipype.interfaces.minc import XfmAvg
    >>> from nipype.testing import example_data

    >>> xfm = example_data('minc_initial.xfm')
    >>> invert = XfmInvert(input_file=xfm)
    >>> invert.run()

Inputs:

    [Mandatory]
    input_file: (a file name)
            input file
            flag: %s, position: -2

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    clobber: (a boolean, nipype default value: True)
            Overwrite existing file.
            flag: -clobber
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, 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
    output_file: (a file name)
            output file
            flag: %s, position: -1
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    verbose: (a boolean)
            Print out log messages. Default: False.
            flag: -verbose

Outputs:

    output_file: (an existing file name)
            output file
    output_grid: (an existing file name)
            output grid file