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# nipype.interfaces.minc.minc module

The minc module provides classes for interfacing with the MINC command line tools. This module was written to work with MINC version 2.2.00.

Author: Carlo Hamalainen

## Average

Link to code

> Bases: CommandLine

> Wrapped executable: `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()

> filelista pathlike object or string representing an existing file

>   Specify the name of a file containing input file names. Maps to a command-line argument: `-filelist %s`. Mutually exclusive with inputs: `input_files`, `filelist`.

> input_filesa list of items which are a pathlike object or string representing an existing file

>   Input file(s). Maps to a command-line argument: `%s` (position: -2). Mutually exclusive with inputs: `input_files`, `filelist`.

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> avgdima string

>   Specify a dimension along which we wish to average. Maps to a command-line argument: `-avgdim %s`.

> binarizea boolean

>   Binarize the volume by looking for values in a given range. Maps to a command-line argument: `-binarize`.

> binrangea tuple of the form: (a float, a float)

>   Specify a range for binarization. Default value: 1.79769e+308 -1.79769e+308. Maps to a command-line argument: `-binrange %s %s`.

> binvaluea float

>   Specify a target value (+/- 0.5) forbinarization. Default value: -1.79769e+308. Maps to a command-line argument: `-binvalue %s`.

> check_dimensionsa boolean

>   Check that dimension info matches across files (default). Maps to a command-line argument: `-check_dimensions`. Mutually exclusive with inputs: `check_dimensions`, `no_check_dimensions`.

> clobbera boolean

>   Overwrite existing file. Maps to a command-line argument: `-clobber`. (Nipype default value: `True`)

> copy_headera boolean

>   Copy all of the header from the first file (default for one file). Maps to a command-line argument: `-copy_header`. Mutually exclusive with inputs: `copy_header`, `no_copy_header`.

> debuga boolean

>   Print out debugging messages. Maps to a command-line argument: `-debug`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> format_bytea boolean

>   Write out byte data. Maps to a command-line argument: `-byte`. Mutually exclusive with inputs: `format_filetype`, `format_byte`, `format_short`, `format_int`, `format_long`, `format_float`, `format_double`, `format_signed`, `format_unsigned`.

> format_doublea boolean

>   Write out double-precision floating-point data. Maps to a command-line argument: `-double`. Mutually exclusive with inputs: `format_filetype`, `format_byte`, `format_short`, `format_int`, `format_long`, `format_float`, `format_double`, `format_signed`, `format_unsigned`.

> format_filetypea boolean

>   Use data type of first file (default). Maps to a command-line argument: `-filetype`. Mutually exclusive with inputs: `format_filetype`, `format_byte`, `format_short`, `format_int`, `format_long`, `format_float`, `format_double`, `format_signed`, `format_unsigned`.

> format_floata boolean

>   Write out single-precision floating-point data. Maps to a command-line argument: `-float`. Mutually exclusive with inputs: `format_filetype`, `format_byte`, `format_short`, `format_int`, `format_long`, `format_float`, `format_double`, `format_signed`, `format_unsigned`.

> format_inta boolean

>   Write out 32-bit integer data. Maps to a command-line argument: `-int`. Mutually exclusive with inputs: `format_filetype`, `format_byte`, `format_short`, `format_int`, `format_long`, `format_float`, `format_double`, `format_signed`, `format_unsigned`.

> format_longa boolean

>   Superseded by -int. Maps to a command-line argument: `-long`. Mutually exclusive with inputs: `format_filetype`, `format_byte`, `format_short`, `format_int`, `format_long`, `format_float`, `format_double`, `format_signed`, `format_unsigned`.

> format_shorta boolean

>   Write out short integer data. Maps to a command-line argument: `-short`. Mutually exclusive with inputs: `format_filetype`, `format_byte`, `format_short`, `format_int`, `format_long`, `format_float`, `format_double`, `format_signed`, `format_unsigned`.

> format_signeda boolean

>   Write signed integer data. Maps to a command-line argument: `-signed`. Mutually exclusive with inputs: `format_filetype`, `format_byte`, `format_short`, `format_int`, `format_long`, `format_float`, `format_double`, `format_signed`, `format_unsigned`.

> format_unsigneda boolean

>   Write unsigned integer data (default). Maps to a command-line argument: `-unsigned`. Mutually exclusive with inputs: `format_filetype`, `format_byte`, `format_short`, `format_int`, `format_long`, `format_float`, `format_double`, `format_signed`, `format_unsigned`.

> max_buffer_size_in_kban integer >= 0

>   Specify the maximum size of the internal buffers (in kbytes). Maps to a command-line argument: `-max_buffer_size_in_kb %d`. (Nipype default value: `4096`)

> no_check_dimensionsa boolean

>   Do not check dimension info. Maps to a command-line argument: `-nocheck_dimensions`. Mutually exclusive with inputs: `check_dimensions`, `no_check_dimensions`.

> no_copy_headera boolean

>   Do not copy all of the header from the first file (default for many files)). Maps to a command-line argument: `-nocopy_header`. Mutually exclusive with inputs: `copy_header`, `no_copy_header`.

> nonormalizea boolean

>   Do not normalize data sets (default). Maps to a command-line argument: `-nonormalize`. Mutually exclusive with inputs: `normalize`, `nonormalize`.

> normalizea boolean

>   Normalize data sets for mean intensity. Maps to a command-line argument: `-normalize`. Mutually exclusive with inputs: `normalize`, `nonormalize`.

> output_filea pathlike object or string representing a file

>   Output file. Maps to a command-line argument: `%s` (position: -1).

> quieta boolean

>   Do not print out log messages. Maps to a command-line argument: `-quiet`. Mutually exclusive with inputs: `verbose`, `quiet`.

> sdfilea pathlike object or string representing a file

>   Specify an output sd file (default=none). Maps to a command-line argument: `-sdfile %s`.

> twoa boolean

>   Create a MINC 2 output file. Maps to a command-line argument: `-2`.

> verbosea boolean

>   Print out log messages (default). Maps to a command-line argument: `-verbose`. Mutually exclusive with inputs: `verbose`, `quiet`.

> voxel_rangea tuple of the form: (an integer, an integer)

>   Valid range for output data. Maps to a command-line argument: `-range %d %d`.

> weightsa list of items which are a string

>   Specify weights for averaging (“<w1>,<w2>,…”). Maps to a command-line argument: `-weights %s`.

> width_weighteda boolean

>   Weight by dimension widths when -avgdim is used. Maps to a command-line argument: `-width_weighted`. Requires inputs: `avgdim`.

> output_filea pathlike object or string representing an existing file

>   Output file.

## BBox

Link to code

> Bases: StdOutCommandLine

> Wrapped executable: `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()

> input_filea pathlike object or string representing an existing file

>   Input file. Maps to a command-line argument: `%s` (position: -2).

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> format_minccropa boolean

>   Output format for minccrop: (-xlim x1 x2 -ylim y1 y2 -zlim z1 z2. Maps to a command-line argument: `-minccrop`.

> format_mincresamplea boolean

>   Output format for mincresample: (-step x y z -start x y z -nelements x y z. Maps to a command-line argument: `-mincresample`.

> format_mincreshapea boolean

>   Output format for mincreshape: (-start x,y,z -count dx,dy,dz. Maps to a command-line argument: `-mincreshape`.

> one_linea boolean

>   Output on one line (default): start_x y z width_x y z. Maps to a command-line argument: `-one_line`. Mutually exclusive with inputs: `one_line`, `two_lines`.

> out_filea pathlike object or string representing a file

>   Maps to a command-line argument: `> %s` (position: -1).

> output_filea pathlike object or string representing a file

>   Output file containing bounding box corners.

> thresholdan integer

>   VIO_Real value threshold for bounding box. Default value: 0. Maps to a command-line argument: `-threshold`.

> two_linesa boolean

>   Write output with two rows (start and width). Maps to a command-line argument: `-two_lines`. Mutually exclusive with inputs: `one_line`, `two_lines`.

> output_filea pathlike object or string representing an existing file

>   Output file containing bounding box corners.

## Beast

Link to code

> Bases: CommandLine

> Wrapped executable: `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()

> input_filea pathlike object or string representing a file

>   Input file. Maps to a command-line argument: `%s` (position: -2).

> library_dira pathlike object or string representing a directory

>   Library directory. Maps to a command-line argument: `%s` (position: -3).

> abspatha boolean

>   File paths in the library are absolute (default is relative to library root). Maps to a command-line argument: `-abspath`. (Nipype default value: `True`)

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> clobbera boolean

>   Overwrite existing file. Maps to a command-line argument: `-clobber`. (Nipype default value: `True`)

> confidence_level_alphaa float

>   Specify confidence level Alpha. Default value: 0.5. Maps to a command-line argument: `-alpha %s`. (Nipype default value: `0.5`)

> configuration_filea pathlike object or string representing a file

>   Specify configuration file. Maps to a command-line argument: `-configuration %s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> fill_holesa boolean

>   Fill holes in the binary output. Maps to a command-line argument: `-fill`.

> flip_imagesa boolean

>   Flip images around the mid-sagittal plane to increase patch count. Maps to a command-line argument: `-flip`.

> load_momentsa boolean

>   Do not calculate moments instead use precalculatedlibrary moments. (for optimization purposes). Maps to a command-line argument: `-load_moments`.

> median_filtera boolean

>   Apply a median filter on the probability map. Maps to a command-line argument: `-median`.

> nlm_filtera boolean

>   Apply an NLM filter on the probability map (experimental). Maps to a command-line argument: `-nlm_filter`.

> number_selected_imagesan integer

>   Specify number of selected images. Default value: 20. Maps to a command-line argument: `-selection_num %s`. (Nipype default value: `20`)

> output_filea pathlike object or string representing a file

>   Output file. Maps to a command-line argument: `%s` (position: -1).

> patch_sizean integer

>   Specify patch size for single scale approach. Default value: 1. Maps to a command-line argument: `-patch_size %s`. (Nipype default value: `1`)

> probability_mapa boolean

>   Output the probability map instead of crisp mask. Maps to a command-line argument: `-probability`.

> same_resolutiona boolean

>   Output final mask with the same resolution as input file. Maps to a command-line argument: `-same_resolution`.

> search_areaan integer

>   Specify size of search area for single scale approach. Default value: 2. Maps to a command-line argument: `-search_area %s`. (Nipype default value: `2`)

> smoothness_factor_betaa float

>   Specify smoothness factor Beta. Default value: 0.25. Maps to a command-line argument: `-beta %s`. (Nipype default value: `0.5`)

> threshold_patch_selectiona float

>   Specify threshold for patch selection. Default value: 0.95. Maps to a command-line argument: `-threshold %s`. (Nipype default value: `0.95`)

> voxel_sizean integer

>   Specify voxel size for calculations (4, 2, or 1).Default value: 4. Assumes no multiscale. Use configurationfile for multiscale. Maps to a command-line argument: `-voxel_size %s`. (Nipype default value: `4`)

> output_filea pathlike object or string representing an existing file

>   Output mask file.

## BestLinReg

Link to code

> Bases: CommandLine

> Wrapped executable: `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()

> sourcea pathlike object or string representing an existing file

>   Source Minc file. Maps to a command-line argument: `%s` (position: -4).

> targeta pathlike object or string representing an existing file

>   Target Minc file. Maps to a command-line argument: `%s` (position: -3).

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> clobbera boolean

>   Overwrite existing file. Maps to a command-line argument: `-clobber`. (Nipype default value: `True`)

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> output_mnca pathlike object or string representing a file

>   Output mnc file. Maps to a command-line argument: `%s` (position: -1).

> output_xfma pathlike object or string representing a file

>   Output xfm file. Maps to a command-line argument: `%s` (position: -2).

> verbosea boolean

>   Print out log messages. Default: False. Maps to a command-line argument: `-verbose`.

> output_mnca pathlike object or string representing an existing file

>   Output mnc file.

> output_xfma pathlike object or string representing an existing file

>   Output xfm file.

## BigAverage

Link to code

> Bases: CommandLine

> Wrapped executable: `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()

> input_filesa list of items which are a pathlike object or string representing an existing file

>   Input file(s). Maps to a command-line argument: `%s` (position: -2).

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> clobbera boolean

>   Overwrite existing file. Maps to a command-line argument: `--clobber`. (Nipype default value: `True`)

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> output_filea pathlike object or string representing a file

>   Output file. Maps to a command-line argument: `%s` (position: -1).

> output_floata boolean

>   Output files with float precision. Maps to a command-line argument: `--float`.

> robusta 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. Maps to a command-line argument: `-robust`.

> sd_filea pathlike object or string representing a file

>   Place standard deviation image in specified file. Maps to a command-line argument: `--sdfile %s`.

> tmpdira pathlike object or string representing a directory

>   Temporary files directory. Maps to a command-line argument: `-tmpdir %s`.

> verbosea boolean

>   Print out log messages. Default: False. Maps to a command-line argument: `--verbose`.

> output_filea pathlike object or string representing an existing file

>   Output file.

> sd_filea pathlike object or string representing an existing file

>   Standard deviation image.

## Blob

Link to code

> Bases: CommandLine

> Wrapped executable: `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()

> input_filea pathlike object or string representing an existing file

>   Input file to blob. Maps to a command-line argument: `%s` (position: -2).

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> determinanta boolean

>   Compute the determinant (exact growth and shrinkage) – SLOW. Maps to a command-line argument: `-determinant`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> magnitudea boolean

>   Compute the magnitude of the displacement vector. Maps to a command-line argument: `-magnitude`.

> output_filea pathlike object or string representing a file

>   Output file. Maps to a command-line argument: `%s` (position: -1).

> tracea boolean

>   Compute the trace (approximate growth and shrinkage) – FAST. Maps to a command-line argument: `-trace`.

> translationa boolean

>   Compute translation (structure displacement). Maps to a command-line argument: `-translation`.

> output_filea pathlike object or string representing an existing file

>   Output file.

## Blur

Link to code

> Bases: StdOutCommandLine

> Wrapped executable: `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.

> fwhma float

>   Full-width-half-maximum of gaussian kernel. Default value: 0. Maps to a command-line argument: `-fwhm %s`. Mutually exclusive with inputs: `fwhm`, `fwhm3d`, `standard_dev`.

> fwhm3da 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. Maps to a command-line argument: `-3dfwhm %s %s %s`. Mutually exclusive with inputs: `fwhm`, `fwhm3d`, `standard_dev`.

> input_filea pathlike object or string representing an existing file

>   Input file. Maps to a command-line argument: `%s` (position: -2).

> standard_deva float

>   Standard deviation of gaussian kernel. Default value: 0. Maps to a command-line argument: `-standarddev %s`. Mutually exclusive with inputs: `fwhm`, `fwhm3d`, `standard_dev`.

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> clobbera boolean

>   Overwrite existing file. Maps to a command-line argument: `-clobber`. (Nipype default value: `True`)

> dimensions3 or 1 or 2

>   Number of dimensions to blur (either 1,2 or 3). Default value: 3. Maps to a command-line argument: `-dimensions %s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> gaussiana boolean

>   Use a gaussian smoothing kernel (default). Maps to a command-line argument: `-gaussian`. Mutually exclusive with inputs: `gaussian`, `rect`.

> gradienta boolean

>   Create the gradient magnitude volume as well. Maps to a command-line argument: `-gradient`.

> no_apodizea boolean

>   Do not apodize the data before blurring. Maps to a command-line argument: `-no_apodize`.

> output_file_basea pathlike object or string representing a file

>   Output file base. Maps to a command-line argument: `%s` (position: -1).

> partiala boolean

>   Create the partial derivative and gradient magnitude volumes as well. Maps to a command-line argument: `-partial`.

> recta boolean

>   Use a rect (box) smoothing kernel. Maps to a command-line argument: `-rect`. Mutually exclusive with inputs: `gaussian`, `rect`.

> gradient_dxyza pathlike object or string representing a file

>   Gradient dxyz.

> output_filea pathlike object or string representing an existing file

>   Blurred output file.

> partial_dxa pathlike object or string representing a file

>   Partial gradient dx.

> partial_dxyza pathlike object or string representing a file

>   Partial gradient dxyz.

> partial_dya pathlike object or string representing a file

>   Partial gradient dy.

> partial_dza pathlike object or string representing a file

>   Partial gradient dz.

> property Blur.cmdline

>   command plus any arguments (args) validates arguments and generates command line

## Calc

Link to code

> Bases: CommandLine

> Wrapped executable: `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()

> expfilea pathlike object or string representing a file

>   Name of file containing expression. Maps to a command-line argument: `-expfile %s`. Mutually exclusive with inputs: `expression`, `expfile`.

> expressiona string

>   Expression to use in calculations. Maps to a command-line argument: `-expression '%s'`. Mutually exclusive with inputs: `expression`, `expfile`.

> filelista pathlike object or string representing a file

>   Specify the name of a file containing input file names. Maps to a command-line argument: `-filelist %s`. Mutually exclusive with inputs: `input_files`, `filelist`.

> input_filesa list of items which are a pathlike object or string representing an existing file

>   Input file(s) for calculation. Maps to a command-line argument: `%s` (position: -2).

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> check_dimensionsa boolean

>   Check that files have matching dimensions (default). Maps to a command-line argument: `-check_dimensions`. Mutually exclusive with inputs: `check_dimensions`, `no_check_dimensions`.

> clobbera boolean

>   Overwrite existing file. Maps to a command-line argument: `-clobber`. (Nipype default value: `True`)

> copy_headera boolean

>   Copy all of the header from the first file. Maps to a command-line argument: `-copy_header`. Mutually exclusive with inputs: `copy_header`, `no_copy_header`.

> debuga boolean

>   Print out debugging messages. Maps to a command-line argument: `-debug`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> eval_widthan integer

>   Number of voxels to evaluate simultaneously. Maps to a command-line argument: `-eval_width %s`.

> format_bytea boolean

>   Write out byte data. Maps to a command-line argument: `-byte`. Mutually exclusive with inputs: `format_filetype`, `format_byte`, `format_short`, `format_int`, `format_long`, `format_float`, `format_double`, `format_signed`, `format_unsigned`.

> format_doublea boolean

>   Write out double-precision floating-point data. Maps to a command-line argument: `-double`. Mutually exclusive with inputs: `format_filetype`, `format_byte`, `format_short`, `format_int`, `format_long`, `format_float`, `format_double`, `format_signed`, `format_unsigned`.

> format_filetypea boolean

>   Use data type of first file (default). Maps to a command-line argument: `-filetype`. Mutually exclusive with inputs: `format_filetype`, `format_byte`, `format_short`, `format_int`, `format_long`, `format_float`, `format_double`, `format_signed`, `format_unsigned`.

> format_floata boolean

>   Write out single-precision floating-point data. Maps to a command-line argument: `-float`. Mutually exclusive with inputs: `format_filetype`, `format_byte`, `format_short`, `format_int`, `format_long`, `format_float`, `format_double`, `format_signed`, `format_unsigned`.

> format_inta boolean

>   Write out 32-bit integer data. Maps to a command-line argument: `-int`. Mutually exclusive with inputs: `format_filetype`, `format_byte`, `format_short`, `format_int`, `format_long`, `format_float`, `format_double`, `format_signed`, `format_unsigned`.

> format_longa boolean

>   Superseded by -int. Maps to a command-line argument: `-long`. Mutually exclusive with inputs: `format_filetype`, `format_byte`, `format_short`, `format_int`, `format_long`, `format_float`, `format_double`, `format_signed`, `format_unsigned`.

> format_shorta boolean

>   Write out short integer data. Maps to a command-line argument: `-short`. Mutually exclusive with inputs: `format_filetype`, `format_byte`, `format_short`, `format_int`, `format_long`, `format_float`, `format_double`, `format_signed`, `format_unsigned`.

> format_signeda boolean

>   Write signed integer data. Maps to a command-line argument: `-signed`. Mutually exclusive with inputs: `format_filetype`, `format_byte`, `format_short`, `format_int`, `format_long`, `format_float`, `format_double`, `format_signed`, `format_unsigned`.

> format_unsigneda boolean

>   Write unsigned integer data (default). Maps to a command-line argument: `-unsigned`. Mutually exclusive with inputs: `format_filetype`, `format_byte`, `format_short`, `format_int`, `format_long`, `format_float`, `format_double`, `format_signed`, `format_unsigned`.

> ignore_nana boolean

>   Ignore invalid data (NaN) for accumulations. Maps to a command-line argument: `-ignore_nan`.

> max_buffer_size_in_kban integer >= 0

>   Specify the maximum size of the internal buffers (in kbytes). Maps to a command-line argument: `-max_buffer_size_in_kb %d`.

> no_check_dimensionsa boolean

>   Do not check that files have matching dimensions. Maps to a command-line argument: `-nocheck_dimensions`. Mutually exclusive with inputs: `check_dimensions`, `no_check_dimensions`.

> no_copy_headera boolean

>   Do not copy all of the header from the first file. Maps to a command-line argument: `-nocopy_header`. Mutually exclusive with inputs: `copy_header`, `no_copy_header`.

> outfiles : a list of items which are a tuple of the form: (a string, a pathlike object or string representing a file) output_file : a pathlike object or string representing a file

> > Output file. Maps to a command-line argument: `%s` (position: -1).

> output_illegala boolean

>   Value to write out when an illegal operation is done. Default value: 1.79769e+308. Maps to a command-line argument: `-illegal_value`. Mutually exclusive with inputs: `output_nan`, `output_zero`, `output_illegal_value`.

> output_nana boolean

>   Output NaN when an illegal operation is done (default). Maps to a command-line argument: `-nan`. Mutually exclusive with inputs: `output_nan`, `output_zero`, `output_illegal_value`.

> output_zeroa boolean

>   Output zero when an illegal operation is done. Maps to a command-line argument: `-zero`. Mutually exclusive with inputs: `output_nan`, `output_zero`, `output_illegal_value`.

> propagate_nana boolean

>   Invalid data in any file at a voxel produces a NaN (default). Maps to a command-line argument: `-propagate_nan`.

> quieta boolean

>   Do not print out log messages. Maps to a command-line argument: `-quiet`. Mutually exclusive with inputs: `verbose`, `quiet`.

> twoa boolean

>   Create a MINC 2 output file. Maps to a command-line argument: `-2`.

> verbosea boolean

>   Print out log messages (default). Maps to a command-line argument: `-verbose`. Mutually exclusive with inputs: `verbose`, `quiet`.

> voxel_rangea tuple of the form: (an integer, an integer)

>   Valid range for output data. Maps to a command-line argument: `-range %d %d`.

> output_filea pathlike object or string representing an existing file

>   Output file.

## Convert

Link to code

> Bases: CommandLine

> Wrapped executable: `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()

> input_filea pathlike object or string representing an existing file

>   Input file for converting. Maps to a command-line argument: `%s` (position: -2).

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> chunkan integer >= 0

>   Set the target block size for chunking (0 default, >1 block size). Maps to a command-line argument: `-chunk %d`.

> clobbera boolean

>   Overwrite existing file. Maps to a command-line argument: `-clobber`. (Nipype default value: `True`)

> compression0 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). Maps to a command-line argument: `-compress %s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> output_filea pathlike object or string representing a file

>   Output file. Maps to a command-line argument: `%s` (position: -1).

> templatea boolean

>   Create a template file. The dimensions, variables, andattributes of the input file are preserved but all data it set to zero. Maps to a command-line argument: `-template`.

> twoa boolean

>   Create a MINC 2 output file. Maps to a command-line argument: `-2`.

> output_filea pathlike object or string representing an existing file

>   Output file.

## Copy

Link to code

> Bases: CommandLine

> Wrapped executable: `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.

> input_filea pathlike object or string representing an existing file

>   Input file to copy. Maps to a command-line argument: `%s` (position: -2).

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> output_filea pathlike object or string representing a file

>   Output file. Maps to a command-line argument: `%s` (position: -1).

> pixel_valuesa boolean

>   Copy pixel values as is. Maps to a command-line argument: `-pixel_values`. Mutually exclusive with inputs: `pixel_values`, `real_values`.

> real_valuesa boolean

>   Copy real pixel intensities (default). Maps to a command-line argument: `-real_values`. Mutually exclusive with inputs: `pixel_values`, `real_values`.

> output_filea pathlike object or string representing an existing file

>   Output file.

## Dump

Link to code

> Bases: StdOutCommandLine

> Wrapped executable: `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()

> input_filea pathlike object or string representing an existing file

>   Input file. Maps to a command-line argument: `%s` (position: -2).

> annotations_brief‘c’ or ‘f’

>   Brief annotations for C or Fortran indices in data. Maps to a command-line argument: `-b %s`. Mutually exclusive with inputs: `annotations_brief`, `annotations_full`.

> annotations_full‘c’ or ‘f’

>   Full annotations for C or Fortran indices in data. Maps to a command-line argument: `-f %s`. Mutually exclusive with inputs: `annotations_brief`, `annotations_full`.

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> coordinate_dataa boolean

>   Coordinate variable data and header information. Maps to a command-line argument: `-c`. Mutually exclusive with inputs: `coordinate_data`, `header_data`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> header_dataa boolean

>   Header information only, no data. Maps to a command-line argument: `-h`. Mutually exclusive with inputs: `coordinate_data`, `header_data`.

> line_lengthan integer >= 0

>   Line length maximum in data section (default 80). Maps to a command-line argument: `-l %d`.

> netcdf_namea string

>   Name for netCDF (default derived from file name). Maps to a command-line argument: `-n %s`.

> out_filea pathlike object or string representing a file

>   Maps to a command-line argument: `> %s` (position: -1).

> output_filea pathlike object or string representing a file

>   Output file.

> precisionan integer or a tuple of the form: (an integer, an integer)

>   Display floating-point values with less precision. Maps to a command-line argument: `%s`.

> variablesa list of items which are a string

>   Output data for specified variables only. Maps to a command-line argument: `-v %s`.

> output_filea pathlike object or string representing an existing file

>   Output file.

## Extract

Link to code

> Bases: StdOutCommandLine

> Wrapped executable: `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()

> input_filea pathlike object or string representing an existing file

>   Input file. Maps to a command-line argument: `%s` (position: -2).

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> counta list of items which are an integer

>   Specifies edge lengths of hyperslab to read. Maps to a command-line argument: `-count %s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> flip_any_directiona boolean

>   Do not flip images (Default). Maps to a command-line argument: `-any_direction`. Mutually exclusive with inputs: `flip_positive_direction`, `flip_negative_direction`, `flip_any_direction`.

> flip_negative_directiona boolean

>   Flip images to always have negative direction. Maps to a command-line argument: `-negative_direction`. Mutually exclusive with inputs: `flip_positive_direction`, `flip_negative_direction`, `flip_any_direction`.

> flip_positive_directiona boolean

>   Flip images to always have positive direction. Maps to a command-line argument: `-positive_direction`. Mutually exclusive with inputs: `flip_positive_direction`, `flip_negative_direction`, `flip_any_direction`.

> flip_x_anya boolean

>   Don’t flip images along x-axis (default). Maps to a command-line argument: `-xanydirection`. Mutually exclusive with inputs: `flip_x_positive`, `flip_x_negative`, `flip_x_any`.

> flip_x_negativea boolean

>   Flip images to give negative xspace:step value (right-to-left). Maps to a command-line argument: `-xdirection`. Mutually exclusive with inputs: `flip_x_positive`, `flip_x_negative`, `flip_x_any`.

> flip_x_positivea boolean

>   Flip images to give positive xspace:step value (left-to-right). Maps to a command-line argument: `+xdirection`. Mutually exclusive with inputs: `flip_x_positive`, `flip_x_negative`, `flip_x_any`.

> flip_y_anya boolean

>   Don’t flip images along y-axis (default). Maps to a command-line argument: `-yanydirection`. Mutually exclusive with inputs: `flip_y_positive`, `flip_y_negative`, `flip_y_any`.

> flip_y_negativea boolean

>   Flip images to give negative yspace:step value (ant-to-post). Maps to a command-line argument: `-ydirection`. Mutually exclusive with inputs: `flip_y_positive`, `flip_y_negative`, `flip_y_any`.

> flip_y_positivea boolean

>   Flip images to give positive yspace:step value (post-to-ant). Maps to a command-line argument: `+ydirection`. Mutually exclusive with inputs: `flip_y_positive`, `flip_y_negative`, `flip_y_any`.

> flip_z_anya boolean

>   Don’t flip images along z-axis (default). Maps to a command-line argument: `-zanydirection`. Mutually exclusive with inputs: `flip_z_positive`, `flip_z_negative`, `flip_z_any`.

> flip_z_negativea boolean

>   Flip images to give negative zspace:step value (sup-to-inf). Maps to a command-line argument: `-zdirection`. Mutually exclusive with inputs: `flip_z_positive`, `flip_z_negative`, `flip_z_any`.

> flip_z_positivea boolean

>   Flip images to give positive zspace:step value (inf-to-sup). Maps to a command-line argument: `+zdirection`. Mutually exclusive with inputs: `flip_z_positive`, `flip_z_negative`, `flip_z_any`.

> image_maximuma float

>   Specify the maximum real image value for normalization.Default value: 1.79769e+308. Maps to a command-line argument: `-image_maximum %s`.

> image_minimuma float

>   Specify the minimum real image value for normalization.Default value: 1.79769e+308. Maps to a command-line argument: `-image_minimum %s`.

> image_rangea tuple of the form: (a float, a float)

>   Specify the range of real image values for normalization. Maps to a command-line argument: `-image_range %s %s`.

> nonormalizea boolean

>   Turn off pixel normalization. Maps to a command-line argument: `-nonormalize`. Mutually exclusive with inputs: `normalize`, `nonormalize`.

> normalizea boolean

>   Normalize integer pixel values to file max and min. Maps to a command-line argument: `-normalize`. Mutually exclusive with inputs: `normalize`, `nonormalize`.

> out_filea pathlike object or string representing a file

>   Maps to a command-line argument: `> %s` (position: -1).

> output_filea pathlike object or string representing a file

>   Output file.

> starta list of items which are an integer

>   Specifies corner of hyperslab (C conventions for indices). Maps to a command-line argument: `-start %s`.

> write_asciia boolean

>   Write out data as ascii strings (default). Maps to a command-line argument: `-ascii`. Mutually exclusive with inputs: `write_ascii`, `write_ascii`, `write_byte`, `write_short`, `write_int`, `write_long`, `write_float`, `write_double`, `write_signed`, `write_unsigned`.

> write_bytea boolean

>   Write out data as bytes. Maps to a command-line argument: `-byte`. Mutually exclusive with inputs: `write_ascii`, `write_ascii`, `write_byte`, `write_short`, `write_int`, `write_long`, `write_float`, `write_double`, `write_signed`, `write_unsigned`.

> write_doublea boolean

>   Write out data as double precision floating-point values. Maps to a command-line argument: `-double`. Mutually exclusive with inputs: `write_ascii`, `write_ascii`, `write_byte`, `write_short`, `write_int`, `write_long`, `write_float`, `write_double`, `write_signed`, `write_unsigned`.

> write_floata boolean

>   Write out data as single precision floating-point values. Maps to a command-line argument: `-float`. Mutually exclusive with inputs: `write_ascii`, `write_ascii`, `write_byte`, `write_short`, `write_int`, `write_long`, `write_float`, `write_double`, `write_signed`, `write_unsigned`.

> write_inta boolean

>   Write out data as 32-bit integers. Maps to a command-line argument: `-int`. Mutually exclusive with inputs: `write_ascii`, `write_ascii`, `write_byte`, `write_short`, `write_int`, `write_long`, `write_float`, `write_double`, `write_signed`, `write_unsigned`.

> write_longa boolean

>   Superseded by write_int. Maps to a command-line argument: `-long`. Mutually exclusive with inputs: `write_ascii`, `write_ascii`, `write_byte`, `write_short`, `write_int`, `write_long`, `write_float`, `write_double`, `write_signed`, `write_unsigned`.

> write_rangea tuple of the form: (a float, a float)

>   Specify the range of output values Default value: 1.79769e+308 1.79769e+308. Maps to a command-line argument: `-range %s %s`.

> write_shorta boolean

>   Write out data as short integers. Maps to a command-line argument: `-short`. Mutually exclusive with inputs: `write_ascii`, `write_ascii`, `write_byte`, `write_short`, `write_int`, `write_long`, `write_float`, `write_double`, `write_signed`, `write_unsigned`.

> write_signeda boolean

>   Write out signed data. Maps to a command-line argument: `-signed`. Mutually exclusive with inputs: `write_signed`, `write_unsigned`.

> write_unsigneda boolean

>   Write out unsigned data. Maps to a command-line argument: `-unsigned`. Mutually exclusive with inputs: `write_signed`, `write_unsigned`.

> output_filea pathlike object or string representing an existing file

>   Output file in raw/text format.

## Gennlxfm

Link to code

> Bases: CommandLine

> Wrapped executable: `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()

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> clobbera boolean

>   Overwrite existing file. Maps to a command-line argument: `-clobber`. (Nipype default value: `True`)

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> identa boolean

>   Generate an identity xfm. Default: False. Maps to a command-line argument: `-ident`.

> likea pathlike object or string representing an existing file

>   Generate a nlxfm like this file. Maps to a command-line argument: `-like %s`.

> output_filea pathlike object or string representing a file

>   Output file. Maps to a command-line argument: `%s` (position: -1).

> stepan integer

>   Output ident xfm step [default: 1]. Maps to a command-line argument: `-step %s`.

> verbosea boolean

>   Print out log messages. Default: False. Maps to a command-line argument: `-verbose`.

> output_filea pathlike object or string representing an existing file

>   Output file.

> output_grida pathlike object or string representing an existing file

>   Output grid.

## Math

Link to code

> Bases: StdOutCommandLine

> Wrapped executable: `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()

> filelista pathlike object or string representing an existing file

>   Specify the name of a file containing input file names. Maps to a command-line argument: `-filelist %s`. Mutually exclusive with inputs: `input_files`, `filelist`.

> input_filesa list of items which are a pathlike object or string representing an existing file

>   Input file(s) for calculation. Maps to a command-line argument: `%s` (position: -2). Mutually exclusive with inputs: `input_files`, `filelist`.

> absa boolean

>   Take absolute value of a volume. Maps to a command-line argument: `-abs`.

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> calc_adda boolean or a float

>   Add N volumes or volume + constant. Maps to a command-line argument: `-add`.

> calc_anda boolean

>   Calculate vol1 && vol2 (&& …). Maps to a command-line argument: `-and`.

> calc_diva boolean or a float

>   Divide 2 volumes or volume / constant. Maps to a command-line argument: `-div`.

> calc_mula boolean or a float

>   Multiply N volumes or volume * constant. Maps to a command-line argument: `-mult`.

> calc_nota boolean

>   Calculate !vol1. Maps to a command-line argument: `-not`.

> calc_ora boolean

>   Calculate vol1 || vol2 (|| …). Maps to a command-line argument: `-or`.

> calc_suba boolean or a float

>   Subtract 2 volumes or volume - constant. Maps to a command-line argument: `-sub`.

> check_dimensionsa boolean

>   Check that dimension info matches across files (default). Maps to a command-line argument: `-check_dimensions`. Mutually exclusive with inputs: `check_dimensions`, `no_check_dimensions`.

> clampa tuple of the form: (a float, a float)

>   Clamp a volume to lie between two values. Maps to a command-line argument: `-clamp -const2 %s %s`.

> clobbera boolean

>   Overwrite existing file. Maps to a command-line argument: `-clobber`. (Nipype default value: `True`)

> copy_headera boolean

>   Copy all of the header from the first file (default for one file). Maps to a command-line argument: `-copy_header`. Mutually exclusive with inputs: `copy_header`, `no_copy_header`.

> count_valida boolean

>   Count the number of valid values in N volumes. Maps to a command-line argument: `-count_valid`.

> dimensiona string

>   Specify a dimension along which we wish to perform a calculation. Maps to a command-line argument: `-dimension %s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> expa tuple of the form: (a float, a float)

>   Calculate c2*exp(c1*x). Both constants must be specified. Maps to a command-line argument: `-exp -const2 %s %s`.

> format_bytea boolean

>   Write out byte data. Maps to a command-line argument: `-byte`. Mutually exclusive with inputs: `format_filetype`, `format_byte`, `format_short`, `format_int`, `format_long`, `format_float`, `format_double`, `format_signed`, `format_unsigned`.

> format_doublea boolean

>   Write out double-precision floating-point data. Maps to a command-line argument: `-double`. Mutually exclusive with inputs: `format_filetype`, `format_byte`, `format_short`, `format_int`, `format_long`, `format_float`, `format_double`, `format_signed`, `format_unsigned`.

> format_filetypea boolean

>   Use data type of first file (default). Maps to a command-line argument: `-filetype`. Mutually exclusive with inputs: `format_filetype`, `format_byte`, `format_short`, `format_int`, `format_long`, `format_float`, `format_double`, `format_signed`, `format_unsigned`.

> format_floata boolean

>   Write out single-precision floating-point data. Maps to a command-line argument: `-float`. Mutually exclusive with inputs: `format_filetype`, `format_byte`, `format_short`, `format_int`, `format_long`, `format_float`, `format_double`, `format_signed`, `format_unsigned`.

> format_inta boolean

>   Write out 32-bit integer data. Maps to a command-line argument: `-int`. Mutually exclusive with inputs: `format_filetype`, `format_byte`, `format_short`, `format_int`, `format_long`, `format_float`, `format_double`, `format_signed`, `format_unsigned`.

> format_longa boolean

>   Superseded by -int. Maps to a command-line argument: `-long`. Mutually exclusive with inputs: `format_filetype`, `format_byte`, `format_short`, `format_int`, `format_long`, `format_float`, `format_double`, `format_signed`, `format_unsigned`.

> format_shorta boolean

>   Write out short integer data. Maps to a command-line argument: `-short`. Mutually exclusive with inputs: `format_filetype`, `format_byte`, `format_short`, `format_int`, `format_long`, `format_float`, `format_double`, `format_signed`, `format_unsigned`.

> format_signeda boolean

>   Write signed integer data. Maps to a command-line argument: `-signed`. Mutually exclusive with inputs: `format_filetype`, `format_byte`, `format_short`, `format_int`, `format_long`, `format_float`, `format_double`, `format_signed`, `format_unsigned`.

> format_unsigneda boolean

>   Write unsigned integer data (default). Maps to a command-line argument: `-unsigned`. Mutually exclusive with inputs: `format_filetype`, `format_byte`, `format_short`, `format_int`, `format_long`, `format_float`, `format_double`, `format_signed`, `format_unsigned`.

> ignore_nana boolean

>   Ignore invalid data (NaN) for accumulations. Maps to a command-line argument: `-ignore_nan`.

> inverta float

>   Calculate 1/c. Maps to a command-line argument: `-invert -const %s`.

> isnana boolean

>   Test for NaN values in vol1. Maps to a command-line argument: `-isnan`.

> loga tuple of the form: (a float, a float)

>   Calculate log(x/c2)/c1. The constants c1 and c2 default to 1. Maps to a command-line argument: `-log -const2 %s %s`.

> max_buffer_size_in_kban integer >= 0

>   Specify the maximum size of the internal buffers (in kbytes). Maps to a command-line argument: `-max_buffer_size_in_kb %d`. (Nipype default value: `4096`)

> maximuma boolean

>   Find maximum of N volumes. Maps to a command-line argument: `-maximum`.

> minimuma boolean

>   Find minimum of N volumes. Maps to a command-line argument: `-minimum`.

> nisnana boolean

>   Negation of -isnan. Maps to a command-line argument: `-nisnan`.

> no_check_dimensionsa boolean

>   Do not check dimension info. Maps to a command-line argument: `-nocheck_dimensions`. Mutually exclusive with inputs: `check_dimensions`, `no_check_dimensions`.

> no_copy_headera boolean

>   Do not copy all of the header from the first file (default for many files)). Maps to a command-line argument: `-nocopy_header`. Mutually exclusive with inputs: `copy_header`, `no_copy_header`.

> nsegmenta tuple of the form: (a float, a float)

>   Opposite of -segment: within range = 0, outside range = 1. Maps to a command-line argument: `-nsegment -const2 %s %s`.

> output_filea pathlike object or string representing a file

>   Output file. Maps to a command-line argument: `%s` (position: -1).

> output_illegala boolean

>   Value to write out when an illegal operationis done. Default value: 1.79769e+308. Maps to a command-line argument: `-illegal_value`. Mutually exclusive with inputs: `output_nan`, `output_zero`, `output_illegal_value`.

> output_nana boolean

>   Output NaN when an illegal operation is done (default). Maps to a command-line argument: `-nan`. Mutually exclusive with inputs: `output_nan`, `output_zero`, `output_illegal_value`.

> output_zeroa boolean

>   Output zero when an illegal operation is done. Maps to a command-line argument: `-zero`. Mutually exclusive with inputs: `output_nan`, `output_zero`, `output_illegal_value`.

> percentdiffa float

>   Percent difference between 2 volumes, thresholded (const def=0.0). Maps to a command-line argument: `-percentdiff`.

> propagate_nana boolean

>   Invalid data in any file at a voxel produces a NaN (default). Maps to a command-line argument: `-propagate_nan`.

> scalea tuple of the form: (a float, a float)

>   Scale a volume: volume * c1 + c2. Maps to a command-line argument: `-scale -const2 %s %s`.

> segmenta tuple of the form: (a float, a float)

>   Segment a volume using range of -const2: within range = 1, outside range = 0. Maps to a command-line argument: `-segment -const2 %s %s`.

> sqrta boolean

>   Take square root of a volume. Maps to a command-line argument: `-sqrt`.

> squarea boolean

>   Take square of a volume. Maps to a command-line argument: `-square`.

> test_eqa boolean or a float

>   Test for integer vol1 == vol2 or vol1 == constant. Maps to a command-line argument: `-eq`.

> test_gea boolean or a float

>   Test for vol1 >= vol2 or vol1 >= const. Maps to a command-line argument: `-ge`.

> test_gta boolean or a float

>   Test for vol1 > vol2 or vol1 > constant. Maps to a command-line argument: `-gt`.

> test_lea boolean or a float

>   Test for vol1 <= vol2 or vol1 <= const. Maps to a command-line argument: `-le`.

> test_lta boolean or a float

>   Test for vol1 < vol2 or vol1 < constant. Maps to a command-line argument: `-lt`.

> test_nea boolean or a float

>   Test for integer vol1 != vol2 or vol1 != const. Maps to a command-line argument: `-ne`.

> twoa boolean

>   Create a MINC 2 output file. Maps to a command-line argument: `-2`.

> voxel_rangea tuple of the form: (an integer, an integer)

>   Valid range for output data. Maps to a command-line argument: `-range %d %d`.

> output_filea pathlike object or string representing an existing file

>   Output file.

## NlpFit

Link to code

> Bases: CommandLine

> Wrapped executable: `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()

> config_filea pathlike object or string representing an existing file

>   File containing the fitting configuration use. Maps to a command-line argument: `-config_file %s`.

> init_xfma pathlike object or string representing an existing file

>   Initial transformation (default identity). Maps to a command-line argument: `-init_xfm %s`.

> sourcea pathlike object or string representing an existing file

>   Source Minc file. Maps to a command-line argument: `%s` (position: -3).

> source_maska pathlike object or string representing an existing file

>   Source mask to use during fitting. Maps to a command-line argument: `-source_mask %s`.

> targeta pathlike object or string representing an existing file

>   Target Minc file. Maps to a command-line argument: `%s` (position: -2).

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> clobbera boolean

>   Overwrite existing file. Maps to a command-line argument: `-clobber`. (Nipype default value: `True`)

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> input_grid_filesa list of items which are a pathlike object or string representing a file

>   Input grid file(s).

> output_xfma pathlike object or string representing a file

>   Output xfm file. Maps to a command-line argument: `%s` (position: -1).

> verbosea boolean

>   Print out log messages. Default: False. Maps to a command-line argument: `-verbose`.

> output_grida pathlike object or string representing an existing file

>   Output grid file.

> output_xfma pathlike object or string representing an existing file

>   Output xfm file.

## Norm

Link to code

> Bases: CommandLine

> Wrapped executable: `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()

> input_filea pathlike object or string representing an existing file

>   Input file to normalise. Maps to a command-line argument: `%s` (position: -2).

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> clampa boolean

>   Force the output range between limits [default]. Maps to a command-line argument: `-clamp`. (Nipype default value: `True`)

> clobbera boolean

>   Overwrite existing file. Maps to a command-line argument: `-clobber`. (Nipype default value: `True`)

> cutoff0.0 <= a floating point number <= 100.0

>   Cutoff value to use to calculate thresholds by a histogram PcT in %. [default: 0.01]. Maps to a command-line argument: `-cutoff %s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> lowera float

>   Lower real value to use. Maps to a command-line argument: `-lower %s`.

> maska pathlike object or string representing an existing file

>   Calculate the image normalisation within a mask. Maps to a command-line argument: `-mask %s`.

> out_ceila float

>   Output files minimum [default: 100]. Maps to a command-line argument: `-out_ceil %s`.

> out_floora float

>   Output files maximum [default: 0]. Maps to a command-line argument: `-out_floor %s`.

> output_filea pathlike object or string representing a file

>   Output file. Maps to a command-line argument: `%s` (position: -1).

> output_threshold_maska pathlike object or string representing a file

>   File in which to store the threshold mask. Maps to a command-line argument: `-threshold_mask %s`.

> thresholda boolean

>   Threshold the image (set values below threshold_perc to -out_floor). Maps to a command-line argument: `-threshold`.

> threshold_blura float

>   Blur FWHM for intensity edges then thresholding [default: 2]. Maps to a command-line argument: `-threshold_blur %s`.

> threshold_bmta boolean

>   Use the resulting image BiModalT as the threshold. Maps to a command-line argument: `-threshold_bmt`.

> threshold_perc0.0 <= a floating point number <= 100.0

>   Threshold percentage (0.1 == lower 10% of intensity range) [default: 0.1]. Maps to a command-line argument: `-threshold_perc %s`.

> uppera float

>   Upper real value to use. Maps to a command-line argument: `-upper %s`.

> output_filea pathlike object or string representing an existing file

>   Output file.

> output_threshold_maska pathlike object or string representing a file

>   Threshold mask file.

## Pik

Link to code

> Bases: CommandLine

> Wrapped executable: `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()

> input_filea pathlike object or string representing an existing file

>   Input file. Maps to a command-line argument: `%s` (position: -2).

> annotated_bara boolean

>   Create an annotated bar to match the image (use height of the output image). Maps to a command-line argument: `--anot_bar`.

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> auto_rangea boolean

>   Automatically determine image range using a 5 and 95% PcT. (histogram). Maps to a command-line argument: `--auto_range`. Mutually exclusive with inputs: `image_range`, `auto_range`.

> clobbera boolean

>   Overwrite existing file. Maps to a command-line argument: `-clobber`. (Nipype default value: `True`)

> depth8 or 16

>   Bitdepth for resulting image 8 or 16 (MSB machines only!). Maps to a command-line argument: `--depth %s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> horizontal_triplanar_viewa boolean

>   Create a horizontal triplanar view. Maps to a command-line argument: `--horizontal`. Mutually exclusive with inputs: `vertical_triplanar_view`, `horizontal_triplanar_view`.

> image_rangea tuple of the form: (a float, a float)

>   Range of image values to use for pixel intensity. Maps to a command-line argument: `--image_range %s %s`. Mutually exclusive with inputs: `image_range`, `auto_range`.

> jpga boolean

>   Output a jpg file. Mutually exclusive with inputs: `jpg`, `png`.

> lookupa string

>   Arguments to pass to minclookup. Maps to a command-line argument: `--lookup %s`.

> minc_rangea tuple of the form: (a float, a float)

>   Valid range of values for MINC file. Maps to a command-line argument: `--range %s %s`.

> output_filea pathlike object or string representing a file

>   Output file. Maps to a command-line argument: `%s` (position: -1).

> pnga boolean

>   Output a png file (default). Mutually exclusive with inputs: `jpg`, `png`.

> sagittal_offsetan integer

>   Offset the sagittal slice from the centre. Maps to a command-line argument: `--sagittal_offset %s`.

> sagittal_offset_perc0 <= an integer <= 100

>   Offset the sagittal slice by a percentage from the centre. Maps to a command-line argument: `--sagittal_offset_perc %d`.

> scalean integer

>   Scaling factor for resulting image. By default images areoutput at twice their original resolution. Maps to a command-line argument: `--scale %s`. (Nipype default value: `2`)

> slice_xa boolean

>   Get a sagittal (x) slice. Maps to a command-line argument: `-x`. Mutually exclusive with inputs: `slice_z`, `slice_y`, `slice_x`.

> slice_ya boolean

>   Get a coronal (y) slice. Maps to a command-line argument: `-y`. Mutually exclusive with inputs: `slice_z`, `slice_y`, `slice_x`.

> slice_za boolean

>   Get an axial/transverse (z) slice. Maps to a command-line argument: `-z`. Mutually exclusive with inputs: `slice_z`, `slice_y`, `slice_x`.

> startan integer

>   Slice number to get. (note this is in voxel coordinates). Maps to a command-line argument: `--slice %s`.

> tile_sizean integer

>   Pixel size for each image in a triplanar. Maps to a command-line argument: `--tilesize %s`.

> titlea boolean or a string

>   Maps to a command-line argument: `%s`.

> title_sizean integer

>   Font point size for the title. Maps to a command-line argument: `--title_size %s`. Requires inputs: `title`.

> triplanara boolean

>   Create a triplanar view of the input file. Maps to a command-line argument: `--triplanar`.

> vertical_triplanar_viewa boolean

>   Create a vertical triplanar view (Default). Maps to a command-line argument: `--vertical`. Mutually exclusive with inputs: `vertical_triplanar_view`, `horizontal_triplanar_view`.

> widthan integer

>   Autoscale the resulting image to have a fixed image width (in pixels). Maps to a command-line argument: `--width %s`.

> output_filea pathlike object or string representing an existing file

>   Output image.

## Resample

Link to code

> Bases: StdOutCommandLine

> Wrapped executable: `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()

> input_filea pathlike object or string representing an existing file

>   Input file for resampling. Maps to a command-line argument: `%s` (position: -2).

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> clobbera boolean

>   Overwrite existing file. Maps to a command-line argument: `-clobber`. (Nipype default value: `True`)

> coronal_slicesa boolean

>   Write out coronal slices. Maps to a command-line argument: `-coronal`. Mutually exclusive with inputs: `transverse`, `sagittal`, `coronal`.

> dircosa 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. Maps to a command-line argument: `-dircos %s %s %s`. Mutually exclusive with inputs: `nelements`, `nelements_x_y_or_z`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> filla boolean

>   Use a fill value for points outside of input volume. Maps to a command-line argument: `-fill`. Mutually exclusive with inputs: `nofill`, `fill`.

> fill_valuea float

>   Specify a fill value for points outside of input volume.Default value: 1.79769e+308. Maps to a command-line argument: `-fillvalue %s`. Requires inputs: `fill`.

> format_bytea boolean

>   Write out byte data. Maps to a command-line argument: `-byte`. Mutually exclusive with inputs: `format_byte`, `format_short`, `format_int`, `format_long`, `format_float`, `format_double`, `format_signed`, `format_unsigned`.

> format_doublea boolean

>   Write out double-precision floating-point data. Maps to a command-line argument: `-double`. Mutually exclusive with inputs: `format_byte`, `format_short`, `format_int`, `format_long`, `format_float`, `format_double`, `format_signed`, `format_unsigned`.

> format_floata boolean

>   Write out single-precision floating-point data. Maps to a command-line argument: `-float`. Mutually exclusive with inputs: `format_byte`, `format_short`, `format_int`, `format_long`, `format_float`, `format_double`, `format_signed`, `format_unsigned`.

> format_inta boolean

>   Write out 32-bit integer data. Maps to a command-line argument: `-int`. Mutually exclusive with inputs: `format_byte`, `format_short`, `format_int`, `format_long`, `format_float`, `format_double`, `format_signed`, `format_unsigned`.

> format_longa boolean

>   Superseded by -int. Maps to a command-line argument: `-long`. Mutually exclusive with inputs: `format_byte`, `format_short`, `format_int`, `format_long`, `format_float`, `format_double`, `format_signed`, `format_unsigned`.

> format_shorta boolean

>   Write out short integer data. Maps to a command-line argument: `-short`. Mutually exclusive with inputs: `format_byte`, `format_short`, `format_int`, `format_long`, `format_float`, `format_double`, `format_signed`, `format_unsigned`.

> format_signeda boolean

>   Write signed integer data. Maps to a command-line argument: `-signed`. Mutually exclusive with inputs: `format_byte`, `format_short`, `format_int`, `format_long`, `format_float`, `format_double`, `format_signed`, `format_unsigned`.

> format_unsigneda boolean

>   Write unsigned integer data (default). Maps to a command-line argument: `-unsigned`. Mutually exclusive with inputs: `format_byte`, `format_short`, `format_int`, `format_long`, `format_float`, `format_double`, `format_signed`, `format_unsigned`.

> half_width_sinc_window5 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. Maps to a command-line argument: `-width %s`. Requires inputs: `sinc_interpolation`.

> input_grid_filesa list of items which are a pathlike object or string representing a file

>   Input grid file(s).

> invert_transformationa boolean

>   Invert the transformation before using it. Maps to a command-line argument: `-invert_transformation`.

> keep_real_rangea boolean

>   Keep the real scale of the input volume. Maps to a command-line argument: `-keep_real_range`. Mutually exclusive with inputs: `keep_real_range`, `nokeep_real_range`.

> likea pathlike object or string representing an existing file

>   Specifies a model file for the resampling. Maps to a command-line argument: `-like %s`.

> nearest_neighbour_interpolationa boolean

>   Do nearest neighbour interpolation. Maps to a command-line argument: `-nearest_neighbour`. Mutually exclusive with inputs: `trilinear_interpolation`, `tricubic_interpolation`, `nearest_neighbour_interpolation`, `sinc_interpolation`.

> nelementsa tuple of the form: (an integer, an integer, an integer)

>   Number of elements along each dimension (X, Y, Z). Maps to a command-line argument: `-nelements %s %s %s`. Mutually exclusive with inputs: `nelements`, `nelements_x_y_or_z`.

> no_filla boolean

>   Use value zero for points outside of input volume. Maps to a command-line argument: `-nofill`. Mutually exclusive with inputs: `nofill`, `fill`.

> no_input_samplinga boolean

>   Use the input sampling without transforming (old behaviour). Maps to a command-line argument: `-use_input_sampling`. Mutually exclusive with inputs: `vio_transform`, `no_input_sampling`.

> nokeep_real_rangea boolean

>   Do not keep the real scale of the data (default). Maps to a command-line argument: `-nokeep_real_range`. Mutually exclusive with inputs: `keep_real_range`, `nokeep_real_range`.

> origina 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. Maps to a command-line argument: `-origin %s %s %s`.

> output_filea pathlike object or string representing a file

>   Output file. Maps to a command-line argument: `%s` (position: -1).

> output_rangea tuple of the form: (a float, a float)

>   Valid range for output data. Default value: -1.79769e+308 -1.79769e+308. Maps to a command-line argument: `-range %s %s`.

> sagittal_slicesa boolean

>   Write out sagittal slices. Maps to a command-line argument: `-sagittal`. Mutually exclusive with inputs: `transverse`, `sagittal`, `coronal`.

> sinc_interpolationa boolean

>   Do windowed sinc interpolation. Maps to a command-line argument: `-sinc`. Mutually exclusive with inputs: `trilinear_interpolation`, `tricubic_interpolation`, `nearest_neighbour_interpolation`, `sinc_interpolation`.

> sinc_window_hamminga boolean

>   Set sinc window type to Hamming. Maps to a command-line argument: `-hamming`. Mutually exclusive with inputs: `sinc_window_hanning`, `sinc_window_hamming`. Requires inputs: `sinc_interpolation`.

> sinc_window_hanninga boolean

>   Set sinc window type to Hanning. Maps to a command-line argument: `-hanning`. Mutually exclusive with inputs: `sinc_window_hanning`, `sinc_window_hamming`. Requires inputs: `sinc_interpolation`.

> spacetypea string

>   Set the spacetype attribute to a specified string. Maps to a command-line argument: `-spacetype %s`.

> standard_samplinga boolean

>   Set the sampling to standard values (step, start and dircos). Maps to a command-line argument: `-standard_sampling`.

> starta 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. Maps to a command-line argument: `-start %s %s %s`. Mutually exclusive with inputs: `nelements`, `nelements_x_y_or_z`.

> stepa tuple of the form: (an integer, an integer, an integer)

>   Step size along each dimension (X, Y, Z). Default value: (0, 0, 0). Maps to a command-line argument: `-step %s %s %s`. Mutually exclusive with inputs: `nelements`, `nelements_x_y_or_z`.

> talairacha boolean

>   Output is in Talairach space. Maps to a command-line argument: `-talairach`.

> transformationa pathlike object or string representing an existing file

>   File giving world transformation. (Default = identity). Maps to a command-line argument: `-transformation %s`.

> transverse_slicesa boolean

>   Write out transverse slices. Maps to a command-line argument: `-transverse`. Mutually exclusive with inputs: `transverse`, `sagittal`, `coronal`.

> tricubic_interpolationa boolean

>   Do tricubic interpolation. Maps to a command-line argument: `-tricubic`. Mutually exclusive with inputs: `trilinear_interpolation`, `tricubic_interpolation`, `nearest_neighbour_interpolation`, `sinc_interpolation`.

> trilinear_interpolationa boolean

>   Do trilinear interpolation. Maps to a command-line argument: `-trilinear`. Mutually exclusive with inputs: `trilinear_interpolation`, `tricubic_interpolation`, `nearest_neighbour_interpolation`, `sinc_interpolation`.

> twoa boolean

>   Create a MINC 2 output file. Maps to a command-line argument: `-2`.

> unitsa string

>   Specify the units of the output sampling. Maps to a command-line argument: `-units %s`.

> vio_transforma boolean

>   VIO_Transform the input sampling with the transform (default). Maps to a command-line argument: `-tfm_input_sampling`. Mutually exclusive with inputs: `vio_transform`, `no_input_sampling`.

> xdircosa float

>   Direction cosines along the X dimension.Default value: 1.79769e+308 1.79769e+308 1.79769e+308. Maps to a command-line argument: `-xdircos %s`. Mutually exclusive with inputs: `dircos`, `dircos_x_y_or_z`. Requires inputs: `ydircos`, `zdircos`.

> xnelementsan integer

>   Number of elements along the X dimension. Maps to a command-line argument: `-xnelements %s`. Mutually exclusive with inputs: `nelements`, `nelements_x_y_or_z`. Requires inputs: `ynelements`, `znelements`.

> xstarta float

>   Start point along the X dimension. Default value: 1.79769e+308. Maps to a command-line argument: `-xstart %s`. Mutually exclusive with inputs: `start`, `start_x_y_or_z`. Requires inputs: `ystart`, `zstart`.

> xstepan integer

>   Step size along the X dimension. Default value: 0. Maps to a command-line argument: `-xstep %s`. Mutually exclusive with inputs: `step`, `step_x_y_or_z`. Requires inputs: `ystep`, `zstep`.

> ydircosa float

>   Direction cosines along the Y dimension.Default value: 1.79769e+308 1.79769e+308 1.79769e+308. Maps to a command-line argument: `-ydircos %s`. Mutually exclusive with inputs: `dircos`, `dircos_x_y_or_z`. Requires inputs: `xdircos`, `zdircos`.

> ynelementsan integer

>   Number of elements along the Y dimension. Maps to a command-line argument: `-ynelements %s`. Mutually exclusive with inputs: `nelements`, `nelements_x_y_or_z`. Requires inputs: `xnelements`, `znelements`.

> ystarta float

>   Start point along the Y dimension. Default value: 1.79769e+308. Maps to a command-line argument: `-ystart %s`. Mutually exclusive with inputs: `start`, `start_x_y_or_z`. Requires inputs: `xstart`, `zstart`.

> ystepan integer

>   Step size along the Y dimension. Default value: 0. Maps to a command-line argument: `-ystep %s`. Mutually exclusive with inputs: `step`, `step_x_y_or_z`. Requires inputs: `xstep`, `zstep`.

> zdircosa float

>   Direction cosines along the Z dimension.Default value: 1.79769e+308 1.79769e+308 1.79769e+308. Maps to a command-line argument: `-zdircos %s`. Mutually exclusive with inputs: `dircos`, `dircos_x_y_or_z`. Requires inputs: `xdircos`, `ydircos`.

> znelementsan integer

>   Number of elements along the Z dimension. Maps to a command-line argument: `-znelements %s`. Mutually exclusive with inputs: `nelements`, `nelements_x_y_or_z`. Requires inputs: `xnelements`, `ynelements`.

> zstarta float

>   Start point along the Z dimension. Default value: 1.79769e+308. Maps to a command-line argument: `-zstart %s`. Mutually exclusive with inputs: `start`, `start_x_y_or_z`. Requires inputs: `xstart`, `ystart`.

> zstepan integer

>   Step size along the Z dimension. Default value: 0. Maps to a command-line argument: `-zstep %s`. Mutually exclusive with inputs: `step`, `step_x_y_or_z`. Requires inputs: `xstep`, `ystep`.

> output_filea pathlike object or string representing an existing file

>   Output file.

## Reshape

Link to code

> Bases: CommandLine

> Wrapped executable: `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()

> input_filea pathlike object or string representing an existing file

>   Input file. Maps to a command-line argument: `%s` (position: -2).

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> clobbera boolean

>   Overwrite existing file. Maps to a command-line argument: `-clobber`. (Nipype default value: `True`)

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> output_filea pathlike object or string representing a file

>   Output file. Maps to a command-line argument: `%s` (position: -1).

> verbosea boolean

>   Print out log messages. Default: False. Maps to a command-line argument: `-verbose`.

> write_shorta boolean

>   Convert to short integer data. Maps to a command-line argument: `-short`.

> output_filea pathlike object or string representing an existing file

>   Output file.

## ToEcat

Link to code

> Bases: CommandLine

> Wrapped executable: `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()

> input_filea pathlike object or string representing an existing file

>   Input file to convert. Maps to a command-line argument: `%s` (position: -2).

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> ignore_acquisition_variablea boolean

>   Ignore information from the minc acquisition variable. Maps to a command-line argument: `-ignore_acquisition_variable`.

> ignore_ecat_acquisition_variablea boolean

>   Ignore information from the minc ecat_acquisition variable. Maps to a command-line argument: `-ignore_ecat_acquisition_variable`.

> ignore_ecat_maina boolean

>   Ignore information from the minc ecat-main variable. Maps to a command-line argument: `-ignore_ecat_main`.

> ignore_ecat_subheader_variablea boolean

>   Ignore information from the minc ecat-subhdr variable. Maps to a command-line argument: `-ignore_ecat_subheader_variable`.

> ignore_patient_variablea boolean

>   Ignore information from the minc patient variable. Maps to a command-line argument: `-ignore_patient_variable`.

> ignore_study_variablea boolean

>   Ignore information from the minc study variable. Maps to a command-line argument: `-ignore_study_variable`.

> no_decay_corr_fctra boolean

>   Do not compute the decay correction factors. Maps to a command-line argument: `-no_decay_corr_fctr`.

> output_filea pathlike object or string representing a file

>   Output file. Maps to a command-line argument: `%s` (position: -1).

> voxels_as_integersa boolean

>   Voxel values are treated as integers, scale andcalibration factors are set to unity. Maps to a command-line argument: `-label`.

> output_filea pathlike object or string representing an existing file

>   Output file.

## ToRaw

Link to code

> Bases: StdOutCommandLine

> Wrapped executable: `minctoraw`.

> Dump a chunk of MINC file data. This program is largely superseded 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()

> input_filea pathlike object or string representing an existing file

>   Input file. Maps to a command-line argument: `%s` (position: -2).

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> nonormalizea boolean

>   Turn off pixel normalization. Maps to a command-line argument: `-nonormalize`. Mutually exclusive with inputs: `normalize`, `nonormalize`.

> normalizea boolean

>   Normalize integer pixel values to file max and min. Maps to a command-line argument: `-normalize`. Mutually exclusive with inputs: `normalize`, `nonormalize`.

> out_filea pathlike object or string representing a file

>   Maps to a command-line argument: `> %s` (position: -1).

> output_filea pathlike object or string representing a file

>   Output file.

> write_bytea boolean

>   Write out data as bytes. Maps to a command-line argument: `-byte`. Mutually exclusive with inputs: `write_byte`, `write_short`, `write_int`, `write_long`, `write_float`, `write_double`.

> write_doublea boolean

>   Write out data as double precision floating-point values. Maps to a command-line argument: `-double`. Mutually exclusive with inputs: `write_byte`, `write_short`, `write_int`, `write_long`, `write_float`, `write_double`.

> write_floata boolean

>   Write out data as single precision floating-point values. Maps to a command-line argument: `-float`. Mutually exclusive with inputs: `write_byte`, `write_short`, `write_int`, `write_long`, `write_float`, `write_double`.

> write_inta boolean

>   Write out data as 32-bit integers. Maps to a command-line argument: `-int`. Mutually exclusive with inputs: `write_byte`, `write_short`, `write_int`, `write_long`, `write_float`, `write_double`.

> write_longa boolean

>   Superseded by write_int. Maps to a command-line argument: `-long`. Mutually exclusive with inputs: `write_byte`, `write_short`, `write_int`, `write_long`, `write_float`, `write_double`.

> write_rangea tuple of the form: (a float, a float)

>   Specify the range of output values.Default value: 1.79769e+308 1.79769e+308. Maps to a command-line argument: `-range %s %s`.

> write_shorta boolean

>   Write out data as short integers. Maps to a command-line argument: `-short`. Mutually exclusive with inputs: `write_byte`, `write_short`, `write_int`, `write_long`, `write_float`, `write_double`.

> write_signeda boolean

>   Write out signed data. Maps to a command-line argument: `-signed`. Mutually exclusive with inputs: `write_signed`, `write_unsigned`.

> write_unsigneda boolean

>   Write out unsigned data. Maps to a command-line argument: `-unsigned`. Mutually exclusive with inputs: `write_signed`, `write_unsigned`.

> output_filea pathlike object or string representing an existing file

>   Output file in raw format.

## VolSymm

Link to code

> Bases: CommandLine

> Wrapped executable: `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()

> input_filea pathlike object or string representing an existing file

>   Input file. Maps to a command-line argument: `%s` (position: -3).

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> clobbera boolean

>   Overwrite existing file. Maps to a command-line argument: `-clobber`. (Nipype default value: `True`)

> config_filea pathlike object or string representing an existing file

>   File containing the fitting configuration (nlpfit -help for info). Maps to a command-line argument: `-config_file %s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> fit_lineara boolean

>   Fit using a linear xfm. Maps to a command-line argument: `-linear`.

> fit_nonlineara boolean

>   Fit using a non-linear xfm. Maps to a command-line argument: `-nonlinear`.

> input_grid_filesa list of items which are a pathlike object or string representing a file

>   Input grid file(s).

> nofita boolean

>   Use the input transformation instead of generating one. Maps to a command-line argument: `-nofit`.

> output_filea pathlike object or string representing a file

>   Output file. Maps to a command-line argument: `%s` (position: -1).

> trans_filea pathlike object or string representing a file

>   Output xfm trans file. Maps to a command-line argument: `%s` (position: -2).

> verbosea boolean

>   Print out log messages. Default: False. Maps to a command-line argument: `-verbose`.

> xa boolean

>   Flip volume in x-plane (default). Maps to a command-line argument: `-x`.

> ya boolean

>   Flip volume in y-plane. Maps to a command-line argument: `-y`.

> za boolean

>   Flip volume in z-plane. Maps to a command-line argument: `-z`.

> output_filea pathlike object or string representing an existing file

>   Output file.

> output_grida pathlike object or string representing an existing file

>   Output grid file.

> trans_filea pathlike object or string representing an existing file

>   Xfm trans file.

## Volcentre

Link to code

> Bases: CommandLine

> Wrapped executable: `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()

> input_filea pathlike object or string representing an existing file

>   Input file to centre. Maps to a command-line argument: `%s` (position: -2).

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> centrea tuple of the form: (a float, a float, a float)

>   Centre to use (x,y,z) [default: 0 0 0]. Maps to a command-line argument: `-centre %s %s %s`.

> clobbera boolean

>   Overwrite existing file. Maps to a command-line argument: `-clobber`. (Nipype default value: `True`)

> coma boolean

>   Use the CoM of the volume for the new centre (via mincstats). Default: False. Maps to a command-line argument: `-com`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> output_filea pathlike object or string representing a file

>   Output file. Maps to a command-line argument: `%s` (position: -1).

> verbosea boolean

>   Print out log messages. Default: False. Maps to a command-line argument: `-verbose`.

> zero_dircosa boolean

>   Set the direction cosines to identity [default]. Maps to a command-line argument: `-zero_dircos`.

> output_filea pathlike object or string representing an existing file

>   Output file.

## Voliso

Link to code

> Bases: CommandLine

> Wrapped executable: `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()

> input_filea pathlike object or string representing an existing file

>   Input file to convert to isotropic sampling. Maps to a command-line argument: `%s` (position: -2).

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> avgstepa boolean

>   Calculate the maximum step from the average steps of the input volume. Maps to a command-line argument: `--avgstep`.

> clobbera boolean

>   Overwrite existing file. Maps to a command-line argument: `--clobber`. (Nipype default value: `True`)

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> maxstepa float

>   The target maximum step desired in the output volume. Maps to a command-line argument: `--maxstep %s`.

> minstepa float

>   The target minimum step desired in the output volume. Maps to a command-line argument: `--minstep %s`.

> output_filea pathlike object or string representing a file

>   Output file. Maps to a command-line argument: `%s` (position: -1).

> verbosea boolean

>   Print out log messages. Default: False. Maps to a command-line argument: `--verbose`.

> output_filea pathlike object or string representing an existing file

>   Output file.

## Volpad

Link to code

> Bases: CommandLine

> Wrapped executable: `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()

> input_filea pathlike object or string representing an existing file

>   Input file to centre. Maps to a command-line argument: `%s` (position: -2).

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> autoa boolean

>   Automatically determine padding distances (uses -distance as max). Default: False. Maps to a command-line argument: `-auto`.

> auto_freqa float

>   Frequency of voxels over bimodalt threshold to stop at [default: 500]. Maps to a command-line argument: `-auto_freq %s`.

> clobbera boolean

>   Overwrite existing file. Maps to a command-line argument: `-clobber`. (Nipype default value: `True`)

> distancean integer

>   Padding distance (in voxels) [default: 4]. Maps to a command-line argument: `-distance %s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> output_filea pathlike object or string representing a file

>   Output file. Maps to a command-line argument: `%s` (position: -1).

> smootha boolean

>   Smooth (blur) edges before padding. Default: False. Maps to a command-line argument: `-smooth`.

> smooth_distancean integer

>   Smoothing distance (in voxels) [default: 4]. Maps to a command-line argument: `-smooth_distance %s`.

> verbosea boolean

>   Print out log messages. Default: False. Maps to a command-line argument: `-verbose`.

> output_filea pathlike object or string representing an existing file

>   Output file.

## XfmAvg

Link to code

> Bases: CommandLine

> Wrapped executable: `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()

> input_filesa list of items which are a pathlike object or string representing an existing file

>   Input file(s). Maps to a command-line argument: `%s` (position: -2).

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> avg_lineara boolean

>   Average the linear part [default]. Maps to a command-line argument: `-avg_linear`.

> avg_nonlineara boolean

>   Average the non-linear part [default]. Maps to a command-line argument: `-avg_nonlinear`.

> clobbera boolean

>   Overwrite existing file. Maps to a command-line argument: `-clobber`. (Nipype default value: `True`)

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> ignore_lineara boolean

>   Opposite of -avg_linear. Maps to a command-line argument: `-ignore_linear`.

> ignore_nonlineara boolean

>   Opposite of -avg_nonlinear. Maps to a command-line argument: `-ignore_nonline`.

> input_grid_filesa list of items which are a pathlike object or string representing a file

>   Input grid file(s).

> output_filea pathlike object or string representing a file

>   Output file. Maps to a command-line argument: `%s` (position: -1).

> verbosea boolean

>   Print out log messages. Default: False. Maps to a command-line argument: `-verbose`.

> output_filea pathlike object or string representing an existing file

>   Output file.

> output_grida pathlike object or string representing an existing file

>   Output grid file.

## XfmConcat

Link to code

> Bases: CommandLine

> Wrapped executable: `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()

> input_filesa list of items which are a pathlike object or string representing an existing file

>   Input file(s). Maps to a command-line argument: `%s` (position: -2).

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> clobbera boolean

>   Overwrite existing file. Maps to a command-line argument: `-clobber`. (Nipype default value: `True`)

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> input_grid_filesa list of items which are a pathlike object or string representing a file

>   Input grid file(s).

> output_filea pathlike object or string representing a file

>   Output file. Maps to a command-line argument: `%s` (position: -1).

> verbosea boolean

>   Print out log messages. Default: False. Maps to a command-line argument: `-verbose`.

> output_filea pathlike object or string representing an existing file

>   Output file.

> output_gridsa list of items which are a pathlike object or string representing an existing file

>   Output grids.

## XfmInvert

Link to code

> Bases: CommandLine

> Wrapped executable: `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()

> input_filea pathlike object or string representing an existing file

>   Input file. Maps to a command-line argument: `%s` (position: -2).

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> clobbera boolean

>   Overwrite existing file. Maps to a command-line argument: `-clobber`. (Nipype default value: `True`)

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> output_filea pathlike object or string representing a file

>   Output file. Maps to a command-line argument: `%s` (position: -1).

> verbosea boolean

>   Print out log messages. Default: False. Maps to a command-line argument: `-verbose`.

> output_filea pathlike object or string representing an existing file

>   Output file.

> output_grida pathlike object or string representing an existing file

>   Output grid file.