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.

  1. 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 ouput 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 co-ordinates). 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 informations from the minc acquisition variable. Maps to a command-line argument: -ignore_acquisition_variable.

ignore_ecat_acquisition_variablea boolean

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

ignore_ecat_maina boolean

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

ignore_ecat_subheader_variablea boolean

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

ignore_patient_variablea boolean

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

ignore_study_variablea boolean

Ignore informations 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 superceded by mincextract (see Extract).

Examples

>>> from nipype.interfaces.minc import ToRaw
>>> from nipype.interfaces.minc.testdata import minc2Dfile
>>> toraw = ToRaw(input_file=minc2Dfile)
>>> toraw.run() 
>>> toraw = ToRaw(input_file=minc2Dfile, write_range=(0, 100))
>>> toraw.run() 
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.