mrinfo

Synopsis

Display image header information, or extract specific information from the header

Usage

mrinfo [ options ]  image [ image ... ]
  • image: the input image(s).

Description

By default, all information contained in each image header will be printed to the console in a reader-friendly format.

Alternatively, command-line options may be used to extract specific details from the header(s); these are printed to the console in a format more appropriate for scripting purposes or piping to file. If multiple options and/or images are provided, the requested header fields will be printed in the order in which they appear in the help page, with all requested details from each input image in sequence printed before the next image is processed.

The command can also write the diffusion gradient table from a single input image to file; either in the MRtrix or FSL format (bvecs/bvals file pair; includes appropriate diffusion gradient vector reorientation)

Options

  • -all print all properties, rather than the first and last 2 of each.
  • -format image file format
  • -ndim number of image dimensions
  • -size image size along each axis
  • -spacing voxel spacing along each image dimension
  • -datatype data type used for image data storage
  • -strides data strides i.e. order and direction of axes data layout
  • -offset image intensity offset
  • -multiplier image intensity multiplier
  • -transform the transformation from image coordinates [mm] to scanner / real world coordinates [mm]
  • -norealign do not realign transform to near-default RAS coordinate system (the default behaviour on image load). This is useful to inspect the image and/or header contents as they are actually stored in the header, rather than as MRtrix interprets them.

Options for exporting image header fields

  • -property key (multiple uses permitted) any text properties embedded in the image header under the specified key (use ‘all’ to list all keys found)
  • -json_keyval file export header key/value entries to a JSON file
  • -json_all file export all header contents to a JSON file

DW gradient table import options

  • -grad file Provide the diffusion-weighted gradient scheme used in the acquisition in a text file. This should be supplied as a 4xN text file with each line is in the format [ X Y Z b ], where [ X Y Z ] describe the direction of the applied gradient, and b gives the b-value in units of s/mm^2. If a diffusion gradient scheme is present in the input image header, the data provided with this option will be instead used.
  • -fslgrad bvecs bvals Provide the diffusion-weighted gradient scheme used in the acquisition in FSL bvecs/bvals format files. If a diffusion gradient scheme is present in the input image header, the data provided with this option will be instead used.
  • -bvalue_scaling mode specifies whether the b-values should be scaled by the square of the corresponding DW gradient norm, as often required for multi-shell or DSI DW acquisition schemes. The default action can also be set in the MRtrix config file, under the BValueScaling entry. Valid choices are yes/no, true/false, 0/1 (default: true).
  • -raw_dwgrad do not modify the gradient table from what was found in the image headers. This skips the validation steps normally performed within MRtrix applications (i.e. do not verify that the number of entries in the gradient table matches the number of volumes in the image, do not scale b-values by gradient norms, do not normalise gradient vectors)

DW gradient table export options

  • -export_grad_mrtrix path export the diffusion-weighted gradient table to file in MRtrix format
  • -export_grad_fsl bvecs_path bvals_path export the diffusion-weighted gradient table to files in FSL (bvecs / bvals) format
  • -dwgrad the diffusion-weighting gradient table, as stored in the header (i.e. without any interpretation, scaling of b-values, or normalisation of gradient vectors)
  • -shell_bvalues list the average b-value of each shell
  • -shell_sizes list the number of volumes in each shell

Options for exporting phase-encode tables

  • -export_pe_table file export phase-encoding table to file
  • -export_pe_eddy config indices export phase-encoding information to an EDDY-style config / index file pair
  • -petable print the phase encoding table

Standard options

  • -info display information messages.
  • -quiet do not display information messages or progress status; alternatively, this can be achieved by setting the MRTRIX_QUIET environment variable to a non-empty string.
  • -debug display debugging messages.
  • -force force overwrite of output files (caution: using the same file as input and output might cause unexpected behaviour).
  • -nthreads number use this number of threads in multi-threaded applications (set to 0 to disable multi-threading).
  • -config key value (multiple uses permitted) temporarily set the value of an MRtrix config file entry.
  • -help display this information page and exit.
  • -version display version information and exit.

Author: J-Donald Tournier (d.tournier@brain.org.au) and Robert E. Smith (robert.smith@florey.edu.au)

Copyright: Copyright (c) 2008-2019 the MRtrix3 contributors.

This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed with this file, You can obtain one at http://mozilla.org/MPL/2.0/.

Covered Software is provided under this License on an “as is” basis, without warranty of any kind, either expressed, implied, or statutory, including, without limitation, warranties that the Covered Software is free of defects, merchantable, fit for a particular purpose or non-infringing. See the Mozilla Public License v. 2.0 for more details.

For more details, see http://www.mrtrix.org/.