MRtrix 0.2 equivalent commands
==============================

For those users moving to *MRtrix3* from the old MRtrix 0.2.x software, this list provides the equivalent command names for the functionalities that they are accustomed to from the older version of the software. The new command naming scheme was carefully designed, so we hope people agree that it makes sense, and allows users to easily find the command functionalities available that are relevant for the data they are processing.

Further information can be found on these commands either through the `documentation <commands_list>`__, or by typing the binary name at the command-line with no arguments to access the help file for that command.

+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| MRtrix 0.2.x          | MRtrix3                          | Comments                                                                                                                                                                                                                             |
+=======================+==================================+======================================================================================================================================================================================================================================+
| ``average``           | :ref:`mrmath`                    | Use ``mean`` statistic as second argument, and ``-axis`` option                                                                                                                                                                      |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``cat_tracks``        | :ref:`tckedit`                   | Simply provide multiple input track files to the command                                                                                                                                                                             |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``cleanup_ANTS_warp`` | *no equivalent*                  |                                                                                                                                                                                                                                      |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``csdeconv``          | :ref:`dwi2fod`                   |                                                                                                                                                                                                                                      |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``dicom_filename``    | *no equivalent*                  | See :ref:`dcminfo`                                                                                                                                                                                                                   |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``dir2amp``           | :ref:`peaks2amp`                 |                                                                                                                                                                                                                                      |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``disp_profile``      | :ref:`shview`                    |                                                                                                                                                                                                                                      |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``dwi2SH``            | :ref:`amp2sh`                    |                                                                                                                                                                                                                                      |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``dwi2tensor``        | :ref:`dwi2tensor`                |                                                                                                                                                                                                                                      |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``erode``             | :ref:`maskfilter`                | Specify ``erode`` or ``dilate`` algorithm as second argument                                                                                                                                                                         |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``estimate_response`` | :ref:`dwi2response` manual       | The :ref:`dwi2response` script also has a number of algorithms for automatically selecting single-fibre voxels in order to estimate the response function; see the relevant help page                                                |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``filter_tracks``     | :ref:`tckedit`                   |                                                                                                                                                                                                                                      |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``find_SH_peaks``     | :ref:`sh2peaks`                  |                                                                                                                                                                                                                                      |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``gen_ROI``           | *no equivalent*                  |                                                                                                                                                                                                                                      |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``gen_WM_mask``       | *no equivalent*                  | Use of this command was discouraged and so it has been discontinued                                                                                                                                                                  |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``gen_unit_warp``     | :ref:`warpinit`                  |                                                                                                                                                                                                                                      |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``gendir``            | :ref:`dirgen`                    | The electrostatic repulsion algorithm now only uses an exponent of 2 by default, rather than increasing in power over iterations; this was found to give poorer minimum-angle values, but superior conditioning of direction schemes |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``import_tracks``     | :ref:`tckconvert`                |                                                                                                                                                                                                                                      |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``median3D``          | :ref:`mrfilter`                  | Specify ``median`` algorithm as second argument                                                                                                                                                                                      |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``mrabs``             | :ref:`mrcalc`                    | Use ``-abs`` operator                                                                                                                                                                                                                |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``mradd``             | :ref:`mrcalc` *or* :ref:`mrmath` | E.g. ``mrcalc A.mif B.mif -add out.mif`` or ``mrmath A.mif B.mif sum out.mif``                                                                                                                                                       |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``mrcat``             | :ref:`mrcat`                     |                                                                                                                                                                                                                                      |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``mrconvert``         | :ref:`mrconvert`                 |                                                                                                                                                                                                                                      |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``mrinfo``            | :ref:`mrinfo`                    |                                                                                                                                                                                                                                      |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``mrmult``            | :ref:`mrcalc` *or* :ref:`mrmath` | E.g. ``mrcalc A.mif B.mif -mult out.mif`` or ``mrmath A.mif B.mif product out.mif``                                                                                                                                                  |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``mrstats``           | :ref:`mrstats`                   |                                                                                                                                                                                                                                      |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``mrtransform``       | :ref:`mrtransform`               |                                                                                                                                                                                                                                      |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``mrview``            | :ref:`mrview`                    |                                                                                                                                                                                                                                      |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``normalise_tracks``  | :ref:`tcktransform`              |                                                                                                                                                                                                                                      |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``read_dicom``        | :ref:`dcminfo`                   |                                                                                                                                                                                                                                      |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``read_ximg``         | *no equivalent*                  |                                                                                                                                                                                                                                      |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``resample_tracks``   | :ref:`tcksample`                 |                                                                                                                                                                                                                                      |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``sample_tracks``     | :ref:`tcksample`                 |                                                                                                                                                                                                                                      |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``sdeconv``           | :ref:`dwi2fod`                   |                                                                                                                                                                                                                                      |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``select_tracks``     | :ref:`tckedit`                   |                                                                                                                                                                                                                                      |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``streamtrack``       | :ref:`tckgen`                    |                                                                                                                                                                                                                                      |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``tensor2ADC``        | :ref:`tensor2metric`             | Use ``-adc`` output option                                                                                                                                                                                                           |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``tensor2FA``         | :ref:`tensor2metric`             | Use ``-fa`` output option                                                                                                                                                                                                            |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``tensor2vector``     | :ref:`tensor2metric`             | Use ``-vector`` output option                                                                                                                                                                                                        |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``tensor_metric``     | :ref:`tensor2metric`             |                                                                                                                                                                                                                                      |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``threshold``         | :ref:`mrthreshold`               | Note that automatic threshold parameter determination (i.e. if you don't explicitly provide an option to specify how the thresholding should be performed) is done using a different heuristic to that in the MRtrix 0.2 command     |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``track_info``        | :ref:`tckinfo`                   |                                                                                                                                                                                                                                      |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``tracks2prob``       | :ref:`tckmap`                    |                                                                                                                                                                                                                                      |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``tracks2vtk``        | :ref:`tckconvert`                |                                                                                                                                                                                                                                      |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``truncate_tracks``   | :ref:`tckedit`                   |                                                                                                                                                                                                                                      |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+