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|
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` | |
+-----------------------+----------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|
