Questions about mrtransform and preservation of fiber orientation

maxpietsch · July 3, 2020, 3:49pm

This is designed to work with Orientation Distribution Functions and does not work for tensors. We currently do not have the functionality to reorient tensors or vector fields. However, (without warranties!) feel free to try below:

mrtransform vector.mif -warp warp.mif vector_transformed.mif
vectorreorient vector_transformed -warp warp.mif vector_transformed_reoriented.mif

using the vectorreorient.cpp command from:

gist.github.com

https://gist.github.com/maxpietsch/25dffa17f19595aa682cf5a30f0c099a

vectorreorient.cpp

/* Copyright (c) 2008-2020 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

This file has been truncated. show original

Either copy this file into cmd/ and rerun ./build or better set up an external module

vectorreorient requires a warp field. You can concatenate your linear and nonlinear transformation using transformcompose (or extend the command or generate a warp from a linear transformation).