<commit_before>/*
 * Copyright (c) 2008-2016 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/
 * 
 * MRtrix is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 * 
 * For more details, see www.mrtrix.org
 * 
 */



#include "command.h"
#include "image.h"

#include "dwi/tractography/properties.h"
#include "dwi/tractography/roi.h"

#include "dwi/tractography/tracking/exec.h"
#include "dwi/tractography/tracking/method.h"
#include "dwi/tractography/tracking/tractography.h"

#include "dwi/tractography/ACT/act.h"

#include "dwi/tractography/algorithms/fact.h"
#include "dwi/tractography/algorithms/iFOD1.h"
#include "dwi/tractography/algorithms/iFOD2.h"
#include "dwi/tractography/algorithms/nulldist.h"
#include "dwi/tractography/algorithms/sd_stream.h"
#include "dwi/tractography/algorithms/seedtest.h"
#include "dwi/tractography/algorithms/tensor_det.h"
#include "dwi/tractography/algorithms/tensor_prob.h"

#include "dwi/tractography/seeding/seeding.h"




using namespace MR;
using namespace App;



const char* algorithms[] = { "fact", "ifod1", "ifod2", "nulldist1", "nulldist2", "sd_stream", "seedtest", "tensor_det", "tensor_prob", nullptr };


void usage ()
{

  AUTHOR = "<NAME> (<EMAIL>) & <NAME> (<EMAIL>)";

  DESCRIPTION
  + "perform streamlines tractography.";

  REFERENCES 
   + "References based on streamlines algorithm used:"

   + "* FACT:\n"
   "<NAME>.; <NAME>.; <NAME>. & <NAME>. "
   "Three-dimensional tracking of axonal projections in the brain by magnetic resonance imaging. "
   "Annals of Neurology, 1999, 45, 265-269"

   + "* iFOD1 or SD_STREAM:\n"
   "<NAME>.; <NAME>. & <NAME>. "
   "MRtrix: Diffusion tractography in crossing fiber regions. "
   "Int. J. Imaging Syst. Technol., 2012, 22, 53-66"

   + "* iFOD2:\n"
   "<NAME>.; <NAME>. & <NAME>. "
   "Improved probabilistic streamlines tractography by 2nd order integration over fibre orientation distributions. "
   "Proceedings of the International Society for Magnetic Resonance in Medicine, 2010, 1670"

   + "* Nulldist1 / Nulldist2:\n"
   "<NAME>.; <NAME>. & <NAME>. "
   "Probabilistic fibre tracking: Differentiation of connections from chance events. "
   "NeuroImage, 2008, 42, 1329-1339"

   + "* Tensor_Det:\n"
   "<NAME>.; <NAME>.; <NAME>.; <NAME>. & <NAME>. "
   "In vivo fiber tractography using DT-MRI data. "
   "Magnetic Resonance in Medicine, 2000, 44, 625-632"

   + "* Tensor_Prob:\n"
   "<NAME>. "
   "Tractography Gone Wild: Probabilistic Fibre Tracking Using the Wild Bootstrap With Diffusion Tensor MRI. "
   "IEEE Transactions on Medical Imaging, 2008, 27, 1268-1274"

   + "References based on command-line options:"

   + "* -rk4:\n"
   "<NAME>.; <NAME>.; <NAME>.; <NAME>. & <NAME>. "
   "In vivo fiber tractography using DT-MRI data. "
   "Magnetic Resonance in Medicine, 2000, 44, 625-632"

   + "* -act, -backtrack, -seed_gmwmi:\n"
   "<NAME>.; <NAME>.; <NAME>. & <NAME>. "
   "Anatomically-constrained tractography: Improved diffusion MRI streamlines tractography through effective use of anatomical information. "
   "NeuroImage, 2012, 62, 1924-1938"

   + "* -seed_dynamic:\n"
   "<NAME>.; <NAME>.; <NAME>. & <NAME>. "
   "SIFT2: Enabling dense quantitative assessment of brain white matter connectivity using streamlines tractography. "
   "NeuroImage, 2015, 119, 338-351";

  ARGUMENTS
    + Argument ("source",
        "the image containing the source data. The type of data depends on the algorithm used:\n"
        "- FACT: the directions file (each triplet of volumes is the X,Y,Z direction of a fibre population).\n"
        "- iFOD1/2, Nulldist2 & SD_Stream: the SH image resulting from CSD.\n"
        "- Nulldist1 & SeedTest: any image (will not be used).\n"
        "- TensorDet / TensorProb: the DWI image.\n"
        ).type_image_in()

    + Argument ("tracks", "the output file containing the tracks generated.").type_tracks_out();

<commit_msg>tckgen: Fix tiny source of confusion in the docs.<commit_after>/*
 * Copyright (c) 2008-2016 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/
 * 
 * MRtrix is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 * 
 * For more details, see www.mrtrix.org
 * 
 */



#include "command.h"
#include "image.h"

#include "dwi/tractography/properties.h"
#include "dwi/tractography/roi.h"

#include "dwi/tractography/tracking/exec.h"
#include "dwi/tractography/tracking/method.h"
#include "dwi/tractography/tracking/tractography.h"

#include "dwi/tractography/ACT/act.h"

#include "dwi/tractography/algorithms/fact.h"
#include "dwi/tractography/algorithms/iFOD1.h"
#include "dwi/tractography/algorithms/iFOD2.h"
#include "dwi/tractography/algorithms/nulldist.h"
#include "dwi/tractography/algorithms/sd_stream.h"
#include "dwi/tractography/algorithms/seedtest.h"
#include "dwi/tractography/algorithms/tensor_det.h"
#include "dwi/tractography/algorithms/tensor_prob.h"

#include "dwi/tractography/seeding/seeding.h"




using namespace MR;
using namespace App;



const char* algorithms[] = { "fact", "ifod1", "ifod2", "nulldist1", "nulldist2", "sd_stream", "seedtest", "tensor_det", "tensor_prob", nullptr };


void usage ()
{

  AUTHOR = "<NAME> (<EMAIL>) & <NAME> (<EMAIL>)";

  DESCRIPTION
  + "perform streamlines tractography.";

  REFERENCES 
   + "References based on streamlines algorithm used:"

   + "* FACT:\n"
   "<NAME>.; <NAME>.; <NAME>. & <NAME>. "
   "Three-dimensional tracking of axonal projections in the brain by magnetic resonance imaging. "
   "Annals of Neurology, 1999, 45, 265-269"

   + "* iFOD1 or SD_STREAM:\n"
   "<NAME>.; <NAME>. & <NAME>. "
   "MRtrix: Diffusion tractography in crossing fiber regions. "
   "Int. J. Imaging Syst. Technol., 2012, 22, 53-66"

   + "* iFOD2:\n"
   "<NAME>.; <NAME>. & <NAME>. "
   "Improved probabilistic streamlines tractography by 2nd order integration over fibre orientation distributions. "
   "Proceedings of the International Society for Magnetic Resonance in Medicine, 2010, 1670"

   + "* Nulldist1 / Nulldist2:\n"
   "<NAME>.; <NAME>. & <NAME>. "
   "Probabilistic fibre tracking: Differentiation of connections from chance events. "
   "NeuroImage, 2008, 42, 1329-1339"

   + "* Tensor_Det:\n"
   "<NAME>.; <NAME>.; <NAME>.; <NAME>. & <NAME>. "
   "In vivo fiber tractography using DT-MRI data. "
   "Magnetic Resonance in Medicine, 2000, 44, 625-632"

   + "* Tensor_Prob:\n"
   "<NAME>. "
   "Tractography Gone Wild: Probabilistic Fibre Tracking Using the Wild Bootstrap With Diffusion Tensor MRI. "
   "IEEE Transactions on Medical Imaging, 2008, 27, 1268-1274"

   + "References based on command-line options:"

   + "* -rk4:\n"
   "<NAME>.; <NAME>.; <NAME>.; <NAME>. & <NAME>. "
   "In vivo fiber tractography using DT-MRI data. "
   "Magnetic Resonance in Medicine, 2000, 44, 625-632"

   + "* -act, -backtrack, -seed_gmwmi:\n"
   "<NAME>.; <NAME>.; <NAME>. & <NAME>. "
   "Anatomically-constrained tractography: Improved diffusion MRI streamlines tractography through effective use of anatomical information. "
   "NeuroImage, 2012, 62, 1924-1938"

   + "* -seed_dynamic:\n"
   "<NAME>.; <NAME>.; <NAME>. & <NAME>. "
   "SIFT2: Enabling dense quantitative assessment of brain white matter connectivity using streamlines tractography. "
   "NeuroImage, 2015, 119, 338-351";

  ARGUMENTS
    + Argument ("source",
        "the image containing the source data. The type of data depends on the algorithm used:\n"
        "- FACT: the directions file (each triplet of volumes is the X,Y,Z direction of a fibre population).\n"
        "- iFOD1/2, Nulldist2 & SD_Stream: the SH image resulting from CSD.\n"
        "- Nulldist1 & SeedTest: any image (will not be used).\n"
        "- Tensor_Det / Tensor_Prob: the DWI image.\n"
        ).type_image_in()

    + Argument ("tracks", "the output file containing the tracks generated.").type_tracks_out();


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