.. _tckmap:

tckmap
===================

Synopsis
--------

Use track data as a form of contrast for producing a high-resolution image

Usage
--------

::

    tckmap [ options ]  tracks output

-  *tracks*: the input track file.
-  *output*: the output track-weighted image

Description
-----------

Note: if you run into limitations with RAM usage, make sure you output the results to a .mif file or .mih / .dat file pair - this will avoid the allocation of an additional buffer to store the output for write-out.

Options
-------

Options for the header of the output image
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

-  **-template image** an image file to be used as a template for the output (the output image will have the same transform and field of view).

-  **-vox size** provide either an isotropic voxel size (in mm), or comma-separated list of 3 voxel dimensions.

-  **-datatype spec** specify output image data type.

Options for the dimensionality of the output image
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

-  **-dec** perform track mapping in directionally-encoded colour (DEC) space

-  **-dixel path** map streamlines to dixels within each voxel; requires either a number of dixels (references an internal direction set), or a path to a text file containing a set of directions stored as azimuth/elevation pairs

-  **-tod lmax** generate a Track Orientation Distribution (TOD) in each voxel; need to specify the maximum spherical harmonic degree lmax to use when generating Apodised Point Spread Functions

Options for the TWI image contrast properties
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

-  **-contrast type** define the desired form of contrast for the output image |br|
   Options are: tdi, length, invlength, scalar_map, scalar_map_count, fod_amp, curvature, vector_file (default: tdi)

-  **-image image** provide the scalar image map for generating images with 'scalar_map' / 'scalar_map_count' contrast, or the spherical harmonics image for 'fod_amp' contrast

-  **-vector_file path** provide the vector data file for generating images with 'vector_file' contrast

-  **-stat_vox type** define the statistic for choosing the final voxel intensities for a given contrast type given the individual values from the tracks passing through each voxel.  |br|
   Options are: sum, min, mean, max (default: sum)

-  **-stat_tck type** define the statistic for choosing the contribution to be made by each streamline as a function of the samples taken along their lengths.  |br|
   Only has an effect for 'scalar_map', 'fod_amp' and 'curvature' contrast types.  |br|
   Options are: sum, min, mean, max, median, mean_nonzero, gaussian, ends_min, ends_mean, ends_max, ends_prod (default: mean)

-  **-fwhm_tck value** when using gaussian-smoothed per-track statistic, specify the desired full-width half-maximum of the Gaussian smoothing kernel (in mm)

-  **-map_zero** if a streamline has zero contribution based on the contrast & statistic, typically it is not mapped; use this option to still contribute to the map even if this is the case (these non-contributing voxels can then influence the mean value in each voxel of the map)

-  **-backtrack** when using -stat_tck ends_*, if the streamline endpoint is outside the FoV, backtrack along the streamline trajectory until an appropriate point is found

Options for the streamline-to-voxel mapping mechanism
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

-  **-upsample factor** upsample the tracks by some ratio using Hermite interpolation before mappping |br|
   (If omitted, an appropriate ratio will be determined automatically)

-  **-precise** use a more precise streamline mapping strategy, that accurately quantifies the length through each voxel (these lengths are then taken into account during TWI calculation)

-  **-ends_only** only map the streamline endpoints to the image

-  **-tck_weights_in path** specify a text scalar file containing the streamline weights

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.

References
^^^^^^^^^^

* For TDI or DEC TDI: |br|
  Calamante, F.; Tournier, J.-D.; Jackson, G. D. & Connelly, A. Track-density imaging (TDI): Super-resolution white matter imaging using whole-brain track-density mapping. NeuroImage, 2010, 53, 1233-1243

* If using -contrast length and -stat_vox mean: |br|
  Pannek, K.; Mathias, J. L.; Bigler, E. D.; Brown, G.; Taylor, J. D. & Rose, S. E. The average pathlength map: A diffusion MRI tractography-derived index for studying brain pathology. NeuroImage, 2011, 55, 133-141

* If using -dixel option with TDI contrast only: |br|
  Smith, R.E., Tournier, J-D., Calamante, F., Connelly, A. A novel paradigm for automated segmentation of very large whole-brain probabilistic tractography data sets. In proc. ISMRM, 2011, 19, 673

* If using -dixel option with any other contrast: |br|
  Pannek, K., Raffelt, D., Salvado, O., Rose, S. Incorporating directional information in diffusion tractography derived maps: angular track imaging (ATI). In Proc. ISMRM, 2012, 20, 1912

* If using -tod option: |br|
  Dhollander, T., Emsell, L., Van Hecke, W., Maes, F., Sunaert, S., Suetens, P. Track Orientation Density Imaging (TODI) and Track Orientation Distribution (TOD) based tractography. NeuroImage, 2014, 94, 312-336

* If using other contrasts / statistics: |br|
  Calamante, F.; Tournier, J.-D.; Smith, R. E. & Connelly, A. A generalised framework for super-resolution track-weighted imaging. NeuroImage, 2012, 59, 2494-2503

* If using -precise mapping option: |br|
  Smith, R. E.; Tournier, J.-D.; Calamante, F. & Connelly, A. SIFT: Spherical-deconvolution informed filtering of tractograms. NeuroImage, 2013, 67, 298-312 (Appendix 3)

Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch, M.; Christiaens, D.; Jeurissen, B.; Yeh, C.-H. & Connelly, A. MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. NeuroImage, 2019, 202, 116137

--------------



**Author:** Robert E. Smith (robert.smith@florey.edu.au) and J-Donald Tournier (jdtournier@gmail.com)

**Copyright:** Copyright (c) 2008-2022 the MRtrix3 contributors.

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Covered Software is provided under this License on an "as is"
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For more details, see http://www.mrtrix.org/.


