# tcksample¶

## Synopsis¶

Sample values of an associated image along tracks

## Usage¶

tcksample [ options ]  tracks image values

• tracks: the input track file
• image: the image to be sampled
• values: the output sampled values

## Description¶

By default, the value of the underlying image at each point along the track is written to either an ASCII file (with all values for each track on the same line), or a track scalar file (.tsf). Alternatively, some statistic can be taken from the values along each streamline and written to a vector file.

## Options¶

• -stat_tck statistic compute some statistic from the values along each streamline (options are: mean,median,min,max)
• -nointerp do not use trilinear interpolation when sampling image values
• -precise use the precise mechanism for mapping streamlines to voxels (obviates the need for trilinear interpolation) (only applicable if some per-streamline statistic is requested)
• -use_tdi_fraction each streamline is assigned a fraction of the image intensity in each voxel based on the fraction of the track density contributed by that streamline (this is only appropriate for processing a whole-brain tractogram, and images for which the quantiative parameter is additive)

### 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).
• -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¶

• If using -precise option: Smith, R. E.; Tournier, J.-D.; Calamante, F. & Connelly, A. SIFT: Spherical-deconvolution informed filtering of tractograms. NeuroImage, 2013, 67, 298-312

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)