R Inputs/Outputs for Tractography

An input-output interface for reading in and writing out common VTK formats that store tractography data. This data comes in the form of 3D polygons with possibly attributes at each point. These are obtained via tracking algorithms from diffusion MRI and are a non-invasive way of studying brain structural connectivity.

riot

Overview

The riot (R Input/Output for Tractography) package provides an R interface for importing and exporting tractography data to and from R. Currently supported importing formats are:

• native VTK .vtk and .vtp files;
• medInria .fds files;
• MRtrix .tck/.tsf files; and,
• TrackVis .trk files.

The package reads tractography data into a tibble in which each row is a point characterized by at least the following five variables:

• X, Y, Z: 3D coordinates of the current point;
• PointId: Identification number of the current point among all points of the streamline it belongs to;
• StreamlineId: Identification number of the streamline which the current point belongs to.

The points might also have attributes or a color assigned to them, in which case, additional variables will be properly created to import them as well. The user can perform statistical analysis on the point cloud and store any new variable that (s)he would deem to be useful as additional column of the tibble. The package also allows to write back the tibble, including all newly created attributes, into the following exporting formats:

• native VTK .vtk and .vtp files; or,
• medInria .fds files.

Installation

You can install the released version of riot from CRAN with:

install.packages("riot")

Alternatively you can install the development version of riot from GitHub with:

# install.packages("remotes")
remotes::install_github("astamm/riot")

Example

library(riot)

Native VTK .vtk and .vtp files

uf_left_vtk  <- read_fascicles(system.file("extdata", "UF_left.vtk",  package = "riot"))
#> Number of data points: 38697
#> Number of streamlines: 2042
#> ✔ The fascicles stored in ']8;;file:///Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/riot/extdata/UF_left.vtk/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/riot/extdata/UF_left.vtk]8;;' have been successfully imported.
uf_left_vtk
#> # A tibble: 38,697 × 5
#>        X     Y      Z PointId StreamlineId
#>    <dbl> <dbl>  <dbl>   <dbl>        <dbl>
#>  1  13.7 -41.8 -13.1        1            1
#>  2  13.0 -40.4 -13.9        2            1
#>  3  13.9 -37.5 -13.8        3            1
#>  4  14.3 -34.7 -12.8        4            1
#>  5  15.2 -32.7 -11.8        5            1
#>  6  14.3 -29.2 -11.3        6            1
#>  7  12.8 -25.5  -9.73       7            1
#>  8  12.4 -22.6  -9.89       8            1
#>  9  11.1 -20.0 -10.7        9            1
#> 10  12.8 -16.6 -12.8       10            1
#> # … with 38,687 more rows

uf_left_vtp  <- read_fascicles(system.file("extdata", "UF_left.vtp",  package = "riot"))
#> Number of data points: 38697
#> Number of streamlines: 2042
#> ✔ The fascicles stored in ']8;;file:///Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/riot/extdata/UF_left.vtp/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/riot/extdata/UF_left.vtp]8;;' have been successfully imported.
uf_left_vtp
#> # A tibble: 38,697 × 5
#>        X     Y      Z PointId StreamlineId
#>    <dbl> <dbl>  <dbl>   <dbl>        <dbl>
#>  1  13.7 -41.8 -13.1        1            1
#>  2  13.0 -40.4 -13.9        2            1
#>  3  13.9 -37.5 -13.8        3            1
#>  4  14.3 -34.7 -12.8        4            1
#>  5  15.2 -32.7 -11.8        5            1
#>  6  14.3 -29.2 -11.3        6            1
#>  7  12.8 -25.5  -9.73       7            1
#>  8  12.4 -22.6  -9.89       8            1
#>  9  11.1 -20.0 -10.7        9            1
#> 10  12.8 -16.6 -12.8       10            1
#> # … with 38,687 more rows

medInria .fds files

uf_left_fds  <- read_fascicles(system.file("extdata", "UF_left.fds",  package = "riot"))
#> Number of data points: 38697
#> Number of streamlines: 2042
#> ✔ The fascicles stored in ']8;;file:///Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/riot/extdata/UF_left.fds/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/riot/extdata/UF_left.fds]8;;' have been successfully imported.
uf_left_fds
#> # A tibble: 38,697 × 5
#>        X     Y      Z PointId StreamlineId
#>    <dbl> <dbl>  <dbl>   <dbl>        <dbl>
#>  1  13.7 -41.8 -13.1        1            1
#>  2  13.0 -40.4 -13.9        2            1
#>  3  13.9 -37.5 -13.8        3            1
#>  4  14.3 -34.7 -12.8        4            1
#>  5  15.2 -32.7 -11.8        5            1
#>  6  14.3 -29.2 -11.3        6            1
#>  7  12.8 -25.5  -9.73       7            1
#>  8  12.4 -22.6  -9.89       8            1
#>  9  11.1 -20.0 -10.7        9            1
#> 10  12.8 -16.6 -12.8       10            1
#> # … with 38,687 more rows

MRtrix .tck/.tsf files

af_left_tck  <- read_fascicles(system.file("extdata", "AF_left.tck",  package = "riot"))
#> ✔ The fascicles stored in ']8;;file:///Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/riot/extdata/AF_left.tck/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/riot/extdata/AF_left.tck]8;;' have been successfully imported.
af_left_tck
#> # A tibble: 140,301 × 5
#>        X     Y     Z PointId StreamlineId
#>    <dbl> <dbl> <dbl>   <int>        <dbl>
#>  1 -56.1 -24.6  9.55       1            1
#>  2 -51.4 -25.0  6.49       2            1
#>  3 -49.2 -25.3  5.80       3            1
#>  4 -46.4 -25.2  5.68       4            1
#>  5 -44.5 -24.7  5.19       5            1
#>  6 -42.2 -24.3  4.06       6            1
#>  7 -40.4 -24.7  3.09       7            1
#>  8 -39.2 -25.5  2.57       8            1
#>  9 -38.4 -26.5  2.70       9            1
#> 10 -37.1 -28.6  3.84      10            1
#> # … with 140,291 more rows

TrackVis .trk files

cc_mid_trk  <- read_fascicles(system.file("extdata", "CCMid.trk",  package = "riot"))
#> ✔ The fascicles stored in ']8;;file:///Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/riot/extdata/CCMid.trk/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/riot/extdata/CCMid.trk]8;;' have been successfully imported.
cc_mid_trk
#> # A tibble: 112,675 × 5
#>        X     Y     Z PointId StreamlineId
#>    <dbl> <dbl> <dbl>   <int>        <int>
#>  1  8.66 -31.4  68.6       1            1
#>  2  8.89 -31.3  68.1       2            1
#>  3  9.11 -31.2  67.7       3            1
#>  4  9.34 -31.2  67.2       4            1
#>  5  9.56 -31.1  66.8       5            1
#>  6  9.79 -31.0  66.4       6            1
#>  7 10.0  -31.0  65.9       7            1
#>  8 10.2  -30.9  65.5       8            1
#>  9 10.5  -30.8  65.0       9            1
#> 10 10.7  -30.8  64.6      10            1
#> # … with 112,665 more rows

Dependencies

The riot package has two dependencies: VTK and TinyXML-2. They both have been slightly altered with respect to the original softwares for compliance with CRAN policy. Specifically, vtk/include/utf8.h header file has been modified to ensure LF line endings and vtkzlib source files have been compiled without checking for protoype warnings when using LLVM clang compiler. Also, tinyxml2.cpp has been modified to avoid the use of stdout and printf as per Writing R Extensions manual recommendations because R has its own input/output mechanism for writing to the console.

The authors would like to thank Tim Schäfer, the author of the freesurferformats package, for his helpful code to read MRtrix and TrackVis tractography file formats.