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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:

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:

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

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

Example

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;
  • some source files of the CommonDataModel and vtkzlib modules have been modified to avoid compilation warnings arising when using LLVM or Apple clang or GNU gcc compilers;
  • 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.

Moreover, riot now ships a shrunk version of VTK source files to avoid unsuccessful downloads from VTK website.

Acknowledgements

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.