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:
.vtk and
.vtp files;.tck/.tsf files; and,.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:
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")library(riot).vtk and .vtp
filesuf_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 '/Users/stamm-a/Library/R/arm64/4.1/library/riot/extdata/UF_left.vtk' 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 rowsuf_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 '/Users/stamm-a/Library/R/arm64/4.1/library/riot/extdata/UF_left.vtp' 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 rowsuf_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 '/Users/stamm-a/Library/R/arm64/4.1/library/riot/extdata/UF_left.fds' 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.tck/.tsf filesaf_left_tck <- read_fascicles(system.file("extdata", "AF_left.tck", package = "riot"))
#> ✔ The fascicles stored in '/Users/stamm-a/Library/R/arm64/4.1/library/riot/extdata/AF_left.tck' 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.trk filescc_mid_trk <- read_fascicles(system.file("extdata", "CCMid.trk", package = "riot"))
#> ✔ The fascicles stored in '/Users/stamm-a/Library/R/arm64/4.1/library/riot/extdata/CCMid.trk' 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 rowsThe 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. 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.