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
.vtkand.vtpfiles; - medInria
.fdsfiles; - MRtrix
.tck/.tsffiles; and, - TrackVis
.trkfiles.
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)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 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 '�]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 rowsmedInria .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 rowsMRtrix .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 rowsTrackVis .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 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 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.