Title: Tools and Operations for Reading, Writing, Viewing, and Manipulating SKIFTI Files
Version: 0.1.0
Description: SKIFTI files contain brain imaging data in coordinates across Tract Based Spatial Statistics (TBSS) skeleton, which represent the brain white matter intensity values. 'skiftiTools' provides a unified environment for reading, writing, visualizing and manipulating SKIFTI-format data. It supports the "subsetting", "concatenating", and using data as data.frame for R statistical functions. The SKIFTI data is structured for convenient access to the data and metadata, and includes support for visualizations. For more information see Merisaari et al. (2024) <doi:10.57736/87d2-0608>.
Depends: R (≥ 4.2.0)
License: GPL-3
Encoding: UTF-8
Imports: RNifti, stringr, R.utils, rmarchingcubes, Rvcg, png, rgl, oce, abind, methods, s2dv
RoxygenNote: 7.3.3
URL: https://github.com/haanme/skiftiTools
Suggests: knitr, rmarkdown, testthat (≥ 3.0.0)
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2025-10-10 11:13:51 UTC; root
Author: Harri Merisaari ORCID iD [aut], Ilkka Suuronen ORCID iD [cre]
Maintainer: Ilkka Suuronen <ilksuu@utu.fi>
Repository: CRAN
Date/Publication: 2025-10-16 12:10:02 UTC

Create a SKIFTI file from fsl TBSS skeleton data

Description

Skeleton mask and corresponding image intensity data must be in Nifti format. The skeleton mask is used to determine the coordinates of intensity data. If optional label file is given, that is used to label the voxels.

Usage

Nifti2Skifti(
  Nifti_data = NULL,
  Nifti_skeleton = NULL,
  selected_volumes = NULL,
  Nifti_labels = NULL,
  write_coordinates = FALSE,
  verbose = FALSE
)

Arguments

Nifti_data

Intensity data in Nifti format (required)

Nifti_skeleton

Skeleton at same imaging space as the data, in Nifti format (required)

selected_volumes

Selected volume indexes starting from 1 (default==NULL, selecting all)

Nifti_labels

Labeling data to be used inside mask, writing extra line to the output about labels (default==NULL, no extra labeling)

write_coordinates

TRUE/FALSE(default) write coordinates of voxels in x,y,z ASCII format, in the same order as they appear in the skifti

verbose

TRUE/FALSE(default) for verbose messages

Value

skifti object with default rownames as vol1, vol2 .... volN as indexes from the nifti data

Examples

#source('../../R/Skifti2Nifti.R')
#source('../../R/Nifti2Skifti.R')
library(RNifti)
data<-array(0,dim=list(10,10,10,10))
for(t in 1:10) {
  for(x in 1:10) {
    for(y in 1:10) {
      for(z in 1:10) {
        data[x,y,z,t]<-t+x
      }
    }
  }
}
data_Nifti<-RNifti::retrieveNifti(data)
RNifti::writeNifti(data_Nifti, "data_Nifti.nii.gz", template = NULL, datatype = "auto")

data_skeleton<-array(0,dim=list(10,10,10))
data_skeleton[5,5,5]<-1
data_skeleton[6,6,6]<-1
data_skeleton[7,7,7]<-1
data_skeleton_Nifti<-RNifti::retrieveNifti(data_skeleton)
RNifti::writeNifti(data_skeleton_Nifti, "data_skeleton_Nifti.nii.gz", datatype = "auto")

data_Skifti<-Nifti2Skifti(Nifti_data="data_Nifti.nii.gz", 
                          Nifti_skeleton="data_skeleton_Nifti.nii.gz", 
                          selected_volumes=c(1), 
                          Nifti_labels=NULL, 
                          write_coordinates=TRUE, 
                          verbose=FALSE)

# Create Skifti
data_Nifti2<-Skifti2Nifti(data_Skifti)
RNifti::writeNifti(data_Nifti2[[1]], "data_Nifti.nii.gz", datatype = "auto")
data_Nifti2<-RNifti::readNifti("data_Nifti.nii.gz", internal = TRUE, volumes = NULL)

Create a Nifti file from Skifti data

Description

Skeleton mask and corresponding image intensity data in Nifti format. The skeleton mask is used to determine the coordinates of intensity data. If optional label file is given, that is used to label the voxels.

Usage

Skifti2CSV(Skifti_data, filename, overwrite = FALSE, sep = ";")

Arguments

Skifti_data

Intensity data in Nifti format

filename

file to read'

overwrite

TRUE/FALSE(default) to overwrite existing data

sep

file separator to be written default ';'

Value

CSV filename

Examples

library(RNifti)
data<-array(0,dim=list(10,10,10,10))
for(t in 1:10) {
  for(x in 1:10) {
    for(y in 1:10) {
      for(z in 1:10) {
        data[x,y,z,t]<-t+x
      }
    }
  }
}
data_Nifti<-RNifti::retrieveNifti(data)
RNifti::writeNifti(data_Nifti, "data_Nifti.nii.gz", template = NULL, datatype = "auto")

data_skeleton<-array(0,dim=list(10,10,10))
data_skeleton[5,5,5]<-1
data_skeleton[6,6,6]<-1
data_skeleton[7,7,7]<-1
data_skeleton_Nifti<-RNifti::retrieveNifti(data_skeleton)
RNifti::writeNifti(data_skeleton_Nifti, "data_skeleton_Nifti.nii.gz", datatype = "auto")

data_Skifti<-Nifti2Skifti(Nifti_data="data_Nifti.nii.gz", 
                          Nifti_skeleton="data_skeleton_Nifti.nii.gz", 
                          selected_volumes=1:10, 
                          Nifti_labels=NULL, 
                          write_coordinates=TRUE, 
                          verbose=FALSE)

Skifti2CSV(data_Skifti, "data_Skifti.csv", overwrite=TRUE, sep=';')
data_csv<-read.csv2("data_Skifti.csv", ';', header = FALSE, row.names = NULL)

Create a Nifti file from Skifti data

Description

Skeleton mask and corresponding image intensity data in Nifti format. The skeleton mask is used to determine the coordinates of intensity data. If optional label file is given, that is used to label the voxels.

Usage

Skifti2Nifti(Skifti_data)

Arguments

Skifti_data

Intensity data in Nifti format

Value

Nifti skeleton file for Skifti data

Examples

#source('../../R/Skifti2Nifti.R')
#source('../../R/Nifti2Skifti.R')
library(RNifti)
data<-array(0,dim=list(10,10,10,10))
for(t in 1:10) {
  for(x in 1:10) {
    for(y in 1:10) {
      for(z in 1:10) {
        data[x,y,z,t]<-t+x
      }
    }
  }
}
data_Nifti<-RNifti::retrieveNifti(data)
RNifti::writeNifti(data_Nifti, "data_Nifti.nii.gz", template = NULL, datatype = "auto")

data_skeleton<-array(0,dim=list(10,10,10))
data_skeleton[5,5,5]<-1
data_skeleton[6,6,6]<-1
data_skeleton[7,7,7]<-1
data_skeleton_Nifti<-RNifti::retrieveNifti(data_skeleton)
RNifti::writeNifti(data_skeleton_Nifti, "data_skeleton_Nifti.nii.gz", datatype = "auto")

data_Skifti<-Nifti2Skifti(Nifti_data="data_Nifti.nii.gz", 
                          Nifti_skeleton="data_skeleton_Nifti.nii.gz", 
                          selected_volumes=c(1), 
                          Nifti_labels=NULL, 
                          write_coordinates=TRUE, 
                          verbose=FALSE)

# Create Skifti
data_Nifti2<-Skifti2Nifti(data_Skifti)
RNifti::writeNifti(data_Nifti2[[1]], "data_Nifti.nii.gz", datatype = "auto")
data_Nifti2<-RNifti::readNifti("data_Nifti.nii.gz", internal = TRUE, volumes = NULL)

Concatenate Skifti data

Description

Concatenate Skifti data

Usage

concat(Skifti_data1, Skifti_data2)

Arguments

Skifti_data1

Skifti data object1

Skifti_data2

Skifti data object2

Value

concatenated Skifti data object

Examples

library(RNifti)
data<-array(0,dim=list(10,10,10,10))
for(t in 1:10) {
  for(x in 1:10) {
    for(y in 1:10) {
      for(z in 1:10) {
        data[x,y,z,t]<-t+x
      }
    }
  }
}
data_Nifti<-RNifti::retrieveNifti(data)
RNifti::writeNifti(data_Nifti, "data_Nifti.nii.gz", template = NULL, datatype = "auto")

data_skeleton<-array(0,dim=list(10,10,10))
data_skeleton[5,5,5]<-1
data_skeleton[6,6,6]<-1
data_skeleton[7,7,7]<-1
data_skeleton_Nifti<-RNifti::retrieveNifti(data_skeleton)
RNifti::writeNifti(data_skeleton_Nifti, "data_skeleton_Nifti.nii.gz", datatype = "auto")

data_Skifti<-Nifti2Skifti(Nifti_data="data_Nifti.nii.gz", 
                          Nifti_skeleton="data_skeleton_Nifti.nii.gz", 
                          selected_volumes=1:10, 
                          Nifti_labels=NULL, 
                          write_coordinates=TRUE, 
                          verbose=FALSE)

data_Skifti_subset<-subset(data_Skifti, c(1,5,10))
m<-matrix(c(6,10,15,7,11,16,8,12,17), nrow=3, ncol=3)
rownames(m)<-c("vol1", "vol5", "vol10")

data_Skifti_subset1<-subset(data_Skifti, c(1,5))
data_Skifti_subset2<-subset(data_Skifti, c(10))  
data_Skifti_concat<-concat(data_Skifti_subset1, data_Skifti_subset2)
m<-matrix(c(6,10,15,7,11,16,8,12,17), nrow=3, ncol=3)
rownames(m)<-c("vol1", "vol5", "")

Read Skifti data

Description

Read Skifti data

Usage

readSkifti(filename, verbose = FALSE)

Arguments

filename

file to read

verbose

TRUE/FALSE(default), for verbosity

Value

Skifti data object

Examples

#source('../../R/Skifti2Nifti.R')
#source('../../R/Nifti2Skifti.R')
library(RNifti)
data<-array(0,dim=list(10,10,10,10))
for(t in 1:10) {
  for(x in 1:10) {
    for(y in 1:10) {
      for(z in 1:10) {
        data[x,y,z,t]<-t+x
      }
    }
  }
}
data_Nifti<-RNifti::retrieveNifti(data)
RNifti::writeNifti(data_Nifti, "data_Nifti.nii.gz", template = NULL, datatype = "auto")

data_skeleton<-array(0,dim=list(10,10,10))
data_skeleton[5,5,5]<-1
data_skeleton[6,6,6]<-1
data_skeleton[7,7,7]<-1
data_skeleton_Nifti<-RNifti::retrieveNifti(data_skeleton)
RNifti::writeNifti(data_skeleton_Nifti, "data_skeleton_Nifti.nii.gz", datatype = "auto")

data_Skifti<-Nifti2Skifti(Nifti_data="data_Nifti.nii.gz", 
                          Nifti_skeleton="data_skeleton_Nifti.nii.gz", 
                          selected_volumes=c(1), 
                          Nifti_labels=NULL, 
                          write_coordinates=TRUE, 
                          verbose=FALSE)

# Create Skifti
data_Nifti2<-Skifti2Nifti(data_Skifti)
RNifti::writeNifti(data_Nifti2[[1]], "data_Nifti.nii.gz", datatype = "auto")
data_Nifti2<-RNifti::readNifti("data_Nifti.nii.gz", internal = TRUE, volumes = NULL)

Create png from mask and data in Nifti format

Description

Skeleton mask and corresponding image intensity data must be in Nifti format. The skeleton mask is used to determine the coordinates of intensity data.

Usage

save_skeleton(
  mask,
  data,
  img_hdr,
  output,
  legend_title,
  scale,
  keep_temp = FALSE,
  palette = "lajolla",
  verbose = FALSE
)

Arguments

mask

Intensity data in Nifti object format

data

Skeleton at same imaging space as the data, in Nifti format

img_hdr

Nifti header object

output

Output PNG filename

legend_title

Title to be shown

scale

scaling for intensity values, tune for better color depth

keep_temp

TRUE/FALSE(default) to keep temporary png images

palette

color palette

verbose

TRUE/FALSE(default), for verbosity

Value

No output, as resuts are saved to a png file

Get subset of Skifti data

Description

Get subset of Skifti data

Usage

subset(Skifti_data, volumes)

Arguments

Skifti_data

Skifti data object

volumes

selection

Value

Skifti data object of subset

Write Skifti data

Description

Write Skifti data

Usage

writeSkifti(
  Skifti_data,
  basename,
  overwrite = FALSE,
  compress = "none",
  verbose = FALSE
)

Arguments

Skifti_data

Skifti data object

basename

basename to write without suffix

overwrite

TRUE/FALSE(default) to overwrite existing data

compress

bz2/zip/none(default) to select compression method

verbose

TRUE/FALSE(default), for verbosity

Value

filename where Skifti data was written

Examples

#source('../../R/Skifti2Nifti.R')
#source('../../R/Nifti2Skifti.R')
library(RNifti)
data<-array(0,dim=list(10,10,10,10))
for(t in 1:10) {
  for(x in 1:10) {
    for(y in 1:10) {
      for(z in 1:10) {
        data[x,y,z,t]<-t+x
      }
    }
  }
}
data_Nifti<-RNifti::retrieveNifti(data)
RNifti::writeNifti(data_Nifti, "data_Nifti.nii.gz", template = NULL, datatype = "auto")

data_skeleton<-array(0,dim=list(10,10,10))
data_skeleton[5,5,5]<-1
data_skeleton[6,6,6]<-1
data_skeleton[7,7,7]<-1
data_skeleton_Nifti<-RNifti::retrieveNifti(data_skeleton)
RNifti::writeNifti(data_skeleton_Nifti, "data_skeleton_Nifti.nii.gz", datatype = "auto")

data_Skifti<-Nifti2Skifti(Nifti_data="data_Nifti.nii.gz", 
                          Nifti_skeleton="data_skeleton_Nifti.nii.gz", 
                          selected_volumes=c(1), 
                          Nifti_labels=NULL, 
                          write_coordinates=TRUE, 
                          verbose=FALSE)

# Create Skifti
data_Nifti2<-Skifti2Nifti(data_Skifti)
RNifti::writeNifti(data_Nifti2[[1]], "data_Nifti.nii.gz", datatype = "auto")
data_Nifti2<-RNifti::readNifti("data_Nifti.nii.gz", internal = TRUE, volumes = NULL)