fix_striatum_rois.Rout

R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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> library("oro.nifti")
oro.nifti 0.11.0
> library("glue")
> 
> sz <- Sys.getenv("sz")
> if (sz == "") sz <- "2.3"
> 
> 
> ##Left
> x <- readNIfTI(glue("l_striatum_tight_7Networks_{sz}mm.nii.gz"), reorient=FALSE)
> x[x==3] <- 0 # 0 voxels to work with at 2.3mm (here for smaller starting resolutions)
> 
> x[x==2] <- 1 #2 -> 1
> highvals <- x[x > 2]
> highvals <- highvals - 2 # 4 ->2; 5 -> 3; etc.
> x[x > 2] <- highvals
> 
> print(table(x))
x
      0       1       2       3       4       5 
7210226    1460    2058    1039    3095    3154 
> 
> writeNIfTI(x, glue("l_striatum_tight_7Networks_{sz}mm"), verbose = TRUE)
  niftiExtension detected!
  vox_offset = 2768
  writing niftiExtension(s) at byte = 352
  writing data at byte = 2768
[1] "l_striatum_tight_7Networks_1.0mm.nii.gz"
Warning message:
In .local(nim, ...) :
  Class is of niftiExtension, extensions can be removed using as.nifti
> 
> ##Right
> x <- readNIfTI(glue("r_striatum_tight_7Networks_{sz}mm.nii.gz"), reorient=FALSE)
> x[x==3] <- 0 #only 9 voxels to work with at 2.3mm
> 
> #same renumbering as above
> x[x==2] <- 1 #2 -> 1
> highvals <- x[x > 2]
> highvals <- highvals - 2 # 4 ->2; 5 -> 3; etc.
> x[x > 2] <- highvals
> 
> print(table(x))
x
      0       1       2       3       4       5 
7210809    1196    2540     994    3685    1808 
> 
> writeNIfTI(x, glue("r_striatum_tight_7Networks_{sz}mm"), verbose = TRUE)
  niftiExtension detected!
  vox_offset = 2768
  writing niftiExtension(s) at byte = 352
  writing data at byte = 2768
[1] "r_striatum_tight_7Networks_1.0mm.nii.gz"
Warning message:
In .local(nim, ...) :
  Class is of niftiExtension, extensions can be removed using as.nifti
> 
> proc.time()
   user  system elapsed 
 20.245   0.803  21.844