Error deface T2w

output console R

> library(RNifti)
> library(fslr)
> getwd()
[1] "/Users/alfoi/Desktop/tst_r"
> setwd("/Users/alfoi/Desktop/tst_r")
> fname = "sub-chibaIngeniasub-chibaIngenia_T2w.nii.gz"
> download.file(url = paste0("https://openneuro.org/crn/datasets/ds002393/", 
+                            "snapshots/1.0.2/files/", 
+                            "sub-chibaIngenia:anat:sub-chibaIngenia_T2w.nii.gz"),
+               destfile = fname)
trying URL 'https://openneuro.org/crn/datasets/ds002393/snapshots/1.0.2/files/sub-chibaIngenia:anat:sub-chibaIngenia_T2w.nii.gz'
downloaded 6.4 MB

> img = RNifti::readNifti(fname)
> out = face_removal_mask(fname)
FSLDIR='/usr/local/fsl'; PATH=${FSLDIR}/bin:${PATH};export PATH FSLDIR; sh "${FSLDIR}/etc/fslconf/fsl.sh"; FSLOUTPUTTYPE=NIFTI_GZ; export FSLOUTPUTTYPE; ${FSLDIR}/bin/flirt -in "/usr/local/fsl/data/standard/MNI152_T1_1mm.nii.gz" -ref "/Users/alfoi/Desktop/tst_r/sub-chibaIngeniasub-chibaIngenia_T2w.nii.gz" -out "/var/folders/_8/wq4mlll97hn7w0hw84bs4stw0000gn/T//RtmpGKYsIW/file2aa03341f9c7" -dof 12 -omat "/var/folders/_8/wq4mlll97hn7w0hw84bs4stw0000gn/T//RtmpGKYsIW/file2aa054f354c3.mat" -cost mutualinfo

FSLDIR='/usr/local/fsl'; PATH=${FSLDIR}/bin:${PATH};export PATH FSLDIR; sh "${FSLDIR}/etc/fslconf/fsl.sh"; FSLOUTPUTTYPE=NIFTI_GZ; export FSLOUTPUTTYPE; ${FSLDIR}/bin/flirt -in "/private/var/folders/_8/wq4mlll97hn7w0hw84bs4stw0000gn/T/RtmpGKYsIW/file2aa076cb4377.nii.gz" -ref "/Users/alfoi/Desktop/tst_r/sub-chibaIngeniasub-chibaIngenia_T2w.nii.gz" -applyxfm -init "/var/folders/_8/wq4mlll97hn7w0hw84bs4stw0000gn/T//RtmpGKYsIW/file2aa054f354c3.mat" -interp nearestneighbour -out "/var/folders/_8/wq4mlll97hn7w0hw84bs4stw0000gn/T//RtmpGKYsIW/file2aa03075921b" 

> out_img = readnii(out)
> xx = which(out_img == 0, arr.ind = TRUE)
> 
> dim3 = 1:(min(xx[,3]) + floor(  (max(xx[,3]) - min(xx[,3]))/2))
Error in 1:(min(xx[, 3]) + floor((max(xx[, 3]) - min(xx[, 3]))/2)) : 
  NA/NaN argument
In addition: Warning messages:
1: In min(xx[, 3]) : no non-missing arguments to min; returning Inf
2: In max(xx[, 3]) : no non-missing arguments to max; returning -Inf
3: In min(xx[, 3]) : no non-missing arguments to min; returning Inf

script R

library(RNifti)
library(fslr)
getwd()
setwd("/Users/alfoi/Desktop/tst_r")
fname = "sub-chibaIngeniasub-chibaIngenia_T2w.nii.gz"
download.file(url = paste0("https://openneuro.org/crn/datasets/ds002393/", 
                           "snapshots/1.0.2/files/", 
                           "sub-chibaIngenia:anat:sub-chibaIngenia_T2w.nii.gz"),
              destfile = fname)
img = RNifti::readNifti(fname)
out = face_removal_mask(fname)
out_img = readnii(out)
xx = which(out_img == 0, arr.ind = TRUE)

dim3 = 1:(min(xx[,3]) + floor(  (max(xx[,3]) - min(xx[,3]))/2))
dim2 = min(xx[,2]):dim(out_img)[2]
eg = expand.grid(dim1 = unique(xx[,1]),
                 dim2 = dim2, dim3 = dim3)
eg = as.matrix(eg)
new_mask = out_img
new_mask[eg] = 0
final_img = img * new_mask

outfile = gsub("_T2w.nii.gz", "_T2w_defaced.nii.gz",image)

writeNifti(final_img, file = outfile)