Rescales an image to be in certain value range. This was created as sometimes DICOM scale and slope parameters may be inconsistent across sites and the data need to be value restricted
rescale_img(
filename,
pngname = NULL,
write.nii = FALSE,
outfile = NULL,
min.val = -1024,
max.val = 3071,
ROIformat = FALSE,
drop_dim = TRUE,
writer = "dcm2nii",
...
)| filename | filename of image to be read into R or nifti object |
|---|---|
| pngname | filename of png of histogram of values of image to be made. For no png - set to NULL (default) |
| write.nii | logical - should the image be written. |
| outfile | if |
| min.val | minimum value of image (default -1024 (for CT)). If no thresholding set to -Inf |
| max.val | maximum value of image (default 3071 (for CT)). If no thresholding set to Inf |
| ROIformat | if TRUE, any values $< 0$ will be set to 0 |
| drop_dim | Should |
| writer | character value to add to description slot of NIfTI header |
| ... | extra methods to be passed to |
Object of class nifti
img = nifti(array(rnorm(10^3, sd = 1000), dim = rep(10, 3)))
outfile = tempfile(fileext = ".nii.gz")
pngname = tempfile(fileext = ".png")
rescale_img(img, write.nii = TRUE, outfile = outfile,
pngname = pngname)
#> [1] "/tmp/RtmpBb1B9G/file16b731b8516d4.png"
#> NIfTI-1 format
#> Type : nifti
#> Data Type : 2 (UINT8)
#> Bits per Pixel : 8
#> Slice Code : 0 (Unknown)
#> Intent Code : 0 (None)
#> Qform Code : 0 (Unknown)
#> Sform Code : 0 (Unknown)
#> Dimension : 10 x 10 x 10
#> Pixel Dimension : 1 x 1 x 1
#> Voxel Units : Unknown
#> Time Units : Unknown