fslr package fslroi function & padding nifti image

[yinkaiming1987]

Thanks John,

Continue to the last question, I have a nifti file in the end. Great! I checked the path /usr/bin which has all just fsl symlinks in the format of fsl5.0-aff2rigid, and the path /usr/share/fsl/5.0 has folders as:

~$ cd /usr/share/fsl/5.0/
5.0$ ls
bin data doc etc tcl
5.0$ ls -l
total 20
lrwxrwxrwx 1 root root 20 Aug 24 2013 bin -> ../../../lib/fsl/5.0
lrwxrwxrwx 1 root root 7 Aug 24 2013 data -> ../data
drwxr-xr-x 6 root root 4096 Oct 22 23:02 doc
drwxr-xr-x 8 root root 4096 Oct 22 23:02 etc
drwxr-xr-x 3 root root 12288 Oct 22 23:02 tcl

Now I have two more questions (unrelated to the above):

1. Does fslr package have function like fslroi? Or could I perform this in other ways?

2. If I have a nifti file in dims of 170 x 240 x 240, could I use fslr package to pad it into a cubic file in dims of 240 x 240 x 240? Or do you know if there are other ways to do this?

Great thank,
Kaiming

[muschellij2]

fslr (the dev version) should have fslroi as a function.

You can pad the image, but there are many ways to do this. You can pad zeros on the left/bottom, the right/top, symmetrically on each side (but there may be asymmetry in the dimensions). You can extract the array of the nifti object using:

arr = out@.Data

And the abind package may be helpful. Why do you want to do this?

[yinkaiming1987]

That's great! I need to pad zeros symmetrically on left, right, and also
slices number so to make it a cubic space, then I will rotate it around the
centre of this cubic, to obtain an isotropic rotation.

Could you show me some commands to to this? Also do you know how to
transform a file of the voxel size e.g. 1.5 x 1.5 x 2 to 1 x 1 x 1 in fslr?

Thanks,
Kaiming

On 28 March 2016 at 18:37, John Muschelli notifications@github.com wrote:

fslr (the dev version) should have fslroi as a function.

You can pad the image, but there are many ways to do this. You can pad
zeros on the left/bottom, the right/top, symmetrically on each side (but
there may be asymmetry in the dimensions). You can extract the array of the
nifti object using:

arr = out@.Data

And the abind package may be helpful. Why do you want to do this?

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#3 (comment)

[muschellij2]

You need to resample the image. You can also register the image to the MNI template (1x1x1).

Here is a function that should symmetrically do this (it favors the right over the left if it's not truly symmetric)

add_zero_dimensions = function(img, 
                    newdim,
                    value = NA){

  dimg = dim(img)

  #   img[1:dimg[1], 1:dimg[2], c(1:7, 36:29)] = 0
  #   img[1:dimg[1], c(1:7, 512:505), 1:dimg[3]] = 0
  #   img[c(1:7, 512:505), 1:dimg[2], 1:dimg[3]] = 0
  stopifnot(length(dimg) == length(newdim))
  stopifnot(all(newdim > 0))

  diff_dim = newdim - dimg
  stopifnot(all(diff_dim >= 0))

  arr = array(value, dim = newdim)

  inds = list()
  idim = 1
  for (idim in seq_along(dimg)){
    adder = diff_dim[idim]
    left = floor(adder/2)
    right = adder - left
    top = newdim[idim]
    ind = seq(left + 1, top - right)
    #     stopifnot(length(ind) == dz)    
    inds[[idim]] = ind
  }
  arr[inds[[1]], inds[[2]], inds[[3]]] = img

  arr = copyNIfTIHeader(img, arr)
  return(arr)
}

You should read the documents on the FSL website. I'm closing this as this is more of how to do an analysis pipeline than issue with the package.