[MINC-users] help on using rawtominc and n3

[Andrew Janke]

On 30/11/05, Runa Parveen <runa at medphys.ucl.ac.uk> wrote:
> 1. I have coronal slices, dimension: 256x256x170, cubic voxel :1mm, T1
> weighted. I could not understand how I could give the command when changing
> from rawtominc? also in world coordinate space?
> the command line I use:
>
> rawtominc -coronal -short -unsigned -origin 0 0 0 -range 0 32767
> -real_range 0 32767 -orange 0 32767 -ystep 1 -zstep 1 -xstep 1 -xdircos 1 0
> 0 -ydircos 0 1 0 -zdircos 0 0 1 -mri data_pix_out.mnc 171 256 256 <
> data_pix_in.img
>
> I am worried about the right way of mentioning dimension and also what
> would be the first voxel of the data in world coordinate.

The command above looks generally right to me, I'd suggest s few
changes if you'd like to position the first voxel (say at -10,-50,-50)

   rawtominc -coronal -short -unsigned -scan_range \
   -xstep 1 -ystep 1 -zstep 1 \
   -xstart -10 -ystart -50 -zstart -50 \
    -mri data_pix_out.mnc 171 256 256 < data_pix_in.img

Although given that your data appears to be in ANALYZE/Nifti format,
the easiest thing may be this:

   nii2mnc data_pix_in.hdr data_pix_out.mnc

> 2. In mincresample, what would be the position of centre of first voxel
> along each of the world dimensions?
> the command line I use:
> mincresample data_pix_out.mnc data_pix_resample.mnc -transform
> data_pix_res.xfm -like average_305.mnc -step 1 1 1 -short -unsigned -range
> 0 32767 -nearest_neighbour -nelements 171 256 256

I am a bit confused as to what you are trying to achive in the above.
I suspect you should drop the -step argument and instead specify one
of -use_input_sampling or -like <target.mnc>.  I'd also drop the type
and range arguments unless you really do want to change the range to
be exactly this.

> The volume of the output in this stage is almost half of the rawtominc output?

Meaning the output file is now 1/2 the original size or the image data?

> 3. In display, the image is showed in some tilting position. Also I would
> like to know when the image_range is used, what would be value of the voxel
> when viewing the image in Display?

The real value of the data in a voxel is displayed in a column on the
left hand side of the image data.

> 4. Also after applying nu_correct, the program runs only for 2 iteration
> and given CV: 0.000878881, is it OK?

Possibly, but without knowing the data it is difficult to answer this.

> 5. As it is stopped after 2 iterations, I use the command:
> nu_correct -iterations 100 -stop 2.e-5 data_pix_resample.mnc data_pix_nu.mnc
> it stopped after 37 iterations and CV of field changes: 1.61641e-05.

> Also, in Display, the view of the image in tilting position. Also I would
> like to know how I could understand the non-uniformity has been corrected?

Look carefully at things like the intensity of the grey/white matter
across the image (in coronal,sagital and axial planes).  Use windowing
with say the spect colour map to best illustrate the differences in
register.

The corrections that N3 makes are often very subtle.

--
Andrew Janke      (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor)
Canada->Montreal                                   Cell: +1 (514) 924 2012