[MINC-users] help on using rawtominc and n3

[Runa Parveen]

Hi,

I have several question to run this package:
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.
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

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

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?

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

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?

I really need your suggestion in these regards, and early reply is 
sincerely appreciable.



Yours sincerely,

Runa

******************************************************************** 

* Runa Parveen                                                          **
* Medical Imaging Group                                               **
* Dept. of Medical Physics & Bioengineering                   **
* University College London                                            **
* 2nd Floor, New Malet Place Engineering Building           **
* Gower Street, off Torrington Place                                 **
* London WC1E 6JA                                                 **
* 
UK 
**

* e-mail: runa at medphys.ucl.ac.uk                                  **
*********************************************************************