[MINC-users] How to use rawtominc with multiple files

[Andrew Janke]

> 2. also, when I check with mincheader command of the "data_pix_out.mnc" the
> image-max = 65285, 65285, 65285, 65285...................
> and
> image_min = _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
>      _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
>      _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
>      _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
>      _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
>      _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
>      _, _, _, _, _, _, _, _,
>
> Is there any information I missed to put in the rawtominc conversion
> command line?

No, this is expected behaviour.


> 3. 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 position of the first voxel is defined by the start information
for each dimension. use mincinfo on the file to get thie information.

> I was trying to resample the input image with average_305.mnc in mritotal
> and mincresample command before using NU_CORRECT. Which would be the better
> solution for NU_CORRECT? directly use on input image or after transforming
> data in a model (average_305) and then use the intensity correction? Please
> give me suggestion in this regard.

Given that N3 has no knowledge of model space and the likes and works
on the raw histogram I would not expect the results to be different
beyond std interpolation and rounding errors.  Typically N3 is run on
the native data.

> 4. I would like to transfer the *.minc image into *.raw after the
> correction to use my own algorithm run on the intensity corrected image. I
> was using the command
> minctoraw -short -unsigned -normalize data_pix_out_nu.mnc > data_pix_out_nu.raw
>
> The value in the raw file are varied from -32767 to 32767. My original
> input image is unsigned short, intensity voxel value min is zero and  max
> 1700. I would like to return back the *.minc image after correction into
> the similar intensity level of input *.raw image.

I suspect you want -nonormalize as opposed to -normalize.  ('minctoraw
-help' or 'man minctoraw' explains the difference between the two.)


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