[MINC-users] transfer integer from MNI to native space

[Jason Lerch]

If you are using mincresample to transfer the values back into native 
space, try using 'mincresample -nearest_neighbour'

Otherwise there was a discussion on the minc-development list a while 
back about label volumes, which I suspect applies. I've pasted one 
message (from Claude Lepage) below in case it helps.

Jason

====

Hi,


> > Correct, the way I have always done this is do a mincreshape to files
> > that are misbehaving..
> > 
> >    mincreshape -image_range 0 255 -valid_range 0 255 ...
>   

This does not correct the problem if the min/max are set per slice and that
they vary for each slice. Once a label file has been "decimalized" by the
ranges, there is no way to recover the original values by the above 
operation.

For example:
   Take a label = 10, with voxel value of 10 if there is a one-to-one 
correspondence with voxel range and image real. Now assume that the slice
has a min=0 and a max=61. That's 62 values over a 256 range, so each bin
has a value of 62/256=0.2421875. The label 10 will be best approximated 
by the 41th bin with value 41*0.2421 = 9.9297. (There might be some
ajustment to do if the values are range-centered, but my argument is still
valid.) Setting back max=255 for the slice will not recover the original
label 10. Now keep doing this repeatedly (minccalc, mincmath, etc) and 
some labels will change value (10 drifts to 9, for example). 

The option -keep_real_range in mincresample does the trick as the global
min/max of the image are applied to each slice, thus not changing the 
internal voxel values. minccalc (which uses voxel_loop as AJ pointed out)
does not.

Despite being ugly, I also think that working in floats might be the best
compromise (on the temporary files, of course).

Claude



Atsuko Nagano wrote:
> Hello all,
>
> I have several ROIs with integers on one MNI space.
> Then I transferred the ROI.mnc into native space for each subject.
>
> However, all integer changed into several values.
> eg. MNI space: ROI A has the value of 33, Native space: ROI A has the
> value between 9 to 33.
>
> I guess it is because of smoothing.
> How can I get same value for each ROI in native space?
>
> Thank you,
> Atsuko
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