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

[Vivek SINGH]

On Tue, 20 Dec 2005, Sridar Narayanan wrote:

> >> 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.

This is not exactly true.  The default behaviour of the nu_estimate script
(called by nu_correct) is to mask volumes in Talairach space using the
average_305_mask_1mm.mnc.  (This is done by attaching an -auto_mask option
when nu_estimate calls the nu_estimate_np_and_em script, for those who
care)  The decision is based on whether the 'spacetype' variables for the
x,y and z dimensions of the minc volume are set to "talairach" or not,
which is done for volumes resampled to an ICBM template using
mincresample.

>
> That's the usual practice, and performing the NU correction first will
> likely improve the registration to the average brain.
>

I believe someone investigated this and found there was little appreciable
difference in registration using mritotal if the NU correction is
performed before or after the fact (given data acquired with the ICBM
protocol), thought it probably doesn't hurt.

In my experience, performing the NU correction after registration can
sometimes improve the result, if I am unhappy with the correction before
registration.

Vivek