Hello,

Ah I think that's what the problem is. My program only checks (and only
reads and writes) the S-form. It's probably something to do with
avwmaths setting Q-form to be consistent with S-form, but then my
program applying new changes only to S-form so that the two are
inconsistent.

I find Q-form much harder to understand, though. I know that they are
both in the NifTI-specification, but had the impression that it is
possible to use one and not the other (I thought that the difference
between the two forms was what what I wrote in my 1st email).

Would there be an easy way to, if all images that I have are axial,
convert an S-form into a Q-form, to fill them in consistemtly? A
StoQform() operation, if you like.

Many thanks
Alle Meije

Mark Jenkinson wrote:
> Hi,
> 
> The qform is a perfectly legitimate part of nifti and, in fact, all
> other supporting packages for nifti started by supporting
> qform before sform.  That's the reason that we now set the
> qform to be the same as the sform by default, as many other
> packages rely on this to work properly.
> 
> The reason people want both qform and sform is so that you
> can know standard space coordinates while, at the same time,
> knowing exactly what the original acquisition directions are,
> which can be important for physics-based corrections where
> the phase-encode, read and slice directions need to be known.
> 
> So there is no way of turning it off at the moment, without also
> losing the sform information.  If you don't care about that then
> you can set both to the "unknown" state by using avwedithd
> (or script it using avwhd -x and avwcreatehd).
> 
> Alternatively, is there a way of making the software that you
> use ignore the qform?  That would seem to be the easiest
> solution.
> 
> All the best,
>     Mark
>