[MINC-users] mincreshape segfault and general behavior

[Soren Christensen]

Andrew, as Alex says mincreshape does do volume averaging - lucky for me it
works for my purposes (at least some basic numerical tests support that).
Thanks for pointing me to the width option of mincresample, but I am not
sure it can do a relatively simple downsample-volume-averaging, it seems to
relate to sinc-windowing.
Does volregrid volume average when downsampling?  If so, then maybe that is
a suitable replacement for mincreshape when it comes to downsampling?



Soren


On Fri, Oct 4, 2013 at 12:44 PM, Alex Zijdenbos <zijdenbos at gmail.com> wrote:

> On Fri, Oct 4, 2013 at 6:35 AM, Andrew Janke <a.janke at gmail.com> wrote:
> >> Let me make sure I understand this right. Are you saying mincreshape
> does
> >> no volume averaging? If you reshape from a dimsize of 512 to 256 for
> >> example, then isn't each voxel a 4x4 average of the input?
> >
> > Correct. mincreshape does no volume averaging/blurring/interpolating
> > that I know of.
>
> So apparently mincreshape does do volume averaging when you use the
> -dimsize option, as Soren noted and Peter confirmed; so it seems that
> in this sense mincreshape -dimsize does the same thing as Vlad's
> EZminc minc_downsample.
>
> > In this case mincresample is what you want. This sort
> > of doubling/halving of step sizes is voered by autocrop with the
> > -isostep style options. Because I like making my own toys I have a few
> > incarnations of this here:
> >
> >    http://packages.bic.mni.mcgill.ca/scripts/voliso
> >
> > I see Vlad has also responded with his own tool to do this.
>
> Not quite - none of these do any kind of volume averaging when you
> downsample. I did some tests using a simple binary sphere, generated
> with 1mm isotropic voxel dims and subsequently downsampling that to
> 3mm voxel dims in a few ways:
>
> https://www.dropbox.com/s/env1l9iorejex92/downsample.jpg
>
> The 4 images are:
>
> 1) orginal 1mm
> 2) resampled to 3mm using mincresample -sinc
> 3) reshaped to 3mm using mincreshape -dimsize
> 4) mincblur -fwhm 3, followed by mincresamle -nearest
>
> Note that for 2), it makes absolutely no difference what interpolant
> you select for mincresample; the result is always identical to this
> image (which is probably not what most people would want/expect). Same
> for autocrop/voliso, which also don't add averaging as they simply
> calls mincresample.
>
> I usually use method 4); and until yesterday wasn't aware that 3)
> works. The difference between them is really the choice of the
> blurring kernel; in 4) a Gaussian, in 3) it's just a rect.
>
> -- A
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