[MINC-users] mincreshape segfault and general behavior

[Alex Zijdenbos]

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