[MINC-users] bug in the mincmorph grouping option

[Andrew Janke]

Hi Pierre,

You are right, however I like to call this behaviour a "feature". :)

This happens because of the shape of the structuring element, in order
to gain a bit of speed and skip doing bounds checking while running
through a 5 deep for loop, I only run the structuring element (for
grouping/dilation/convolution) on the central chunk of the volume
which guarantees me to not get edge problems.

The simple fix is to first pad your volume before running the group.
the Pad option pads by 1/2 the size of the current structuring
element/kernel.

So instead of doing this:

   mincmorph -successive 'G' in.mnc out.mnc

do this:

   mincmorph -successive 'PG' in.mnc out.mnc

Hope this helps,


--
Andrew Janke
(a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883


On Thu, Feb 11, 2010 at 15:08, Pierre Bellec <pbellec at bic.mni.mcgill.ca> wrote:
> Hi everyone,
>
> I have recently been using mincmorph to perform various morphomat
> operations, and I am really happy with that tool which is quite powerful.
> However, I noticed a small bug. The first slice/column/line get set to zero
> with the argument '-successive G'. Maybe I am just using an old version of
> the program (I believe the latest version is not available for my system,
> which is hardy) and that bug has already been fixed. The '-version' tells me
> it is mincmorph 1.4.
>
> Regards,
>
> Pierre
>
> --
> Pierre Bellec
> Post-doctoral fellow
> McConnel Brain Imaging Center, Webster 2B
> Montreal Neurological Institute
> 3801 University Street
> Montreal, Quebec, Canada H3A 2B4
> http://wiki.bic.mni.mcgill.ca/index.php/PierreBellec
> tel:       (001)(514) 398 5220
> fax:      (001)(514) 398 8948
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