[MINC-users] Isolated Spots in mincbeast masks?

[Simon Eskildsen]

Hi Gabriel,

The -fill option simply performs a post-processing step where possible
holes in the mask are filled. Holes are in this context defined as
background objects completely surrounded by foreground object (the mask).

mincbeast always removes isolated mask components as a post-processing step
(irrespective of the -fill option). If the isolated mask components, which
can be seen in the sagittal view of your figure, are truly isolated in 3D,
then mincbeast has a bug. However, I suspect that these voxels are
connected to the main component in 3D.

Let me know if this is not the case and I can take a closer look at your
example.

Simon

On Wed, Jan 28, 2015 at 11:33 PM, Gabriel A. Devenyi <gdevenyi at gmail.com>
wrote:

> Hi all,
>
> I’m having some trouble with mincbeast producing masks with isolated
> spots, despite using the -fill option when invoking. See attached
> screenshot of a brain-mask overlay.
>
> I would’ve expected that the mask would be expanded to encompass the
> isolated mask component, is that not the case?
>
> I invoked mincbeast with the following
>
> mincbeast -clobber -verbose -fill -median -same_res -flip -conf /opt/quarantine/resources/BEaST_libraries/combined/default.1mm.conf /opt/quarantine/resources/BEaST_libraries/combined preprocessed/OAS1_0019_MR1_mpr_n4_anon_sbj_111.n4correct.affine_register_masked.cutneckapply.beastnormalize.mnc preprocessed/OAS1_0019_MR1_mpr_n4_anon_sbj_111.n4correct.affine_register_masked.cutneckapply.beastnormalize.beastmask.mnc
>
> ​
> ​Am I missing something or is this a bug?​
>
>
> --
> Gabriel A. Devenyi B.Eng. Ph.D.
> Research Computing Associate
> Computational Brain Anatomy Laboratory
> Cerebral Imaging Center
> Douglas Mental Health University Institute
> McGill University
> t: 514.761.6131x4781
> e: gdevenyi at gmail.com
>