[MINC-users] Isolated Spots in mincbeast masks?

[Gabriel A. Devenyi]

Simon,

You are correct, the region was connected elsewhere, it was the slice I was
looking at that showed no connection. Thanks for your help.

Thanks for your feedback!

-- 
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

On Mon, Feb 2, 2015 at 5:17 AM, Simon Eskildsen <eskild at gmail.com> wrote:

> 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
>>
>
>