From gabriel.devenyi at mcgill.ca  Thu Jun 21 11:05:52 2018
From: gabriel.devenyi at mcgill.ca (Gabriel A. Devenyi)
Date: Thu, 21 Jun 2018 11:05:52 -0400
Subject: [MINC-users] Display's "Fill 3D" on the command line?
Message-ID: <CAFQOoOqpPW4ke-CH7amq+7nETHeObpnAHr+Pivwdpw=v43qwQA@mail.gmail.com>

Hi minc-users,

I'm wondering if anyone knows of a command/tool which implements Display's
3D fill function on the command line.

Ideally, I'd like something like
```
mincfill3d input.mnc <x y z coordinate, in voxel or world> threshold_low
threshold_high output.mnc
```

This function would drop a point at XYZ and then do region filling
according to the threshold limits (maybe would have an option to specify
the connectivity type.

Does such a thing exist?

Thanks!

--
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
Affiliate, Department of Psychiatry
McGill University
t: 514.761.6131x4781
e: gabriel.devenyi at mcgill.ca

From a.janke at gmail.com  Thu Jun 21 16:58:02 2018
From: a.janke at gmail.com (Andrew Janke)
Date: Fri, 22 Jun 2018 06:58:02 +1000
Subject: [MINC-users] Display's "Fill 3D" on the command line?
In-Reply-To: <CAFQOoOqpPW4ke-CH7amq+7nETHeObpnAHr+Pivwdpw=v43qwQA@mail.gmail.com>
References: <CAFQOoOqpPW4ke-CH7amq+7nETHeObpnAHr+Pivwdpw=v43qwQA@mail.gmail.com>
Message-ID: <CAG0CB23S0jUTPXxv6ep0Wv=d=zSpYeQdNx4B56cvdM4bhJ4SGg@mail.gmail.com>

Hi Gabriel,

Not that I am aware of, unless Vlad has written something. Which is
highly likely.

However I think you could do this a round about way with mincmorph (probably)

First binarise the image

   $ mincmorph -successive B[floor:ceil] in.mnc ...

Then do Connected Component Labelling (note that the components are
labelled in ascending order of #voxels. Might be useful, might not be
for what you are doing.

   $ mincmorph -successive B[floor:ceil]G in.mnc CCL.mnc

Then determine the value at your point

   $ value=$(mincextract -nonormalize -ascii -start x,y,z -count 1,1,1 CCL.mnc)

Then use this value with minccalc / mincmorph / mincmath

   $ minccalc -expression 'A[0] = $value CCL.mnc mask.mnc
   $ mincmorph -successive K[$value:$value] CCL.mnc mask.mnc
   $ mincmath -const2 $value $value -clamp ...blah tiddly something,
Hrm perhaps not with mincmath, it's two steps I think.

I suggest mincmorph as you will have complete control over the
structuring element/kernel. See the -kernel option if you don't want
to use one of the standard ones.

ta


a

On Fri, 22 Jun 2018 at 01:07, Gabriel A. Devenyi
<gabriel.devenyi at mcgill.ca> wrote:
>
> Hi minc-users,
>
> I'm wondering if anyone knows of a command/tool which implements Display's
> 3D fill function on the command line.
>
> Ideally, I'd like something like
> ```
> mincfill3d input.mnc <x y z coordinate, in voxel or world> threshold_low
> threshold_high output.mnc
> ```
>
> This function would drop a point at XYZ and then do region filling
> according to the threshold limits (maybe would have an option to specify
> the connectivity type.
>
> Does such a thing exist?
>
> Thanks!
>
> --
> Gabriel A. Devenyi B.Eng. Ph.D.
> Research Computing Associate
> Computational Brain Anatomy Laboratory
> Cerebral Imaging Center
> Douglas Mental Health University Institute
> Affiliate, Department of Psychiatry
> McGill University
> t: 514.761.6131x4781
> e: gabriel.devenyi at mcgill.ca
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From thomas.funck at mail.mcgill.ca  Thu Jun 28 14:49:22 2018
From: thomas.funck at mail.mcgill.ca (Thomas Funck)
Date: Thu, 28 Jun 2018 18:49:22 +0000
Subject: [MINC-users] Surface AAL Atlas Labels
Message-ID: <YTOPR0101MB2268DF7C940BC4B5D1A7B2E8A64F0@YTOPR0101MB2268.CANPRD01.PROD.OUTLOOK.COM>

Hi,


Does anyone have a surface version of the AAL1 atlas (i.e. AAL surfaces interpolated onto a cortical surface mesh)? I tried to generate some surfaces using CIVET and the Colins27 brain, but the results aren't great and I figure someone must have already done this.


Cheers


Thomas