Whole Brain Volume

[Brandee Winstead]

Is there a simplified way of doing this to get a rough estimate of whole
brain volume? Currently the only method I can think of is drawing ROIs
on every 3rd slice of the MRI, but this will take up a large chunk of time.

I've also been exploring the BET Tool on MRIcroN but I'm finding it less
than user friendly and cannot find any assistance online.

Thank you!

Brandee Winstead
Emory University

[Ahearn, Dr Trevor S.]

Hello Brandee,
 if you're doing neuro work it may be an idea to try implementing the FSL package http://www.fmrib.ox.ac.uk/fsl/ this is where the BET algorithm comes from. There's a bunch of other usefull tools on there as well such as segmentation and registration. You'll need to install VMWare player if you're using windows but it's fairly painless.

How can you get a brain volume measurement by drawing a ROI on every third slice? Surely you'll want to draw on every slice where there is brain tissue?


Regards

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Brandee Winstead
Sent: 26 September 2008 17:05
To: [hidden email]
Subject: Whole Brain Volume

Is there a simplified way of doing this to get a rough estimate of whole brain volume? Currently the only method I can think of is drawing ROIs on every 3rd slice of the MRI, but this will take up a large chunk of time.

I've also been exploring the BET Tool on MRIcroN but I'm finding it less than user friendly and cannot find any assistance online.

Thank you!

Brandee Winstead
Emory University


The University of Aberdeen is a charity registered in Scotland, No SC013683.

[Lambright, Geoffrey]

Hi Everybody,

Can anyone point me in a direction to analyze fiber meshwork structures?
I have z-stack series of collagen fiber meshworks, and I need to
quantify and compare structure differences in varying samples. Basic
differences include spacing and fiber density, branching angles, length,
geometry of open spaces in meshwork, but I would also be interested in
any other structural aspects that may help me identify differences in
these meshworks.

Image J plug-ins was my first target for answers, but I am open to other
platforms as well. If anyone knows of other folks who have done similar
things, I would be interested in references to articles that may contain
information of how they analyzed fiber meshwork structural differences
and what they quantified as well.

The images are quite similar to what you might find in textile meshworks
and paper fiber meshworks as well - any sources in those fields is also
certainly welcome.

Thanks very much!!!

Geoff

[Sudhakar Jaganathan]

Hi,

I don't know about imagej, you could try 3dma-fiber or 3dma software for
3-d medial axis analysis.it use to be open source.

Sudhakar



Hi Everybody,

>
> Can anyone point me in a direction to analyze fiber meshwork structures?
> I have z-stack series of collagen fiber meshworks, and I need to
> quantify and compare structure differences in varying samples. Basic
> differences include spacing and fiber density, branching angles, length,
> geometry of open spaces in meshwork, but I would also be interested in
> any other structural aspects that may help me identify differences in
> these meshworks.
>
> Image J plug-ins was my first target for answers, but I am open to other
> platforms as well. If anyone knows of other folks who have done similar
> things, I would be interested in references to articles that may contain
> information of how they analyzed fiber meshwork structural differences
> and what they quantified as well.
>
> The images are quite similar to what you might find in textile meshworks
> and paper fiber meshworks as well - any sources in those fields is also
> certainly welcome.
>
> Thanks very much!!!
>
> Geoff
>

--
Sudhakar Jaganathan

North Carolina State University
Nonwovens Cooperative Research Center
College of Textile
NC-USA

[Markko Merzin]

Ühel kenal päeval, R, 2008-09-26 kell 12:05, kirjutas Brandee Winstead:

> Is there a simplified way of doing this to get a rough estimate of whole
> brain volume? Currently the only method I can think of is drawing ROIs
> on every 3rd slice of the MRI, but this will take up a large chunk of time.

Hi! Have You seen http://www.ut.ee/~markkom/volumest ?
It gives you volume and error estimations.

--
Markko Merzin <[hidden email]>