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ROI Thresholding

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Brandee Winstead

ROI Thresholding

I'm new to ImageJ, having only done simple ROI measurements
successfully. Now I am needing to get total intracranial volume from an
MRI and I am hoping to find an easier way to do this than manually
tracing the brain on each slice. I thought that if I had a tool similar
to the wand select tool in Photoshop that I could adjust thresholds and
automatically have an ROI of the brain, since everything but the brain
is black. Are there any suggestions as how to go about doing this? Thank
you.

Brandee Winstead
Emory University

Fabrice Cordelières

Re: ROI Thresholding

Hi Brandee,

Try first to make a threshold (Image/Adjust/Threshold), then use the
magic wand tool: click on the "red" zone on the image, and the ROI
will be drawn around the thresholded area.

Alternatively, you may use this macro to automate the measurement over
all slices: simply copy the following lines, go to plugins/macro/new
and paste the text:

8<------------------------------------------
roiManager("Reset");
x=getWidth/2;
y=getHeight/2;
setThreshold(1, pow(2,bitDepth()));
for (i=1; i<=nSlices; i++){
setSlice(i);
doWand(x, y);
roiManager("Add");
roiManager("Select", i-1);
roiManager("Rename", "ROI on slice n°"+i);
}
roiManager("Deselect");
run("Set Measurements...", "area redirect=None decimal=3");
roiManager("Multi Measure");
8<------------------------------------------

Open your image then go to the macro window: macro/run macro. In the
result table, the value indicate the area for each ROI.

NB: in this example, the threshold is set to 1 (change the value if
necessary). I tried it on the sample MRI stack it worked well except
on some slices such as n°12... I can't figure out why the doWand
fails: any idea ?

Fabrice

Le 10 sept. 08 à 17:10, Brandee Winstead a écrit :

> I'm new to ImageJ, having only done simple ROI measurements
> successfully. Now I am needing to get total intracranial volume from
> an MRI and I am hoping to find an easier way to do this than
> manually tracing the brain on each slice. I thought that if I had a
> tool similar to the wand select tool in Photoshop that I could
> adjust thresholds and automatically have an ROI of the brain, since
> everything but the brain is black. Are there any suggestions as how
> to go about doing this? Thank you.
>
> Brandee Winstead
> Emory University
>

Fabrice Cordelières, PhD

Institut Curie - Section de recherche/ CNRS UMR 146
Plateforme d'Imagerie Cellulaire et Tissulaire
Bâtiment 112 - Centre universitaire
91405 Orsay Cedex
FRANCE

Tél. : +33 1 69 86 31 30
Fax. : +33 1 69 86 17 03

Consultez mes disponibilités sur http://www.google.com/calendar/embed?src=fabrice.cordelieres%40gmail.com

Benjamin Schmid-2

Re: ROI Thresholding

In reply to this post by Brandee Winstead

Hi Brandee,

You may want to have a look at our Segmentation editor:

http://132.187.25.13/home/?category=Download&page=SegmentationEditor

The movie on this page shows how to use the actual version. There
are some features, like defining a threshold for a ROI.

Best wishes,
Benjamin

On 11:10 Wed 10 Sep , Brandee Winstead wrote:

> I'm new to ImageJ, having only done simple ROI measurements
> successfully. Now I am needing to get total intracranial volume from an
> MRI and I am hoping to find an easier way to do this than manually
> tracing the brain on each slice. I thought that if I had a tool similar
> to the wand select tool in Photoshop that I could adjust thresholds and
> automatically have an ROI of the brain, since everything but the brain
> is black. Are there any suggestions as how to go about doing this? Thank
> you.
>
> Brandee Winstead
> Emory University

Mario Guarracino

Re: ROI Thresholding

A wand selection tool for 8 and 16 bits CT/NMR images in available here:
http://yawi3d.sourceforge.net

Mario

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Benjamin Schmid
Sent: Wednesday, September 17, 2008 10:17 AM
To: [hidden email]
Subject: Re: ROI Thresholding

Hi Brandee,

You may want to have a look at our Segmentation editor:

http://132.187.25.13/home/?category=Download&page=SegmentationEditor

The movie on this page shows how to use the actual version. There
are some features, like defining a threshold for a ROI.

Best wishes,
Benjamin

On 11:10 Wed 10 Sep , Brandee Winstead wrote:

Dianne Patterson

Re: ROI Thresholding

In reply to this post by Benjamin Schmid-2

You might want to look for BET (Brain Extraction Tool) which is included in
MRIcro...and FSL. With BET you can generate a pretty quick estimate of what
is brain and what is not...it isn't perfect, but it is nice to have a first
estimate in a few minutes...and go from there.

-Dianne

On Wed, Sep 17, 2008 at 4:01 AM, Mario Guarracino <[hidden email]
> wrote:

> A wand selection tool for 8 and 16 bits CT/NMR images in available here:
> http://yawi3d.sourceforge.net
>
> Mario
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Benjamin Schmid
> Sent: Wednesday, September 17, 2008 10:17 AM
> To: [hidden email]
> Subject: Re: ROI Thresholding
>
> Hi Brandee,
>
> You may want to have a look at our Segmentation editor:
>
> http://132.187.25.13/home/?category=Download&page=SegmentationEditor
>
> The movie on this page shows how to use the actual version. There
> are some features, like defining a threshold for a ROI.
>
> Best wishes,
> Benjamin
>
> On 11:10 Wed 10 Sep , Brandee Winstead wrote:
> > I'm new to ImageJ, having only done simple ROI measurements
> > successfully. Now I am needing to get total intracranial volume from an
> > MRI and I am hoping to find an easier way to do this than manually
> > tracing the brain on each slice. I thought that if I had a tool similar
> > to the wand select tool in Photoshop that I could adjust thresholds and
> > automatically have an ROI of the brain, since everything but the brain
> > is black. Are there any suggestions as how to go about doing this? Thank
> > you.
> >
> > Brandee Winstead
> > Emory University
>
>

--
Dianne Patterson, Ph.D.
[hidden email]
University of Arizona
SHLS 328
621-5105