[Mristudio-users] human brain atlas

Tue Apr 28 09:28:52 EDT 2009

Hi Arun,

It is likely that the difference is just 0 padding at the 182th, 218th, and
182th line. You can convert our 181x217x181 atlas to 182x218x182 using the
"Crop" function in Landmarker. Another possibility is that it was
interpolated, which can also be done by Landmarker. You may want to make
sure by subtracting the images (you can do it in RoiEditor). 

We also got ICBM-152 from UCLA and don't know why there are two versions
with different dimensions. 

Susumu

  _____  

From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Arun Bokde, PhD
Sent: Tuesday, April 28, 2009 6:49 AM
To: DTI Studio, ROI Editor, Landmarker Questions/Support
Subject: Re: [Mristudio-users] human brain atlas

Hello,

The ICBM-152 Atlas that comes from the UCLA web site has dimensions of 182 x
218 x 182 .  Within DTI Studio it is 181 x 217 x 181.  There seems to be a
single slice  difference between both templates?  Where would the single
slice need to be added for both templates to match?

Regards,

Arun

From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu
Sent: 26 January 2009 17:50
To: 'DTI Studio, ROI Editor, Landmarker Questions/Support'
Subject: Re: [Mristudio-users] human brain atlas

1) Landmarker can normalize your data to ICBM-152. It comes with the ICBM
(including our ICBM-DTI contrasts) and you can doa linear or non-linear
method.

2) If you already normalized to the ICBM-152, the first step can be skipped.
Just make sure the following;

> our ICBM-152 has 181x217x181 matrix with 1 mm resolution

> You can load our ICBM-152 and your normalized images to Landmarker (or any
other software) to make sure that the compatibility of two ICBM-152 (one you
used and the other one implemented in Landmarker and RoiEditor).

> Also, all of our software follows the Radiology convention (right is
left). If you find your image is loaded upside down, that is because of the
brain orientation issue. It is a good practice to make sure right-left is
correct in your entire procedure using a subject with some characteristic
asymmetry

3) Once you confirm that your ICBM atlas was compatible with the one
implemented in our software, do the following;

> Load your normalized data. If you have lesion volume data (I assume it is
1/0 binary data), load it with some anatomical image such as T2.

> Make sure that the image dimension is 181x217x181 / 1mm

> Then, choose "ICBM" as an atlas in the right column

> There is a button looks like the lung. Click it. This automatically
segment your data into many white matter and gray matter regions and give
you a report. For your lesion image, you can get how many "1 = lesion pixel"
are in each segmented white matter area.

> If you want to see the segmentation visually, use the "load" button in the
"atlas" section and load one of the "WMPM". You can visually see the
superimiposition of the segmentation on the loaded images.

Try

  _____  

From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of WangPing
Sent: Monday, January 26, 2009 11:32 AM
To: mristudio-users at mristudio.org
Subject: Re: [Mristudio-users] human brain atlas
Importance: High

Susumu,

I just played with RoiEditor for a while, and found the atlas with the
software.  I am wondering if the tool (or you may recommend other tool) can
use the atlas to label my subjects.  Right now my subjects have been
normalized to MNI152 space (non-linear registration), there are white matter
lesions on some subjects, I want to calculate the lesion volume on the white
matter regions.  IF I can label my subjects, I will know the lesion volume
on each parcellation. I do not have to need a very detailed label atlas at
this point, maybe a atlas that can divide a brain into a few parcellations
will be okay.
Thanks, any suggestion is  high appreciated.
Best Regards,
Ping

Date: Sun, 25 Jan 2009 08:38:18 -0500
From: susumu at mri.jhu.edu
To: mristudio-users at mristudio.org
Subject: Re: [Mristudio-users] human brain atlas

Hi Ping,

We have several white matter atlases in lbam.med.jhmi.edu, but the easiest
way is to download Landmarker/RoiEditor from www.mristudio.org
<http://www.mristudio.org/> , which come with different types of electronic
atlases. One of them is population-averaged atlas in the MNI coordinates. If
you use linear normalization, I recommend using this atlas (named
ICBM_DTI-81 for GE/Siemens and JHU-MNI-GA for Philips). If you use highly
non-linear normalization, I recommend the single-subject atlas (named
JHU-MNI-SS). Both atlases come with a hand-segmented white matter
parcellation map (WMPM). If you download RoiEditor, this software can apply
the WMPM for various types of image quantification. Please refer to
www.mristudio.org <http://www.mristudio.org/>  for more info.

Susumu

  _____  

From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of WangPing
Sent: Saturday, January 24, 2009 11:53 PM
To: mristudio-users at mristudio.org
Subject: [Mristudio-users] human brain atlas
Importance: High

Dear Dr. Mori and the List:

Could anyone recommend a brain atlas (label atlas) that covers the main
white matters?  It will be great if this atlas is easy to register to MNI
template.

Thanks a lot!
Ping

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