[Mristudio-users] human brain atlas

[WangPing]

Susumu, thank you very much.  Ping

Date: Mon, 26 Jan 2009 12:50:23 -0500
From: susumu at mri.jhu.edu
To: mristudio-users at mristudio.org
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, 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 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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