[Brains-users] How to convert a mask file to analyze file format

[Ronald Pierson]

Image orientation is a constant problem when going between packages.
Hans and his folks here at Iowa have worked hard to make brains2 as
compliant as possible with analyze format, but it is apparent some
fields are interpreted differently across software.  The default
orientation the BRAINS uses is coronal when it saves the image, which is
different from some packages.  That is written into the header.  Most
other imaging packages assume axial orientation, and some don't check
the header, or may interpret it differently.  Hans probably has a much
better explanation, but he is out of town right now.

The easiest is to save the image in axial format; just change it on the
dialog box when you save it.  Then it should work fine.

Ron

-----Original Message-----
From: Lee, Buyean [mailto:BuyeanLee at mednet.ucla.edu] 
Sent: Tuesday, March 14, 2006 6:20 PM
To: 'Ronald Pierson'
Subject: RE: [Brains-users] How to convert a mask file to analyze file
format

Dear Ron,

I confirm that I have successfully saved the mask as analyze file
format.

But, when I opened the T1 MRI in which I drew the ROI for the mask and
the
analyze mask image using AMIDE, the planes of the mask are all changed.

The axial plane was displayed in the coronal plane of the T1 MRI, and so
on.
Basically, the mask did not match the T1 MRI.

Do you have any idea why this happened?
 
Buyean


-----Original Message-----
From: Ronald Pierson [mailto:ronald-pierson at uiowa.edu] 
Sent: Tuesday, March 14, 2006 3:42 PM
To: 'Lee, Buyean'
Subject: RE: [Brains-users] How to convert a mask file to analyze file
format

Since it is displayed by default on a 0-255 scale you won't see a pixel
of intensity 1.  You can go to view, tracker and see what the
intensities are.  Or, go through the selector button to bring up the
various objects, then edit the pallet to show 1-255 as white, and you'll
see it.

ron

-----Original Message-----
From: Lee, Buyean [mailto:BuyeanLee at mednet.ucla.edu] 
Sent: Tuesday, March 14, 2006 4:41 PM
To: 'ronald-pierson at uiowa.edu'
Subject: RE: [Brains-users] How to convert a mask file to analyze file
format

Hi Ronald,

>>On the toolbar, under convert, there is an option to convert mask to
>>image.  This creates a code image with 1's inside the mask and 0's
>>outside it.

I just have tried this instruction.
But, Brains2 made an image object called TalairachMaskSum, which is
basically black screen.  
I can't find any white ('1') image in the TalairachMaskSum image.

Buyean


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