[Mristudio-users] apply transformation to landmarkers & commandfile

[Yi Jiang]

Dear Dr Mori,

 

Thank you very much for your quick and detailed answers. 

 

1.	One thing I need to note is that the transformation matrix I have is
a "final" combined matrix of AIR rigid, AIR affine, and LDDMM K map (so it
should be in the raw data format). Can I extract the "vector" information at
the specified location in this transformation matrix? And how?

 

2.	I agree that checking the result after each step is necessary. I
have manually processed and checked all my data. If there is a way to
automate the process by a command file after I have finalized the methods
and steps, it will be nice so that it can help avoid any unintended mistake
(forget to change a parameter, typo, misclick a button etc) which might
happen when I manually process a lot images. So it will be a nice feature,
but of course not a must yet.

 

Best,

Yi

 

 

  _____  

From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori
Sent: Saturday, January 30, 2010 8:30 AM
To: Yi Jiang; DTI Studio, ROI Editor, Landmarker Questions/Support; Xin Li;
Jiangyang Zhang
Subject: Re: [Mristudio-users] apply transformation to landmarkers &
commandfile

 

Hi Yi,

On Fri, Jan 29, 2010 at 5:25 PM, Yi Jiang <yj3 at duke.edu> wrote:

Hello, dear all,

 

I have two questions and am wondering if someone can help.

 

1.	I have already had a transformation matrix to map the subject image
onto the template image, which was generated by combining AIR rigid, AIR
affine, and LDDMM matrix. I want to define some landmarkers on the subject
image, and apply the transformation matrix to the landmarkers (to see their
corresponding location on the template image). How can I do that?


I think this is exactly what the K and H maps are. I need  confirmation from
Xin, but in my understanding, these transformation matrices contain vectors
at each coordinate, indicating where is the new location. If I'm not
mistaken, it is Vector (x, y, z) x X-dimension x Y-dimension x Z-dimension.
There must be a way to extarct the "Vector" information at the specified
coordinate.

 

2.	I would like to use the "load command file" function. I will do AIR
linear rigid transformation, AIR linear affine transformation, image format
change to byte, automatic intensity correction by histogram, and 2-channel
LDDMM. Is it possible to put all these into one command file? If yes, can
anyone give me an example file?

I believe the command file is only for the functions within the same box,
including byte-integer-float conversion, axial-sagittal-coronal conversion,
resampling, etc. They don't include transformation functions. We are working
on automation, which will take several months. Meanwhile, I believe it is
good idea to use the current way, which forces you to check the result after
each step. Transformation sometimes does silly things. Some images may have
quality problems. You may want compare different methods (e.g. Mutual Info
linear transformation vs AIR, intensity correction methods, contrast of
choice). I think it's very important to get a feel about your data and each
transformation step. Also, depending on pathology, the transformation
strategy may change. Some disease groups have severe intensity changes (e.g.
stroke), some have severely enlarged ventricles. You may find the same
methods may work for one but not the other. Automation is still a difficult
matter for transformation-based analysis.
 

 

Thank you very much!

 

Have a nice weekend!

 

Best

Yi

 

 


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