[Mristudio-users] [developers] Landmarker -Transformation matrix -normalization issues

[Xin Li]

Tilak,

Landmarker is a user-interacted software. If you want to do the batch work of AIR transformation, you can run AIR applications in the command prompt window. Please check the website of AIR http://bishopw.loni.ucla.edu/AIR5/programs.html. 


Xin



----- Original Message -----
From: ramtilak gattu <tilakgattu at gmail.com>
Date: Thursday, May 14, 2009 7:52 am
Subject: Re: [developers] Landmarker -Transformation matrix -normalization issues
To: mristudio-users at mristudio.org, susumu <susumu at mri.jhu.edu>, developers at mristudio.org
Cc: "Benson, Randall" <rbenson at med.wayne.edu>


> Hello mristudio Users,
>  
>  I have two questions regarding Normalization using Landmarker
>  
>  1) I normalized one subject' FA brain to the Icbm Mni space FA template
>  using Landmarker using linear algorithm. The issue is - I am trying 
> to use
>  the transformation matrix (Alignlinearoutput.air) file to batch up "n"
>  number of subjects at a time to save time and to avoid some tedious 
> work in
>  loading up all the images and doing them individually. The output 
> image is
>  very very bad and it doesn't show up clearly while normalizing using 
> this
>  transformation matrix ( with a single subject or 'n' subjects). My question
>  is ' Am I missing some step' to get a proper result?
>     In simple words , We have 50 brains which are in our template 
> space.  We
>  would like to apply the same transformation matrix to all 50 brains 
> to get
>  them into your template space so we can do the regional analysis.  We 
> have
>  found that all we need is a simple linear normalization to get there. 
>  So
>  how to apply the Alignlinearoutput.air transform to all 50 brains.
>  
>  2) I even tried loading up "n" images and tried linear normalization 
> it
>  gives updated images-"n".img but some look good some look translated 
> and
>  some look rotated. Doesn't landmarker normalize ' n' images at a time 
> as SPM
>  does?
>  
>   One last question,  Couple of weeks back I loaded up one FA image 
> for non
>  linear processing using the option of remote processing in 
> Landmarker. I
>  still didnt get any reply from the remote site, normally how long 
> does it
>  take for us to see the results (retrieve the results)? FYI , My user 
> name is
>  ao3080 at wayne.edu.
>  
>  Thanks for your time and help.
>  
>  Regards
>  Tilak
>  
>  On Sat, Jun 14, 2008 at 4:11 PM, ramtilak gattu <tilakgattu at gmail.com>
>  wrote:
>  
>  > Hello Dr Susumu Mori,
>  >
>  > I have two questions regarding Normalization using Landmarker
>  > 1) I normalized one subject' FA brain to the Icbm Mni space FA template
>  > using Landmarker using linear algorithm. The issue is - I am trying 
> to use
>  > the transformation matrix (AIRlinearoutput.air) file to batch up 
> "n" number
>  > of subjects at a time to save time and to avoid some tedious work 
> in loading
>  > up all the images and doing them individually. The output image is 
> very very
>  > bad and it doesn't show up clearly while normalizing using this
>  > transformation matrix ( with a single subject or 'n' subjects). My 
> question
>  > is ' Am I missing some step' to get a proper result?
>  >
>  > 2) I even tried loading up "n" images and tried linear 
> normalization it
>  > gives updated images-"n".img but some look good some look 
> translated and
>  > some look rotated. Doesn't landmarker normalize ' n' images at a 
> time as SPM
>  > does?
>  >
>  >  One last question,  Couple of weeks back I loaded up one FA image 
> for non
>  > linear processing using the option of remote processing in 
> Landmarker. I
>  > still didnt get any reply from the remote site, normally how long 
> does it
>  > take for us to see the results (retrieve the results)? FYI , My 
> user name is
>  > ao3080 at wayne.edu.
>  >
>  > Thanks for your time and help.
>  >
>  > Regards
>  > Tilak
>  > --
>  > Ramtilak Gattu
>  > 21530 Green Hill Rd
>  > #127
>  > Farmington Hills
>  > Michigan-48335
>  > ph: 313-887-1766
>  >       313-820-8862
>  >       313-745-1388
>  >
>  
>  
>  
>  -- 
>  Ramtilak Gattu
>  21530 Green Hill Rd
>  #127
>  Farmington Hills
>  Michigan-48335
>  ph: 313-887-1766
>  313-820-8862
>  313-745-1388 
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