[Mristudio-users] DiffeoMap - Returning Image to the native subject space after LDDMM

[Bill Quinn]

Hi Xin,
 
Thank you very much, the problem was my selection of the template as you described.
 
Thanks again for a quick and effective response.
 
Bill


________________________________
From: Xin Li <xli16 at jhmi.edu>
To: Bill Quinn <billquinndme at yahoo.com>; "DTI Studio, ROI Editor, DiffeoMap Questions/Support" <mristudio-users at mristudio.org> 
Sent: Friday, 23 December 2011, 14:17
Subject: Re: [Mristudio-users] DiffeoMap - Returning Image to the native subject space after LDDMM

Hello Bill,

Your original data is 256*256*55. When the template is your original data (256*256*55) and the inverted air is applied, the WMPM is supposed to be converted to your original data space that is 256*256*55. 

Please take a look at the second slide on the webpage https://www.mristudio.org/wiki/user_manual/diffeomap/GetStarted_DualChannelNormalizationPipeline%3A
It shows the steps to convert the WMPM to the original data space.


By the way, when the WMPM is applied, please make sure to choose nearest neighbor as the interpolation method.


Xin


----- Original Message -----
From: Bill Quinn <billquinndme at yahoo.com>
Date: Friday, December 23, 2011 7:48 am
Subject: Re: [Mristudio-users] DiffeoMap - Returning Image to the native subject space after LDDMM
To: "mristudio-users at mristudio.org" <mristudio-users at mristudio.org>


> Hi all,
>  
>  
>  Just looking for a bit of help in using diffeomap as I seem to be 
> doing something wrong in converting the Talairach_SS_WMPM to the 
> native subject space. When I apply the Hmap from the LDDMM analysis to 
> the WMPM the WMPM is converted perfectly. When I then apply the 
> inverted AIR file I am running into a problem. The file does not seem 
> to convert it correctly. 
>  
>  I have searched through the forum and applied the approach suggested 
> in a couple of posts but I am still having the same issue. If anyone 
> has experience of this and could help me out it would be much appreciated.
>  
>  The atlas is 192*192*136 while my data is 256*256*55. When I apply 
> the Inverted air file the WMPM gets converted but seems to remain in 
> the original dimensions. For example, there are originally 136 slices 
> and the air_inverted file also has 136 slices but an image occurs in 
> only 55 of them. The image is also compressed to the bottom right of 
> the frame.
>  
>  Procedure
>  ·         Load Template
>  o   Talairach b0
>  ·         Load Sample
>  o   b0
>  o   FA
>  ·         Run AIR LINEAR
>  o   Ensure both b0 images active
>  o   Affine/Trilinear
>  o   Save .air file
>  o   Save converted files
>  ·         Run air invert_air_file
>  o   Choose saved air file
>  ·         Close Diffeomap
>   
>  ·         Open Template in Diffeomap
>  o   Open FA image as subject (2nd time use WMPM of Talairach)
>  o   Select Load Transformation Matrix
>  o   Choose inverted file air
>  o   Choose Trilinear or Nearest Neighbour
>  
>   If required I can send  the results I have gotten from the process. 
>  Thank you in advance,
>  Bill
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