[Mristudio-users] viewing automated tract details from LDMM

[susumu]

Hi Elizabeth,

Landmarker is a software program to normalize images to a template space. If
you are interested in normalizing tractography results, the only way is to
convert the tracking results (streamline information for each tract) to a
binary "images", in which pixels that contain the streamlines are 1 and all
the other pixels are 0. 

The Landmarker has two image normalization tools. One is AIR that can do
linear and low-order non-linear transformation. For a high-order
transformation, you need to use LDDMM.

Either way, you first have to do AIR-based normalization as initialization.
This will not only bring the subject brain shape closer to the atlas, it
also makes the matrix and pixel dimensions identical to those of the atlas.
For example, if you choose our template (JHU or ICBM), they are 181x217x181
(1x1x1mm). Then the images are ready for LDDMM. If LDDMM sees the dimensions
of the atlas and the subject data are different, it won't run.

Hope this will help. We are currently working on more detailed documents
about how to use LDDMM.

Susumu

-----Original Message-----
From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Elizabeth Finger
Sent: Wednesday, September 17, 2008 11:58 AM
To: mristudio-users at mristudio.org
Subject: Re: [Mristudio-users] viewing automated tract details from LDMM

Thanks Xin-

I have completed fiber tracking and saved the file with all fibers in DTI
studio.  When I try to load this file into Landmarker, no matter the image
parameters or Image data format I enter, I cannot pull up the correct image.
If I draw an ROI in fiber tracking and save this in binary format, I can
open up the fiber file in Landmarker, however when I try to apply the K-Map
using the button using the Load Transformation Matrix button, and then the
LDDMM matrix option, I receive an error message that the load images must be
isotropic images.  Perhaps I have misunderstood what you mean by fiber file?

Thank you,
Elizabeth

>>> XIN LI <xli16 at jhmi.edu> 09/17/08 11:13 AM >>>
Elizabeth,

Please also apply the Kimap to the fiber file to get the updated fiber file.
Then load the updated target image into ROIEditor and load the updated fiber
file as a raw ROI data file. In that way, you can get what you want.


Xin




----- Original Message -----
From: Elizabeth Finger <Elizabeth.Finger at lhsc.on.ca>
Date: Tuesday, September 16, 2008 3:45 pm
Subject: Re: [Mristudio-users] viewing automated tract details from	LDMM
To: mristudio-users at mristudio.org


> Thank you Xin-
>  
>  That has seemingly worked so far. Can you tell me after the new 
> subject image is updated (it shows up as Updated_Target.img in 
> Landmarker, how I then can visualize the automated tracts which have 
> been segmented, and how to find the # fibers and FA values for those
tracts?
>  
>  Elizabeth
>  
>  >>> XIN LI <xli16 at jhmi.edu> 09/16/08 3:21 PM >>>
>  Elizabeth,
>  
>  There are two image files in the LDDMM processing result, "Template" 
> and "Target". Please load them to Landmarker, "Template" as a template 
> and "Target" as a subject. Please click the button "Load 
> Transformation Matrix" in the subject window, select the radio box 
> "LDDMM Matrix (VTK Format)" and load the file "Kimap.vtk" that is in 
> the LDDMM processing result. Landmarker will show you a new subject 
> image updated based on the LDDMM matrix. 
>  
>  
>  Xin
>  
>  
>  
>  ----- Original Message -----
>  From: Elizabeth Finger <Elizabeth.Finger at lhsc.on.ca>
>  Date: Tuesday, September 16, 2008 2:48 pm
>  Subject: [Mristudio-users] viewing automated tract details from LDMM
>  To: mristudio-users at mristudio.org
>  
>  
>  > Hello-
>  >  
>  >  Are there any step- by step instructions available after 
> retrieving 
>  > results from the LDMM remote processing?  I was able to retrieve my 
> 
>  > results, but it is not clear to me which templates and files should 
> be 
>  > loaded next into Landmarker and how I can view the automated white 
> 
>  > matter tracts and associated stastistics?
>  >  
>  >  Thank you,
>  >  Elizabeth Finger
>  >
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