[Mristudio-users] viewing automated tract details from LDMM

[XIN LI]

Elizabeth,

If you would like to load the fiber file into Landmarker, you have to save it as binary image or analyze image in DtiStudio. Other file formats don't work in Landmarker.

Landmarker only apply LDDMM matrix to isotropic images. But since you already got the updated target image, it means that the subject is an isotropic image. Are the size of the fiber image different from that of the subject image?


Xin





----- Original Message -----
From: Elizabeth Finger <Elizabeth.Finger at lhsc.on.ca>
Date: Wednesday, September 17, 2008 11:58 am
Subject: Re: [Mristudio-users] viewing automated tract details	from	LDMM
To: mristudio-users at mristudio.org


> 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
>  >  >   --------------------------------------------------------------------------------
>  >  >  This information is directed in confidence solely to the person 
> 
>  > named 
>  >  > above and may contain confidential and/or privileged material. 
> This 
>  > 
>  >  > information may not otherwise be distributed, copied or 
> disclosed. 
>  > If 
>  >  > you have received this e-mail in error, please notify the sender 
> 
>  >  > immediately via a return e-mail and destroy original message. 
> Thank 
>  > 
>  >  > you for your cooperation.
>  >  >  
>  >  >  _______________________________________________
>  >  >  Mristudio-users mailing list
>  >  >  Mristudio-users at mristudio.org
>  >  >   
>  >  _______________________________________________
>  >  Mristudio-users mailing list
>  >  Mristudio-users at mristudio.org
>  >  
>  >  
>  >   --------------------------------------------------------------------------------
>  >  This information is directed in confidence solely to the person 
> named 
>  > above and may contain confidential and/or privileged material. This 
> 
>  > information may not otherwise be distributed, copied or disclosed. 
> If 
>  > you have received this e-mail in error, please notify the sender 
>  > immediately via a return e-mail and destroy original message. Thank 
> 
>  > you for your cooperation.
>  >  
>  >  _______________________________________________
>  >  Mristudio-users mailing list
>  >  Mristudio-users at mristudio.org
>  >   
>  _______________________________________________
>  Mristudio-users mailing list
>  Mristudio-users at mristudio.org
>  
>  
>   --------------------------------------------------------------------------------
>  This information is directed in confidence solely to the person named 
> above and may contain confidential and/or privileged material. This 
> information may not otherwise be distributed, copied or disclosed. If 
> you have received this e-mail in error, please notify the sender 
> immediately via a return e-mail and destroy original message. Thank 
> you for your cooperation.
>  
>  _______________________________________________
>  Mristudio-users mailing list
>  Mristudio-users at mristudio.org
>