[Mristudio-users] Color schemes for DTI imaging and fibers?

[wukeqin]

Dear all, I need to know more about the coloring schemes provided in DTI Studio. Surely, we can get the fibers' geometry out and render them in any way that we like. I just wonder what is the default color setting currently. It seems to me that the DTI fiber part assigns random color to each fibers or ask users to manually assign selected fibers a color.   I am sure about the  the volume rendering part (in DTI mapping). Does it use rainbow coloring (maping value of high to low to red -  green - blue specturm) to color FA value? The color-coded orientation maps mentioned in the user manner maps colors red to left-right, green to anterior-posterior, and blue to superior-inferior directions (based on Sinisa Pajevic and Carlo Pierpaoli's 1999 "Color Schemes to Represent the Orientation of Anisotropic Tissues From Diffusion Tensor Data: Application to White Matter Fiber Tract Mapping in the Human Brain" paper). Am I right about this? Do I miss anything? Thanks, Keqin WuVis Lab, UMBC
 From: alb.net at gmail.com
Date: Sun, 24 Mar 2013 17:36:32 -0400
To: mristudio-users at mristudio.org
Subject: Re: [Mristudio-users] Flags file mismatch when reloaded

Dear all,
This is a follow up of my previous email. After checking several factors, it seems overall the "flags" file works, but the realignment has shifted the slices. Therefore, after realignment good slices (previously bad) are tagged as bad slices. An example of what happens can be found here:

http://img69.imageshack.us/img69/4112/artifactsandrealigment.jpg
In order to understand better the issue, realignment parameters can tell something. For example the volume on the figure has these realignment values:


  -- AIR-Matrix for: Scan10.REC - 9 --          Path-Name: C:\Scan10.REC -- AIR 4x4 matrix   1.0000    0.0025    0.0022   -0.5762  -0.0025    1.0000    0.0006   -0.5945

  -0.0022   -0.0006    1.0000    0.9537   0.0000    0.0000    0.0000    1.0000
Which of these paramters is rotation and which is shift? Are the values in millimeters or in voxels?



Your comments on the issue are much appreciated.

Dorian


2013/3/22 Dorian P. <alb.net at gmail.com>



Hi everybody,
I am using the "flags" file to label bad volumes in 3 loaded datasets. After labeling bad volumes, I save the dataset in raw format (all 3 datasets become a single .dat file). I load back the raw format, which now is only 1 long line of volumes, and the flagged volumes do not correspond. As a result, corrupted slices are still visible in FA maps, compromising the study.




I had the impression that the "flags" file can be reloaded on the same dataset, even when saved as raw, but now I am confused. Can you please explain how does a flags work when loaded with a concatenated long dataset? I can send you the par/rec files and the .dat file if necessary.




Thank you and enjoy the weekend.
DorianThomas Jefferson University



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