You must be logged in to post Login Register


Lost Your Password?
Search Forums:


 






Wildcard Usage:
*    matches any number of characters
%    matches exactly one character

Forum TrackVis Usage ROI problems

ROI problems
Page:   1  
UserPost

4:23 am
April 2, 2010


aurely1310

Member

posts 9
Print this Post
1

Hi,

 

I have antoher question and would like to have some help…

 

When I put a ROI on an image, principale fibers are shown. But no ramifications (feeding the whole brain) coming from this ROI are available.

(May be is there an option to activate ?) How can I see them?

 

Thanks,

Aurélie.

10:03 am
April 2, 2010


Ruopeng

Admin

posts 406
Print this Post
2

You need to either associated an existing track group to the ROI (by adding the ROI to its filter list), or create a new track group from the ROI. These demos may help:

http://trackvis.org/demo/?2

http://trackvis.org/demo/?3

Ruopeng

10:20 am
April 8, 2010


aurely1310

Member

posts 9
Print this Post
3

Dear Ruopeng,

 

Thank you for your answer…

but I already looked at the demo and did the same process.

I did a screenshot where the problem was visible : only the main directions (no ramifications) are drawn.

(I cannot insert the file because I can not put it on the web…how can I send it to you? Confused)

 

What can I solve the problem?

 

Regards,

Aurélie.

1:30 pm
April 9, 2010


Ruopeng

Admin

posts 406
Print this Post
4

I just changed the settings of the forum to allow uploading images. You can do that by clicking "Insert Image" button then "Browse".

Ruopeng

3:21 am
April 12, 2010


aurely1310

Member

posts 9
Print this Post
5

Thank you for the new settings.

I add a picture with my message where you can see that just the principal ramifications are shown.

How can I do to have ALL the fiber (more important degree of ramification) ?

Thank you!

 

2:20 pm
April 12, 2010


Ruopeng

Admin

posts 406
Print this Post
6

Sorry I'm still not quite sure what you're trying to look at. Is that picture of a fiber bundle from an ROI? Is there any other filters applied to it? What do you mean by "all the fibers"? All the fibers in the track file?

Ruopeng

3:37 am
April 13, 2010


aurely1310

Member

posts 9
Print this Post
7

This picture is a picture of a fiber bundle from a ROI, and there are no others filters applied to it.

The problem is not to have all the fibers in the track file, but all the fibers from a ROI. It seems (on the picture) that it's not the case. We just have the main direction. That's why I said "no ramifications"…

 

Do these explanations help you ? Confused

12:34 pm
April 14, 2010


Ruopeng

Admin

posts 406
Print this Post
8

If that's all you get from that ROI, then that's probably what you get out of that data. DTK/TrackVis uses deterministic tractography algorithm. There is only one way to go for each track. There is no branching, etc.

There're some adjustable parameters such as mask and angle threshold that may give you better result. But keep in mind DTI tractography is not a gold standard, nor going to reveal every known fibers/connections in the brain. 

Ruopeng

9:15 am
April 15, 2010


aurely1310

Member

posts 9
Print this Post
9

thank you for your answer.

 

How can I change the angle threshold and others parameters ?

The only things i can change seem to be the length threshold…

 

Thank you!

11:41 am
April 15, 2010


Ruopeng

Admin

posts 406
Print this Post
10

Oh, you will need to change them in Diffusion Toolkit when you do the tracking.

Ruopeng

3:09 am
April 19, 2010


aurely1310

Member

posts 9
Print this Post
11

Thank you, I'll try to do some changments on these parameters.

 

Regards,

Aurely1310
Page:   1