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Forum Diffusion Toolkit Usage DIffusion tool kit

DIffusion tool kit
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3:25 pm
January 11, 2012


alim

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Hello, 

I am new to diffusion toolkit. I've been using fsl for a while now.

I understand that the toolkit requires that all bo of a particular dti data set to be the first volumes. does that mean that when i upload my dicom data to the reconstruction softweare it automatically arranges them that way, or is that a parameter that i should myself arrange?

second, is there a way i can use a data set (.nii) from fsl to track using the tool kit? what would be my input?

 

third, the tracks i get seem to be contaminated by skull tissue, is that normal?

 

thank you

3:51 pm
January 17, 2012


Ruopeng

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Hi,

No, the software will not automatically arrange your volumes. It will simply repack them from the dicoms to a 4D nifti volume (by default), keeping its original order. With the latest version, it is not required b0 must be the first volumes. You can simply put 0, 0, 0, in your gradient table so that the software will know where to extract b0's. Please refer to this post: http://trackvis.org/blog/2010/…..ent-table/.

Yes, you can use any data set you want for tracking, as long as they fits the required format. See here: http://trackvis.org/dtk/?subsect=format.

It is normal that you see skull in the tracks. You just need a better mask, or simply ignore it.

Ruopeng

2:53 pm
January 18, 2012


alim

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Thank you.

may you please recommend a link that shows what and how complex are the statistics possible with the software.

thank you

 

3:43 pm
January 18, 2012


Ruopeng

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Post edited 8:44 pm – January 18, 2012 by Ruopeng

Quantification is one of the challenges for deterministic tractogrpahy. One common approach is to use fiber count and/or mean scalar values (for example, FA values) for statistical comparision.

Ruopeng

4:23 pm
January 18, 2012


alim

Member

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Does Track vis or diffusion toolkit perform any sort of statistics?

can you average seveal maps or data points?

thank you

12:19 pm
January 19, 2012


Ruopeng

Admin

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TrackVis can provide some scalar statistics for trackgroups and ROIs. Yes, you can average multiple data repeats in DTK, but you need to prepare the data in the right order and also set the settings correctly in DTK. (Click "more options" button).

Ruopeng
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