Confirm DTI-TK Normalization and TBSS Integration Steps

[Cristina Roman]

Hello, 

I am just starting to learn DTI-TK and would like to use it prior to running TBSS. Before doing this, however, I was hoping to get confirmation about the steps I am to follow. Here is what I have (questions in blue):  

1. Pre-process data using TORTOISE (motion correction, eddy current correction, etc.)

2. Confirm the diffusivity unit and ensure it is DTI-TK compatible, confirm there are no outliers, and make sure volumes share one common voxel space

3. Spatial Normalization using DTI-TK

    a. Create a txt file of all subject DTI volumes

    b. Bootstrap the initial template mean

    c. Affine alignment

    d. Deformable alignment with the final refined template estimate     from affine alignment

  **Group-specific template created from this stem, and data fitted (normalized) to the template**

4. Run a custom implementation of tbss_3_postreg, which replaces the general TBSS postreg step. 

** During this step, the template and DTI data is brought into a standard space. In this case, it will spatially normalized to 1mm^3, and an FA skeleton and 4-D FA map will be created** 

How is this different than what you do in the spatial normalization and template generation step (#3)? Is it that you are putting things in standard space here? 

5. Rename data to be compatible with TBSS

6. Create FA skeleton (How do you assign/check the FA threshold?)

7. Generate FA map of spatially normalized data

8. Put TBSS relevant files in mytbss folder

9. Run tbss_4_prestats

10. Run voxelwise stats on the skeletonized FA data. 

11. Repeat with MD, AD, and RD as necessary. 

Am I on the right path? Any input or clarifications would be GREATLY appreciated. 

Thank you, 

Cristina

[Hui Zhang]

Hi Cristina,

Have you seen the following tutorial?

http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.TBSS

Gary

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[Rowena]

Hi Gary,

Sorry to hijack this thread, but if I read correctly, basically to integrate FSL and DTI-TK, I would do the preprocessing steps in FSL (eddy current and motion correction), then follow the tutorial in the link you posted?

Just to be sure - I would not have to do the tensor-fitting step in FSL prior to feeding the preprocessed data into DTI-TK?

Thanks very much for the clarification in advance, especially for those new to DTI analyses.

Rowena

[Hui Zhang]

Hi Rowena,

In theory, any correctly implemented tensor fitting can be used to produce diffusion tensor volumes from diffusion-weighted volumes.  In practice, different software packages don't always produce results that are easily interoperable.  As a result, I had to write a whole tutorial to address this topic.  (I can't provide a direct link to the tutorial right now, as SourceForge, the host of the DTI-TK website, is broken at the moment.)

So you can use tools other than FSL but if you run into difficulties we may not always be able to help you out.

Gary

[Rowena]

Dear Gary,

Thanks for your reply. I have seen the TBSS integration tutorial.

I guess what I was trying to ask was: For the registration step in DTI-TK (http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.Registration), would "input DTI volumes" to be used in the normalization pipeline (bootstrapping step onwards) refer to DTI volumes that have only been motion-corrected, BET, etc up till the point before tensor fitting, or is this referring to the volumes that have been tensor fitted eg. in FSL?

Sorry if this is a question that seems a little obvious, but I was a little confused.

Thanks very much,
Rowena

[Hui Zhang]

Hi Rowena,

The volumes before tensor fitting are not DTI volumes; they are diffusion-weighted volumes.  I tried to explain this distinction here:

http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.Format

The DTI volumes are produced by tensor fitting.  They can be stored in a variety of ways and different software tools can choose any one of these ways to store the DTI volumes.  I explained how to convert between different DTI volume format here:

http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.Interoperability

Gary