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Hi Lena,

there is no spatial path information in the seed_to_target images. You need the fdt_paths.
 
There have been many posts on deriving the FA from a tract. In short, you need to make sure that the same tract is extracted in each subject using as much anatomical information as possible. If you cannot achieve that in native space, you can look for the overlapping regions across subjects in a common space. 

Some indicative discussions that you can go through in more detail:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0803&L=FSL&D=0&1=FSL&9=A&J=on&K=2&d=No+Match%3BMatch%3BMatches&z=4&P=69759
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0807&L=FSL&D=0&1=FSL&9=A&J=on&K=1&d=No+Match%3BMatch%3BMatches&z=4&P=118951
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1001&L=FSL&D=0&1=FSL&9=A&I=-3&J=on&d=No+Match%3BMatch%3BMatches&z=4&P=338787

Cheers,
Stam



On 26 Jan 2011, at 12:04, Lena Palaniyappan wrote:

Sorry for hijacking this, but Stam can you explain how to derive FA and MD etc from an fdt_path_seed_to_target?

Many thanks
Lena


On 26/01/2011 11:55, "Stamatios Sotiropoulos" <[log in to unmask]">[log in to unmask]> wrote:

Dear Robert,

you can normalize the path distributions using the waytotal number, i.e. the number of "valid" streamlines in each case. Regarding comparing between subjects, it would be more interpretable to compare DTI indices along tracts, such as the FA or the MD, rather than comparing the connection probabilities. The latter reflect the uncertainty on the principal connection between regions, which can be driven by several different factors.

Cheers,
Stam


On 25 Jan 2011, at 18:41, Robert Schulz wrote:

> dear fslers,
>
> i just performed a lot of intracortical tracking between different specific individual (subject's) cortical masks, 2 way, so one way in this, one way the other direction, averaging the waytotals. so what i get are extensively differing values within one subject and even more comparing different subjects. is there a way of comparing the different averaged connections between 2 hemispheres and between subjects (controls and stroke patients). but i can't figure out a method of normalizing the data at all.
>
> is there any approach? i am looking for your comments and suggestions.
>
> regards, robert
>


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