Dear James -

Sorry for the delay.

In general our advice is this -

1) Comparing probabilities should be done with great care - there are  
really only a two or three of reasons why probabilities might be  
different.
i) - a diffuse reduction in FA along a whole pathway will add  
uncertainty and lower probabilities - This should be detectable by  
examining FA along the pathway, and will be much more interpretable  
in this fashion.
ii) A focal change in FA may cause a focal spread, which is likely to  
be detectable with probability, but not group FA comparisons (as this  
focal change is unlikely to align across subjects).
iii) A focal change in the orientation of diffusion across groups -  
this might be caused by changes in routes taken by pathways between  
the groups.

If you see a change in probabilities, it is therefore essential to  
perform many follow-up studies to confirm the exact mechanism causing  
a change in probability.


2) Using tractography to generate ROIS.
We have not had conceptual problems with this idea - It should be  
possible to generate consistent ROIs using probtrackx outputs, with  
which you can later measure the volume, mean FA etc. etc.

In order to do this you should be able to use a mixture of waypoint  
masks, and termination masks to generate consistent ROIs. We have  
found that this works very well.
In order to compute the volume, we would usually play with these  
different masks as much to isolate the relevant pathway as well as we  
can. We would then threshold at a low level to remove the noise, and  
binarise.
We have found that the thresholding technique that is most consistent  
across subjects is to threshold using a percentage of the total  
number of pathways that made it from seedmask to waypoints. This  
number is stored in waytotal - however, if you have been following  
recent emails, you will know that the current version of probtrackx  
has a slight bug in the computation of waytotal. However, the number  
you get out will still be approximately proportional to the right  
number, so it should still be fine to threshold at a consistent  
percentage of this number.

I will try to answer some of your more specific Qs below.


> My thesis advisor and I are wondering if it is even valid to  
> compare mean
> FA, MD, and Volume when using: 2 roi's, an exclusion mask, and  
> probability
> tracking. If one subject has a many fibers connecting the two roi's  
> while
> another subject has many that do not connect and only a few that  
> do, then
> the probabilities will be weighted very differently.


You are right that you have to be able to track the pathway robustly  
in each subject.
If you cannot, then it is a bit of a non-starter. If you can,  
however, then, if you threshold as described above, there is no  
reason I can see that will make you biased towards subjects where the  
pathway is easier to track, as this will also be visible in the  
number in waytotal .


> Are these probabilities
> subjective and not comparable. Does this make comparisons between  
> groups
> when using 2 roi's not valid?

I think they are comparable - see above.


> How does an exclusion mask effect probability
> when a tract hits the exclusion is it removed from the probability  
> calculation?
>


An exclusion mask will not count any streamline that passes through  
it. A termination mask will count it and then stop it.

> I am still wondering about the questions below(from july 7th) as well.
>
> Perhaps, my question should be... what is the best way to evaluate  
> group
> differences in volume, FA (TBSS I'm guessing), and MD on a specific  
> tract?
> What is probabilistic tractography best used for? Can I use it for  
> group
> comparisons when trying to connect 2 regions of interest?
>


  TBSS and tractography-based analysis are complementary. We find  
that it is very useful to do both - they are sensitive to different  
things.

see above for discussion of 2 mask tractography analysis - we, and  
many others, find that this is a very sensitive way to define ROIs  
for further analysis.


> Any enlightenment on this would be awesome.
>
> Thanks,
>
> _J Sheehan
>
> On Mon, 7 Jul 2008 03:39:45 +0100, James Sheehan  
> <[log in to unmask]> wrote:
>
>> Hey all,
>>
>> just a few quick questions.
>>
>> 1. After running a few probtrackX with 2 roi masks on different  
>> subjects. I
>> am wondering what the intensities mean. I have a few tracts which  
>> are 1000+
>> max and some which are as low as 1 max. With 2 masks are these  
>> numbers more
>> subjective? What concerns should I have about the tracts with max
>> intensities of 1?

As above, if you threshold based on a % of the waytotal, this effect  
will be removed except in extreme cases.
You do have to be able to track the pathway robustly though, so if  
you have a max of 1, you are always in trouble.
I would think you want a max of greater than 100 before you can  
realistically be confident.


>>
>> 2. Is the Volume calculation dependent on the probability of voxel  
>> to the
> tract?

No, if you follow the instructions above.

>>
>> 3. How is probability calculated with two masks, is it dependent  
>> on the roi
>> and seed points, or on the number of total tracts found to the  
>> number that
>> reach the 2nd roi, or something completely different?
>>


Total number of pathways that pass through a voxel and pass through  
waypoints, and do not pass through exclusion ...

>> Thanks so much for any light that you can shed!!
>>

Hope this helps - sorry (everyone) that I am slow at the moment -  
lots on.


Cheers

T



>> -J
>> ===================================================================== 
>> ===
>