Are you normalizing by total number of samples or waytotal?

 

Peace,

 

Matt.

 

 

Hi Andreas:

 

Thank you for all the explanation!

 

We will hold a meeting to discuss about which way of threshold is the best for our population, as you mentioned sometimes it is just a personal taste.

 

By the way, do you have some idea on the probability, which we could also get from the fslmaths. We found that the P (probability) in lower in the assistant tracts, e.g. SLF; and usually they are the results from bigger ROIs. If P is smaller than 0.2, that means the probability of the tract is very low? And could we still believe that the probabilistic tract is correct? In reality, how could we use the information of P? I found P is quite variable in across subjects.

 

Regards,

 

Yan

 
> Date: Mon, 30 Mar 2009 18:05:09 +0200
> From: [log in to unmask]
> Subject: [FSL] AW: [FSL] AW: [FSL] asymmetires
> To: [log in to unmask]
>
> Hi,
>
> >fslmaths fdt_paths.nii.gz –div waytotal – thr % fdt_paths_norm –odt float
> strictly spaking you would have to multiply by 100 (after -div waytotal) to use a percent threshold. Note, however, that the magnitude of peak probability in waytotal %, for example, may seem low and that you may want to retain even low probability voxels (i.e. apply a threshold much below 1%) to "clean up" your data. See Matt's previous posts.
> >how could you threshold fdt_paths normalized to the total number of samples? Is it based on the absolute pathway intensities?
> Same story: just replace the waytotal by the total number of samples send out (=number of samples send out from each voxels x number of voxels in yourt ROI). Again note that the waytotal is also a "total number" of samples, i.e. those which made their way from seed to target (that's why the name;).
> >found much less volume in the ipsilateral hemisphere with respect to the contralateral hemisphere
> Right, that is what you would expect.
> >if we use waytotal based threshold, the asymmetries are not so evident and in some tracts they are changed to be symmetrical
> Exactly. In a way you may think of it like atrophy studies normalize to brain size (if your skull is small your brain must be small as well but may still be "normal" for its size; the only difference here is that normally you don't measure the hemiskull - even though only half of the skull may be small;). So does the asymmetry you see >primarily< affect your tract of interest or can it be a secondary phenomenon? Hard to tell, isn't it? Then, if you have other evidence to support one or the other notion you may ask yourself if you need tractography at all to answer your particular question or if - like quite often - we end up in circulary reasoning;)
> >However, sometimes it is difficult to say which one is false-positive or false negative.
> ...and sometimes it remains impossible. Practising bad science you will pick whatever will meet your purpose. Being serious you think of it before you analyze your data and decide for one or the other. I.e. do you have evidence for every single case (not just in general!) that the tract must exist in the particular brain / hemisphere? Then you may want to enforce "trackablility" despite the thresholding and use the waytotal. In normals, you may want to retain variability despite thresholding and be better of using the total number of samples send out. In some regards, the thresholding itself is just a way to "clean up " your results.
> <book of Heidi and Tim
> See Timi's post.
> Cheers-
> Andreas

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