Hi,
you would simply divide the fdt_paths by the waytotal using fslmaths.
Cheers,
Andreas
Am 05.03.14 12:35 schrieb "Irina" unter <[log in to unmask]>:
>Hi Stam,
>
>I am planning to do fibertracking in 2 groups (patients and controls). I
>have a very similar question as Jeff, is it so that I can not use the
>"waytotal" number right away to assess connectivity within certain
>pathway (e.g., between the seed A and target B)?
>
>You wrote that "the ³waytotal² is just a normalisation factor and its
>absolute value mostly reflects your choices for different algorithmic
>options in probtrackx. Depending on how you run tractography this can be
>very similar across subjects for a given seed or quite different".
>
>I traced connections from the seeds of exactly the same volume in each
>subjects (to equalize the initial number of samples) and always got very
>different numbers. The definition of the "waytotal" on the FSL web page
>was very clear ("waytotal" - a text file containing a single number
>corresponding to the total number of generated tracts that have not been
>rejected by inclusion/exclusion mask criteria". So, nothing made me
>hesitating whether I was doing this correctly or not. I was sure that
>"waytotal" gives me the number of tracts going from A to B but not C (an
>exclusion mask). Now I feel confused...
>
>You suggested "to normalise the fdt_paths of every subject with the
>respective waytotal to get directly path probabilities (now normalised
>from 0 to 1)". Would you please be so kind as to explain in more details
>how to do it?
>
>I would really appreciate your help,
>I.
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