Thanks Stam! I've just started using the classification targets mode and
proj_thresh and they look promising. I tried your first suggestion, using
fdt_paths, but my probtrackx runs don't create this file. I have all other
expected output files, just not this one.
I use only command-line version of probtrackx2, not the gui - could
this be why I don't get a fdt_paths file?
Thank you,
Jeff
> Hi Jeff
>
> The numbers you are after are probably the ones contained in fdt_paths.
> The “waytotal” 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. It makes more sense
> to normalise the fdt_paths of every subject with the respective waytotal
> to get directly path probabilities (now normalised from 0 to 1).
>
> Another way to compare connectivity for given tracts is to use
> classification targets. Have a look at the online documentation and
> proj_thresh. Seed_to_target results are more easily comparable across
> subjects rather than fdt_paths, because they have some anatomical priors
> on. These values can be further transformed to proportions (using
> proj_thresh) that further reduces undesired variability across subjects
> (e.g. due to noise, partial volume effects).
>
> Cheers
> Stam
>
>
>
>
>
> On 11 Feb 2014, at 21:01, Jeff Waugh <[log in to unmask]> wrote:
>
>> Hello experts,
>> I am interested in assessing the absolute number of tracts generated
>> from a given seed ROI, and comparing that number between my patient and
>> control groups. Why? I want to know whether my tractography results
>> represent an anatomically-isolated change in tract number, or merely
>> the area of largest change in tract number. Probtrackx generates a file
>> that might be used in this manner, the waytotal. From the FSL page for
>> probtrackx: "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."
>>
>> Have any of you tried to use the waytotal in this manner?
>>
>> One interesting/confounding thing I've found so far: when I correct the
>> waytotal number by the volume of the native-space ROI used to seed
>> probtrackx, all subjects correct to almost exactly the same number (625
>> +/- 0.1). This would lead me to believe that the total number of tracts
>> generated by a voxel is always the same, regardless of subject
>> characteristics. Is this right? I have done the same waytotal and ROI
>> correction for over 40 regions and always come up with this same number,
>> 625.
>>
>> Thank you for any insight you can provide.
>>
>> - Jeff
>>
>>
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