Hi Monica,
this is not so easy to answer and I think the method to choose depends
on your ROIs and research questions.
It might be ok to choose a single direction if you have a good
(anatomical) explanation why only this direction makes sense.
As you said, it is common practice to track in both directions. You
would not count every fibre track twice because you get different tracks
every time - you just get about twice the number of tracks.
This is an interesting publication about anatomical connectivity that
also addresses the question of normalization:
Eickhoff, S.B., Jbabdi, S., Caspers, S., Laird, A.R., Fox, P.T., Zilles,
K., Behrens, T.E.J., 2010. Anatomical and Functional Connectivity of
Cytoarchitectonic Areas within the Human Parietal Operculum. Journal of
Neuroscience 30, 6409–6421. doi:10.1523/JNEUROSCI.5664-09.2010
Cheers,
Jan
On 05/27/2014 04:11 AM, Monica G Chica wrote:
> Hi Jan, thank you very much for the explanation. But then, if I get
> different results depending on where I seed, how should I decide which
> one to use in my analysis? Would it be correct to select the option that
> gives better results visually and just ignore the other one?
>
> I read in other post that if one wants to do comparisons between
> population then should track in both directions (using A as seed and
> then A as target) and then add the results of the waytotal. But does it
> really make sense to add this numbers? Wouldnt it be counting twice
> every fibre? And in that case, if I want to see differences in the
> fdt_paths too, which one I select? or I average them? Because if I use
> the two waytotals I guess I have to use the two fat_paths, right?
>
> Also, is there a way to normalize the waytotal? because I'm having quite
> different values between subjects of the same population. Would be be
> correct to divide by the number of voxels in the seed?
>
> Thank you!!
>
>
> 2014-05-26 1:48 GMT-07:00 Jan Schreiber <[log in to unmask]
> <mailto:[log in to unmask]>>:
>
> Hi Monica,
>
> the results should look different. Let's assume you have a third
> region C and and a bifurcation, the configuration looks like this:
>
> A C
> | |
> \ /
> |
> B
>
> When you seed in A than (almost) all tracks will go to B.
> When you seed in B than a similar number of tracks might go to A and C.
> The results look different.
>
> Additionally, you are doing _probabilistic_ tractography. Hence, you
> will get slightly different results every time even if you always
> use A as seed and B as target.
>
> Hope that helps.
>
> Cheers,
> Jan
>
>
>
>
>
> On 05/26/2014 01:50 AM, Monica G Chica wrote:
>
> Hi FSL experts, I am doing tractography between two regions: A
> and B. When I use A as a seed and B as a target I get very
> different results compared to when I use B as a seed and A as a
> target. I thought tractography doesn't recognize de direction of
> the fibres so I was expecting to have similar results. Is it
> normal to get so different results? Does tractography recognizes
> then the directions of the fibres?
>
> Also, I would like to double check that I am using the correct
> command:
>
> probtrackx2 -x left_LGN -l --xfm=freesurfer2fa.mat
> --meshspace=freesurfer --seedref=freesurferdir/mri/__nifti/brain
> --stop=freesurferdir/label/__nifti/lh_V1 --opd -s
> $BEDPOST_DIR/merged -m $BEDPOST_DIR/nodif_brain_mask.__nii.gz
> --dir=L_LGN_2_V1 --waypoints=freesurferdir/__label/nifti/lh_V1
> --targetmasks=freesurferdir/__label/nifti/lh_V1 --os2t
>
> Also, I am tracking through the mayer's loop, I am using the
> default parameters of probtrackx for -c, -s etc. But just
> wondering if the mayer's loop needs any different parameters
> since it's special in the way it is a very curved angle and also
> goes through grey matter.
>
> Thanks!
>
>
>
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