Hi Kasia,
> Hi Gwenaëlle,
> I'm sorry but I'm a novice and I don't really get
> everything of what you did.
No worries...
> I'll try to translate it the way I understand it.
> First you did a classification of the seed voxels twice,
> once with association target and exclusion masks, and once
> with projection target and exclusion masks.
> Then you took a command:
> fslstats seed_to _projection_fib -m -k (seed_mask)
> and the same for seed_to_association_fib
> is that correct?
Yes and no, I did the classification for association and projection indeed, but twice for *each*, once using an initialisation with the first fibre orientation, a second time using an initialisation with the first fibre orientation. It is equivalent to using *once* the option of --randfib which samples randomly amongst the fibre orientations for the initialisation of the tractography.
> you are saying that using -M produced more less the same
> results, but I do have very different values:
> fslstats seeds_to_proj_target_mask1.nii.gz -M -m -k
> /home/jednorog/final_tbss/tbss/stats/atlas/crossing_fib.nii.gz
>
> 3041.000000 0.082121
...using -M vs using -m -k, so in your case:
fslstats seeds_to_proj_target_mask1.nii.gz -m -k /home/jednorog/final_tbss/tbss/stats/atlas/crossing_fib.nii.gz
vs
fslstats seeds_to_proj_target_mask1.nii.gz -M
Try typing the help of the fslstats command to see how this works...
> > As I performed the tractography using both fibre
> orientations crossing in my seed region as an
> initialisation, I then took the mean over the two
> tractography results > (so if you want, seed_to_target_f1
> and seed_to_target_f2).
>
> I don't get it. What was the mean for? When did use it?
See above...
One more important point: I did the tractography from the 3D (as opposed to skeletonised) increase of FA, so this was in the right "standard-space" for each subject. However, if you run the tractography from TBSS results, you *must* project the results back either in the "standard-space" for each subject (option 1 of tbss_deproject and giving the warpfield and inverted warpfield to probtrackx) or in the native spacee for each subject (option 2 of tbss_deproject).
Hope this helps,
Gwenaelle
> --------------------------------------------------------------------
>
> Gwenaëlle Douaud, PhD
>
> FMRIB Centre, University of Oxford
> John Radcliffe Hospital, Headington OX3 9DU
> Oxford UK
>
> Tel: +44 (0) 1865 222 523 Fax: +44 (0) 1865 222 717
>
> www.fmrib.ox.ac.uk/~douaud
>
> --------------------------------------------------------------------
>
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