Hi Katharina
> Since we created our own atlas (grey matter), we want to apply it on our data now. The first problem we are running into is the registration of the atlas to the DTI data. The FLIRT nearest neighbour interpolation gives us non-natural numbers and therefore creates too many regions. Do you have any tipps on that?
I am assuming your atlas consists of a parcellation of the grey matter into regions and the different regions are encoded with different numbers in a NIFTI file? You can use fslmaths to separate the different subregions and FLIRT them separately?
Note also that probtrackx does not require that the seed regions be diffusion space. If you provide probtrackx with a transformation between your atlas and the diffusion data, the tractography will run in diffusion space and the results will be saved for you in the atlas space.
> The second problem I have is with probtrackX. For one atlas region I get a nice looking fdt_path and for other regions I get a NIFTI only containing zeros even though both atlas regions are very close to each other and definitely inside the brain image. For the multiple mask option I do not get any non Zero-values either even though the voxel size and the size of the picture is the same as in the single mask that works. I was wondering if there is an explanation for that.
It is difficult for me to help on this without knowing more details of what exactly your are doing. A copy-paste of the command would help.
Cheers
Saad
> I would be very thankful if someone could help me.
>
> Regards
> Katharina
>
>
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