Hello Saad,
Thank you for your reply. I did look at the "vector lines" but those I generated them with matlab and those looked fine (I wrote it as a nifti volume and opened them up in fslview and they were ok). However, you are right: with make_dyadic_vectors, the generated vectors are indeed oriented S-I. What could be causing that? What is the FDT convention you were mentioning? Can I find any detail about it somewhere?
Thank you again for your help,
Giorgia
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From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Saad Jbabdi [[log in to unmask]]
Sent: Thursday, July 13, 2017 2:44 AM
To: [log in to unmask]
Subject: Re: [FSL] Problems running probtrackx
Hi Giorgia
You can check if your theta/phi representation is compatible with the FDT convention by using “make_dyadic_vectors” on the merged_* files. Once you run this command, load the resulting vectors onto fslview and check that the white matter orientations look correct on all views using *vector lines* visualisation mode (i.e. not just RGB).
Cheers,
Saad
> On 13 Jul 2017, at 06:50, Giorgia Grisot <[log in to unmask]> wrote:
>
> Hello FSL experts,
>
> I am trying to run probtrackx on indipendently generated samples (i.e. instead of using bedpost, I used my own code). I have calculated phi and th angles for each of my 50 samples and saved them in the required merged_* files. I have checked the angles of each samples by calculating the resulting vectors and they all look correct. However, when I try to run tractography on it with probtrackx (with simple default settings), even though I don't get any error per se (all the files are read correctly), streamlines are wrong and only travel superior to inferior. Streamlines behave as if all the samples where oriented on the S-I axis, even though when I plot them, as I previously mentioned, they look fine.
>
> I would really appreciate any suggestions on what could be going wrong or other things I could check. Also, 'd be happy to send you a sample of my data, if you'd like to take a look.
>
> Thank you in advance for your time,
>
> Giorgia Grisot
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