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Hi Davide,
We are looking into this issue. It might have to do with the way fslview displays vectors in neurological orientation..

In the mean time, the best thing for you to do is to change convention to radiological. I hope it is not a problem for you?
You can do it using both these two commands:

fslswapdim -z y z <volume> <volume>
fslorient -forceradiological <volume>

Cheers,
Saad.


On 4 Oct 2009, at 02:19, Davide Imperati wrote:

Hi Saad,
I'm sure I did not reoriented the images after bedpostx
I bedposted the image once again to be sure I did not update fsl inbetween and I'm still having this inconsistency.
The dyads are correct and probtrackx delivers those flipped tractograms.
Unfortunately at the moment I'm not able to double check the process on an other machine.
Can you try to reproduce this strange behaviour?

THanks.
Davide.


----- Original Message -----
From: Saad Jbabdi <[log in to unmask]>
Date: Saturday, October 3, 2009 18:03
Subject: Re: [FSL] bedpostx - probtrack inconsitency
To: [log in to unmask]

> Hi - 
> Is it possible that you may have changed the orientation info in your header (radiological to neurological) after you've ran bedpostx?
> (e.g. using fsl_orient etc.) - if you did that, then the sample fibre orientation, encoded as angles in spherical coordinates, will have the wrong orientation. 
>
> A quick fix is to replace phi by pi-phi as follows:
>
> fslmaths merged_phsamples -mul -1 -add 3.14159265 merged_phsamples
>
> But a safer thing to do is to rerun bedpostx..
>
> Cheers,
> Saad.
>
>
> On 3 Oct 2009, at 16:46, Davide Imperati wrote:
>
> Hello everyone,
> I found an inconsitency between bedpost dyads and probtrack tractograms. on linux ubuntu, fsl 4.1.4, fslview 3.1.2, fdt toolbox 2.0.
> The bedpost dyads seem to be consitent with neural anatomy in vivo and are consitent with the model used to generate the synthetic data.
> When I run probtrack (see below) on bedpostx data, the tractogram is not consistent with the dyads. The tract seems to follow a directions mirrored  on the x axis (see attachment).
> Thank you.
>
> Best.
> Davide
>
>
> --- command line generated by the ffdt graphical interface---
>
> mkdir -p /media/.../circle.bedpostX/fdt_24_5_5b
> /usr/share/fsl/bin/probtrackx --mode=simple --seedref=/media/.../circle.bedpostX/./nodif_brain_mask -o /media/.../circle.bedpostX/fdt_24_5_5b/fdt_24_5_5b -x /media/.../circle.bedpostX/fdt_24_5_5b/fdt_coordinates.txt  -l -c 0.2 -S 2000 --steplength=0.5 -P 5000 --forcedir --opd -s /media/.../circle.bedpostX/./merged -m /media/.../circle.bedpostX/./nodif_brain_mask  --dir=/media/.../circle.bedpostX/fdt_24_5_5b
>
> ---
>

>

> <probtrack_inconsistency_smaller.jpg>
>
>
--
> Saad Jbabdi
> University of Oxford, FMRIB Centre
>
> JR Hospital, Headington, OX3 9DU, UK
> +44 (0) 1865 222523  (fax 717)
>
>
>
>
>
>
>
>
>


--
Saad Jbabdi
University of Oxford, FMRIB Centre

JR Hospital, Headington, OX3 9DU, UK
+44 (0) 1865 222523  (fax 717)