Personally, I would keep the whole brain mask. If you are worried that tracts may enter non-brain regions such as CSF, you can use CSF as a stopping mask.
If you really want to use the "all-white" strategy, then you need to make sure that your seed masks (and target masks) are in the brain mask, and that they are connected to the white matter!
Cheers,
Saad.
On 4 Feb 2010, at 11:59, Versace, Amelia wrote:
> Hi Saad,
> actually that was done on purpose!! I read in the forum that this is a good strategy (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0903&L=FSL&P=R101079&D=0), so I wouldn't go back to the original one. In order to fit the "new" nodif_brain_mask (WM only) to my bedpostx folder, should I rerun bedpostx?? Is there an easiest/faster way??
> Thanks again for all of your help!
> Best -Amelia
>
> ________________________________________
> From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf Of Saad Jbabdi [[log in to unmask]]
> Sent: Thursday, February 04, 2010 5:34 AM
> To: [log in to unmask]
> Subject: Re: [FSL] "empty" seed-classification map
>
> Hi Amelia
> Your "nodif_brain_mask" is restricted to the white matter - was that on purpose? you must have changed this after you ran bedpostx since the mask that has been used for bedpostx covered the whole brain...
>
> When probtrackx internally transforms the seed masks onto diffusion space, most of the seed mask end up outside the brain mask, so no tracts are calculated.
>
> I suggest you calculate the nodif_brain_mask again (e.g.in the bedpostx directory, type: fslmaths mean_f1samples -bin nodif_brain_mask) and then re-run probtrackx.
>
> Cheers,
> Saad.
>
> On 3 Feb 2010, at 19:11, Versace, Amelia wrote:
>
> Done!!
> Here is the reference number: 903024
> Thanks a lot!!
> Amelia
>
--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
www.fmrib.ox.ac.uk/~saad
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