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
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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, 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
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