Saad,
I tried running one probtrackx following your hints. The fdt_paths.nii.gz looks definitively better and now the seed_to_?.nii.gz makes a lot more sense!!!
Thank you sooooo much!!!!
Best
Amelia
Amelia Versace, MD
Loeffler Building
121 Meyran Avenue
Suite 202
Pittsburgh, PA 15213
Phone 412- 383-8202
Fax 412-383-8336
CONFIDENTIAL UPMC HEALTH SYSTEM INFORMATION Any unauthorized or improper disclosure, copying, distribution, or use of the contents of this email or attached documents is PROHIBITED. The information contained in this e-mail message is intended only for the personal and confidential use of the recipient(s) named above. If you have received this communication in error, please notify the sender IMMEDIATELY by e-mail and DELETE the original message.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Saad Jbabdi
Sent: Thursday, February 04, 2010 9:07 AM
To: [log in to unmask]
Subject: Re: [FSL] "empty" seed-classification map
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
|