Hi Matt,
I did!!! .. I mean, I was defining what WM is in my seed space. So, If I understand correctly you suggest to use as "stop mask" a cvs+cortices mask. Even if targets are 1mm-ribbons projected into the wm??
Thanks!!
Amelia
Amelia Versace, MD
Loeffler Building
121 Meyran Avenue
Suite 202
Pittsburgh, PA 15213
Phone 412- 383-8202
Fax 412-383-8336
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-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Matt Glasser
Sent: Thursday, February 04, 2010 12:18 PM
To: [log in to unmask]
Subject: Re: [FSL] "empty" seed-classification map
Yeah I have abandoned the white matter nodif_brain_mask "hack" described in
that thread for a stop mask now that stop masks stop paths when they enter
(rather than when they leave as they used to). You do have to be very
careful that everything lines up, and one of the issues with the previous
method was that even if everything was in alignment one could still end up
with differences between what was called white matter in your
nodif_brain_mask in diffusion space and in your seed space because of
interpolation differences.
I recommend you define what is white matter in your seed space, then do the
following: fslmaths <whitemattermaskfile> -sub 1 -mul -1
<inverseofwhitemattermaskfile> and use that as your stop mask.
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Versace, Amelia
Sent: Thursday, February 04, 2010 10:55 AM
To: [log in to unmask]
Subject: Re: [FSL] "empty" seed-classification map
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
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