Hi Reem,
this should not affect your results...
If it does, it might simply be in this way:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1010&L=FSL&P=R64206&I=-3&d=No+Match%3BMatch%3BMatches&m=32143
so this should be fine.
However, without seeing this template and your final results, I am not
sure what's causing this GM around the ventricles. Sometimes it can
also be a problem of partial volume effect with voxels between CSF and
white matter being "recognised" as grey matter. Again, this might not
cause any problem when it comes to your final results.
Keep me posted!
Cheers,
Gwenaelle
De: Reem Jan <[log in to unmask]>
Objet: Re: [FSL] VBM: GM_mask including non-GM tissue!
À: [log in to unmask]
Date: Jeudi 11 novembre 2010, 21h49
Hi Steve There was some non-brain tissue around the brain stem and I think that might have been due to 3 of my 37 subjects struc_brain images still incorporating non-brain tissue around that area, I have fixed that manually and re-ran fslvbm_2_template and fslvbm_3_proc. The template_GM image seems to cover some non-GM areas such as the ventricles. Is this something to worry about? I’m not sure how to get rid of that because it’s not a BET issue? Many thanks for your help.Reem From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Stephen Smith
Sent: Thursday, November 11, 2010 11:53 PM
To: [log in to unmask]
Subject: Re: [FSL] VBM: GM_mask including non-GM tissue! Hi - is this just a slight amount of result 'outside' of the brain, caused by the spatial smoothing?Cheers. On 8 Nov 2010, at 21:36, Reem Jan wrote:
Dear VBMers
I have run a full VBM analysis and am now looking at the outputs from
randomise. I noticed I get activations outside of the GM (and sometimes
outside of brain tissue).
I have checked the following images:
1. All the brain extracted structural images (which were extracted
using fslvbm_1_bet -N as my scans had some neck tissue). The _brain*
images look fine (only 1 image out of 37 has very little left over
non-brain tissue)
2. Template_GM - looks fine
3. GM_mask (overlayed on the template_GM) - the GM_mask includes
more out of brain and out of GM voxels.
So my question is, how does the GM_mask get created and how do you
optimize it or fix it so that it only includes GM?
Any suggestions would be greatly appreciated.
Kind regards
Reem
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Gwenaëlle Douaud, PhD
FMRIB Centre, University of Oxford
John Radcliffe Hospital, Headington OX3 9DU Oxford UK
Tel: +44 (0) 1865 222 523 Fax: +44 (0) 1865 222 717
www.fmrib.ox.ac.uk/~douaud
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