 |
 |
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
__________ Information from ESET NOD32 Antivirus, version of virus
signature database 5602 (20101108) __________
The message was checked by ESET NOD32 Antivirus.
http://www.eset.com
---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
---------------------------------------------------------------------------
__________ Information from ESET NOD32 Antivirus, version of virus signature database 5612 (20101111) __________
The message was checked by ESET NOD32 Antivirus.
http://www.eset.com