Many thanks for the response Steve.
After I have chosen less smoothing and higher value for cluster thresholding, I got much better results.
cheers,
Kosta
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----- Original Message ----
From: Steve Smith <[log in to unmask]>
To: [log in to unmask]
Sent: Sunday, January 25, 2009 1:16:30 PM
Subject: Re: [FSL] WM detected as GM in fslvbm
It is possible to get a difference in GM within regions that are on average (across subjects) more WM than GM, because they can still contain some "GM", particularly when you have applied smoothing to the data. I would overlay this on your mean GM map that the scripts generated to reassure yourself, but they may be ok.
Cheers.
On 24 Jan 2009, at 14:10, Kosta Markov wrote:
> Dear FSL users,
>
>
> I am trying to use FSL-VBM v1.1 on two groups of subjects (young vs old) to
> look at effects of ageing in GM. The VBM output revealed some strange results -
> highly significant clusters of voxels (showing decrease of GM with age)
> within white matter areas (attached snapshot). Do you have any idea what
> could possibly be the reason for these ambiguous results?
>
> Here are the steps I have done:
>
> - individual BET with varying -f and -c option to provide proper brain
> extraction
> - fslvbm_2_template -n
> - fslvbm_3_proc 0.2
> - randomise -i GM_mod_merg_s4 -o GM_mod_merg_s4 -GM_mask -d design.mat -t
> design.con -n 5000 -tfce(-c 3) -V
> - the design was created in the Glm wizard with two contrasts (A>B: 1 -1;
> B>A:-1 1)
> - the attached snapshot shows the GM_mod_merg_s4_tfce_corrp_tstats1
> (intensity threshold 0.999-1) overlaid on the standart MNI152_2mm
>
> Any suggestions are greatly appreciated.
>
> thanks,
> Kosta
>
> <p_value-0.001.jpg>
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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
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