Hi Gwenaëlle,
You are right!! thank you very much for the hint.
Kindly I have one more question:
In the guide http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLVBM/UserGuide
Under the title "D - Processing the native GM images: fslvbm_3_proc"
It was mentioned the following:
"These tstats maps should help you decide which smoothing is the most relevant to feed into a full run of randomise, and which threshold to use for the cluster-based thresholding (option -c in the randomise command); however, in general we would recommend using the TFCE option (-T) instead of the cluster-based thresholding."
Please what is the meaning of this? How can these tsytats maps help me decide which smoothing must be used?
Thank you very much for clarifying this
Jon
Hi Jon,
I suspect that your first contrast is something like 1 0, and not 1 -1 (or -1 1) which are the only two contrasts you should run if you indeed want to compare both populations. If this is not the case, then please send us your design.mat and design.con.
Cheers,
Gwenaëlle
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Gwenaëlle Douaud, PhD
Associate Professor & MRC Career Development Fellow
FMRIB Centre, University of Oxford
John Radcliffe Hospital, Headington
OX3 9DU Oxford UK
Switchboard: +44 (0) 1865 222 493
Fax: +44 (0) 1865 222 717
www.fmrib.ox.ac.uk/team/principal-investigators/gwenaelle-douaud
www.fmrib.ox.ac.uk/research/translational-image-analysis-group
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De : Jon Anderson <[log in to unmask]>
À : [log in to unmask]
Envoyé le : Lundi 1 août 2016 13h21
Objet : [FSL] vbm -statistical map
Dear experts,
I ran vbm analysis between two groups ( 10 patients and 10 controls ). I followed the same steps mentioned in the guide http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLVBM/UserGuide
Finally I ran randomise as follow:
randomise -i GM_mod_merg_s3 -m GM_mask -o fslvbm -d design.mat -t design.con -T -n 5000
The final statistical map of interest (attached) showing that the whole mask is significant ?!
Please what I am doing wrong here?
Thank you for your help
Jon
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