Hi Gwenaelle and Andreas
Thank you, I've tried both ways and I don't get results surviving FDR, so I guess I don't have significant results after all :(
Thank you for your advice.
Have a great weekend
Cheers
Reem
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Gwenaëlle DOUAUD
Sent: Thursday, June 02, 2011 11:19 PM
To: [log in to unmask]
Subject: Re: [FSL] fsl VBM -clusters - FDR command question
Hi Reem,
I would actually advise you to use the GM_mask built in the FSL-VBM preprocessing, as this is what you'd also use in the recommended randomise VBM statistical analysis...
Cheers,
Gwenaelle
> Thank you Mark for clearing that up,
> so is it okay to use the GM mask or should I be generating a
> whole brain mask with fslmaths?
>
> Many thanks
> Reem
>
> On 2/06/2011, at 19:28, "Mark Jenkinson" <[log in to unmask]>
> wrote:
>
> > Hi Reem,
> >
> > The mask should be a mask of the non-zero probability
> voxels
> > (so typically the brain mask).
> >
> > A threshold of 0 means that nothing passes FDR.
> > It will hopefully change when you use the right mask.
> >
> > All the best,
> > Mark
> >
> >
> > On 2 Jun 2011, at 07:15, Reem Jan wrote:
> >
> >> Hi Steve, Gwenaelle and Hannah
> >>
> >> I’ve followed this thread and I had a similar
> question to Hannah which has been answered very well by
> Steve and Gwenaelle.
> >>
> >> As a consequence of this thread, I have applied
> FDR correction to my grot_vox_p_tstat images (after
> inverting them and obtaining the 1_minus_grot_vox_p_tstat
> images), and I had a simple question regarding the fdr
> command:
> >>
> >> Fdr –i 1_minus_grot_vox_p_tstat1 –m mask –q
> 0.05
> >>
> >> What kind of mask can we input here?
> >> I tried running the fdr command without a mask and
> got the output “Probability threshold is 0”. What does
> this mean? Will this change if include a mask in the
> command?
> >>
> >> Your advice on this is much appreciated.
> >>
> >> Kind regards
> >> Reem
--------------------------------------------------------------------
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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