Thanks, I was missing the equal sign Stefano
-----Original Message-----
From: Gwenaëlle DOUAUD [mailto:[log in to unmask]]
Sent: Thursday, March 27, 2008 7:53 PM
To: [log in to unmask]
Subject: [FSL] RE : Re: [FSL] mask usage and duration of calculations in randomise for TBSS
Hi,
you should type:
randomise -i all_FA_skeletonised -o tbss_FA -d
design.mat -t design.con -m ALIC_mask -n 500 -T
--tfce_H=1 --tfce_E=1 --tfce_C=26 -V
Cheers,
Gwenaëlle
--- "Marenco, Stefano (NIH/NIMH) [E]"
<[log in to unmask]> a écrit :
> Sorry to bug the whole list again, but here is the
> command I used. Are
> the tfce options specified correctly?
>
> randomise -i all_FA_skeletonised -o tbss_FA -d
> design.mat -t design.com
> -m ALIC_mask -n 500 -T 1 1 26
>
> The randomise help shows --tfce_H --tfce_E --tfce_C,
> but when I try to
> type these characters in the command I get errors...
>
>
> Stefano
>
> -----Original Message-----
> From: Steve Smith [mailto:[log in to unmask]]
> Sent: Thursday, March 27, 2008 11:58 AM
> To: [log in to unmask]
> Subject: Re: [FSL] mask usage and duration of
> calculations in randomise
> for TBSS
>
> Yes - for 3D data, H=2, E=0.5 has been found to be
> optimal (see the
> techrep announced this morning).
>
> However, in 2D (e.g. TBSS) this is different. We
> have not finished
> quantiatively optimising this yet, but it seems
> likely that E=1, H=1
> is good.
>
> The units of E are voxel count (volume) and H is in
> the units of the
> input data intensity.
>
>
>
>
> On 27 Mar 2008, at 15:45, Marenco, Stefano
> (NIH/NIMH) [E] wrote:
> > The website says E=0.5 (is this voxels, mm or
> what?)
> > And H=2 (I assume the height of the t statistic I
> am using),
> > Why this discrepancy? Have you found out something
> empirically that
> > was
> > not obvious when the website was created? Or are
> these parameters
> > better
> > suited for TBSS skeletons? Stefano
> >
> > -----Original Message-----
> > From: Steve Smith [mailto:[log in to unmask]]
> > Sent: Thursday, March 27, 2008 4:41 AM
> > To: [log in to unmask]
> > Subject: Re: [FSL] mask usage and duration of
> calculations in
> > randomise
> > for TBSS
> >
> > Hi - depending on what options you used for the
> template specification
> > in TBSS this is not necessarily surprising. If you
> used the "find the
> > most typical subject" then this template is only
> affine-registered
> > into MNI space and so will not exactly correspond
> to all labels in all
> > the FSL atlases. Even if you register directly to
> the FMRIB58_FA,
> > exact matching is not guaranteed as the atlases
> are defined with
> > different templates, different registration
> programs etc - so will be
> > close but not necessarily exact.
> >
> > Your approach for resolving this is indeed the
> most obvious sensible
> > thing to do - e.g. dilate the atlas mask of
> interest sufficiently to
> > overlap your skeleton. Yes, dependingon how you
> then extract
> > information from the new mask, it probably makes
> sense to AND the
> > dilated mask with your mean_FA_skeleton_mask.
> >
> > Yes, cluster-based thresholding inside randomise
> is much slower than
> > voxel-based, but is also more sensitive to
> extended regions of signal.
> > You might also try TFCE (E=1 H=1, nperm=500 to
> start with) instead of
> > cluster-based.
> >
> > Variance smoothing does probably slow things down
> even more, though I
> > don't have a feel for by how much. It seems that
> if your Nsubjects>~15
> > you may not see much (if any) benefit from
> variance smoothing.
> >
> > Cheers.
> >
> >
> > On 26 Mar 2008, at 20:30, Marenco, Stefano
> (NIH/NIMH) [E] wrote:
> >> I am trying to use a mask for the ant limb of the
> internal capsule
> >> after running TBSS. I am using randomise for my
> stats.
> >> One thing I noticed is that the
> AnteriorLimbInternalCapsule mask
> >> available in FSL does not cover fully the ant
> limb of the skeleton
> >> (obtained with MNI152) in the lower portions of
> the structure. I was
> >> perplexed by this discrepancy, I don't quite
> understand how this
> >> arises. I addressed this by a modal dilation of
> the mask with
> >> fslmaths.
> >>
> >> One question is the following: to take full
> advantage of the mask,
> >> do I have to do an AND operation between this
> mask (that exceeds the
> >> boundaries of the skeleton) and the skeleton
> itself, and obtain a
> >> more restricted mask?
> >>
> >> I noticed that when running randomise the
> duration of the
> >> computations increases tremendously when a
> cluster correction is
> >> requested of the program. However, in the same
> analysis I also set
> >> the variance smoothing to 6. Does variance
> smoothing contribute to
> >> the duration of calculations? And is the size of
> the variance
> >> smoothing kernel related to the extra time it
> takes to do the
> >> analysis?
> >>
> >> Does tfce take even more time than simple cluster
> extent?
> >>
> >> Stefano Marenco, MD
> >> NIMH/GCAP
> >> Building 10, room 4S235
> >> 10 Center Drive
> >> Bethesda, MD 20892
> >> tel 301 435-8964
> >> fax 301 480-7795
> >> email: [log in to unmask]
> >>
> >
> >
> >
>
------------------------------------------------------------------------
> > ---
> > 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
> >
>
------------------------------------------------------------------------
> > ---
> >
>
>
>
------------------------------------------------------------------------
> ---
> 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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