Hi Matt,
it seems that you have not demeaned your ev in your
stats.mat. You should do so and run exactly the same
command you've used without forgetting the -D option.
Cheers,
Gwenaelle
--- Matt Glasser <[log in to unmask]> a écrit :
> Tom and others,
>
>
>
> I am helping Bhargav with this project. We tried
> using the -D option,
> however now all of our t statistics are very small
> (between -1 and 1, with
> most very close to zero). This doesn't make sense,
> however, as we would
> expect at least some voxels to show t statistics
> greater than 1, just by
> chance. Our randomize commandline, our design
> matrix and our contrast file
> follow this message. We have verified that our 4D
> FA skeleton file and mean
> skeleton mask files are okay. Does anyone know why
> we are getting such low
> t values? Would it be possible to get r values
> instead using something
> other than randomise?
>
>
>
> Thanks,
>
>
>
> Matt.
>
>
>
> randomise commandline:
>
> randomise -i all_FA_skeletonised -o tbss -m
> mean_FA_skeleton_mask -d
> stats.mat -t stats.con -n 5000 -c 3 -D
>
>
>
> stats.mat:
>
>
>
> /NumWaves 1
>
> /NumPoints 10
>
> /PPheights 7.800000e+02
>
>
>
> /Matrix
>
> 6.700000e+02
>
> 5.400000e+02
>
> 5.300000e+02
>
> 6.000000e+02
>
> 5.800000e+02
>
> 7.800000e+02
>
> 7.500000e+02
>
> 6.100000e+02
>
> 7.000000e+02
>
> 7.200000e+02
>
>
>
> stats.con:
>
>
>
> /ContrastName1 Positive
>
> /ContrastName2 Negative
>
> /NumWaves 1
>
> /NumContrasts 2
>
> /PPheights 7.800000e+02
> 7.800000e+02
>
> /RequiredEffect 3.726 3.726
>
>
>
> /Matrix
>
> 1.000000e+00
>
> -1.000000e+00
>
>
>
> _____
>
> From: FSL - FMRIB's Software Library
> [mailto:[log in to unmask]] On Behalf
> Of Thomas Nichols
> Sent: Wednesday, October 10, 2007 5:10 AM
> To: [log in to unmask]
> Subject: Re: [FSL] TBSS-voxelwise correlations
> between FA and Test scores
>
>
>
> Bhargav,
>
> Did you include an intercept in the model? Or
> specify the -D option and use
> a centered covariate? That might well explain the
> large t values (without
> an intercept you may be testing if the FA values are
> non-zero, not a very
> interesting question).
>
> randomise uses the general linear model and
> contrasts to test effects of
> interest with t-tests and so doesn't produce
> correlation coefficients.
>
> You can threshold on the basis of corrected or
> uncorrected P-values with
> fslmaths/avwmaths, the -thr option, and the
> corresponding One-Minus-P-value
> images; see the randomise help page
> http://www.fmrib.ox.ac.uk/fsl/randomise/ for the
> exact filename extensions
> for each of these types of images.
>
> Hope this helps!
>
> -Tom
>
> On 10/9/07, Bhargav Kumar Errangi
> <[log in to unmask]> wrote:
>
> Hello,
>
> We are using TBSS to look for voxel-wise
> correlations between FA and test
> scores. Could you please answer the following
> questions for us?
>
> 1) Using the GLM tool, we specificy 1 covariate and
> provide values for each
> of 10 subjects in the EV tab. Then in the contrast
> tab, we specify 2
> contrasts (1 and -1)
> 2) The output is a t statistic image. We were
> exepcting an r statistic map.
> Does FSL calculate the t from the r?
> 3) Will the "1" contrast yield positive correlations
> and the "-1" contrast
> yield negative correlations?
> 4) The t statistic values are very, very large. We
> only get reasonbable maps
> when we threshold at t>20. Do you know why this
> might be?
> 5) Is there a way to threshold the map based on
> p-values rather than t
> statistics?
>
>
>
> ____________________________________________
> Thomas Nichols, PhD
> Director, Modelling & Genetics
> GlaxoSmithKline Clinical Imaging Centre
>
> Senior Research Fellow
> Oxford University FMRIB Centre
>
>
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