I'm afraid not at the moment (although we have a semi-finished work on that)
so, for now, randomise is THE ONLY straight-forward way.
2010/6/30 Grimm, Oliver <[log in to unmask]>
> Thanks for your fast answer. Is it possible at all, to use a parametric
> test and get p-values out of the TCFE-image?
>
>
>
> Oliver
>
>
> ------------------------------
>
> *Von:* FSL - FMRIB's Software Library [mailto:[log in to unmask]] *Im
> Auftrag von *Reza Salimi
> *Gesendet:* Mittwoch, 30. Juni 2010 13:58
>
> *An:* [log in to unmask]
> *Betreff:* Re: [FSL] TFCE with SPM-Toolbox
>
>
>
> Oliver,
>
> at the moment, TFCE can be utilized for the second-level type analyses
> where you have a exchangeable design matrix (under the H0). This
> exchangeability makes the formation of distribution of the statistic of
> interest (i.e., maximum TFCE per volume, as recommended) under H0. Having
> this null distribution, you will be able to assess the actual TFCE-image's
> significance at each voxel, i.e., a nonparametric hypothesis test.
>
>
>
> Now, in order to use *fslmaths* jointly with some SPM nonparametric tests
> (which I think might be SnPM), you might need to add a T->TFCE
> transformation (using *fslmaths*) whenever you form your T-stat and use
> the null distribution of the *max* statistic of these new images for
> converting you actual t-stat into a P-image.
>
>
>
> Anyway, to summarise, it might be much easier to use FSL-randomise,
> however, you can use any nonparametric test on max{T-images}, *IF* you
> correctly transform your T-images to TFCE-images.
>
>
>
> 2010/6/30 Grimm, Oliver <[log in to unmask]>
>
> Dear FSL-Team, dear Stephen,
>
> we have read your paper about TFCE with great interest and we would like to
> make use of this cool technique.
>
> As we do net (yet...) use FSL, but have a very well established
> MATLAB/SPM-pipeline, we would like to compare our old results with new
> TFCE-statistics.
> We wonder wether it would be possible to combine TFCE (via
> fslmaths-command) with SPM, e.g. like this ...
>
> a) Pre-processing and the first-level-analyses have been performed
> in SPM
>
> b) the first-level SPM-t-images will be fed into the fsl/TFCE
> procedure
>
> c) the resulting TFCE images should be fed into second-level
> analysis in SPM
>
>
>
> However, we do not really know if this strategy is adequate and it would be
> great if you, as the expert, can help us with the following points:
>
>
>
> 1) Would you recommend to use the SPM t-images for the TFCE
> procedure or should we take z-images or something else?
>
> both T and Z should be fine
>
>
> 2) Do we have to feed the second-level-analysis with the TFCE-weighted
> images from the first-level or is TFCE applied afterwards on a second-level
> result image?
>
> currently, the existing nonparametric TFCE scheme is ONLY applicable to
> the second-level type analyses.
>
>
>
> We know that you are getting plenty of these emails and your time is
> limited, however, maybe we will be lucky and get some brief helping
> comments.
>
>
>
> All the best
>
> Michael Plichta
>
> Oliver Grimm
>
>
>
> _____________________________________
>
> Department of Psychiatry
>
> Division for Imaging in Psychiatry
>
> Central Institute of Mental Health
>
>
>
>
>
>
> -----Ursprüngliche Nachricht-----
> Von: FSL - FMRIB's Software Library [mailto:[log in to unmask]] Im Auftrag
> von Andreas Bartsch
> Gesendet: Mittwoch, 30. Juni 2010 12:05
> An: [log in to unmask]
> Betreff: [FSL] AW: [FSL] corpus callosum waytotal
>
> no - you need to add the waytotal, given that the fdt_path is the sum of
> the tracking forth and back in the symm mode.
> spatial extent of the tract is NOT modified by the normalization but only
> by later thresholding. depending on your masks, the numbers can seem quite
> low.
> cheers-
> andreas
> ________________________________________
> Von: FSL - FMRIB's Software Library [[log in to unmask]] im Auftrag von
> LiuYan [[log in to unmask]]
> Gesendet: Mittwoch, 30. Juni 2010 12:04
> An: [log in to unmask]
> Betreff: Re: [FSL] corpus callosum waytotal
>
> Hi Stam:
>
> Thank you for your advice! I also thought of that, to use the sum for the
> normalization. But the waytotal number of the corpus callosum is big, if I
> add these two numbers and divide the fdt_path by the sum, I will have a very
> low probability for the entire tract. After using the threshold, I get very
> few fibres. Could I use the average of these two numbers, as it is the same
> tract going through the two seeds twice?
>
> Regards,
>
> Yan
> ________________________________
> Date: Wed, 30 Jun 2010 10:21:43 +0100
> From: [log in to unmask]
> Subject: Re: [FSL] corpus callosum waytotal
> To: [log in to unmask]
>
> Hi Yan,
>
> you are right, you will get two waytotal numbers, one per specified seed
> mask. I would add these numbers and use the sum for normalization.
>
> Cheers,
> Stam
>
>
>
> On 30 Jun 2010, at 09:50, LiuYan wrote:
>
> Hi FSL specialists:
>
> Recently, we try to do the tractography for the corpus callosum. Two seed
> masks are defined either side of the midline in the sagittal images. In the
> tools box, we choose the multiple masks to get the tract. However, we have
> two waytotal numbers in the result, and we don't know which one to use for
> the normalization. Any one who has also worked on the corpus callosum could
> give us some advice? Many thanks in advance!
>
> Regards,
>
> Yan
>
>
>
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>
>
> --
> Reza Salimi-Khorshidi,
> DPhil Candidate, Dept. of Clinical Neurology, University of Oxford (Linacre
> College).
> [log in to unmask]
> FMRIB Centre, John Radcliffe Hospital, Oxford OX3 9DU
> Tel: +44 (0) 1865 222704 Fax: +44 (0)1865 222717
>
--
Reza Salimi-Khorshidi,
DPhil Candidate, Dept. of Clinical Neurology, University of Oxford (Linacre
College).
[log in to unmask]
FMRIB Centre, John Radcliffe Hospital, Oxford OX3 9DU
Tel: +44 (0) 1865 222704 Fax: +44 (0)1865 222717
