[MINC-users] t threshold for corrected p value of Aston's method

Tue May 6 09:07:29 EDT 2008

Thank you so much!
This is exactly what I wanted, a reference that I dig in.

Thanks,

Ji Hyun

On Tue, 6 May 2008, Sylvain Milot wrote:

>
> Hello,
>
> Greg Ward's scripts will work under linux with some fiddling - they are
> written in perl after all but they also make system calls to a wide
> variety of tools! I have used them under linux but they will
> require more work before making them available for mass comsumption. The
> bulk of the work resides in rewriting the code used for the creation of
> verification images since the current versions use an Irix image toolbox
> based on Irix's ImageVision Library. Also the code using batch needs
> revamping!
>
> So use do_mritotal -noverify -resample all -background ... and verify the
> images in the mrital_rsl directory.
>
> Better yet, do the following:
>
> qbatch do_mritotal -noverify -resample all
>
> qbatch is available on all linux systems and I hopefully fixed all
> the bugs ... but do_mritotal is NOT yet available - I suppose a version
> could be made available with a few options disabled to prevent havoc. I'll
> see what I can do in the next couple of weeks.
>
> do_mritopet needs to be revamped and I don't use do_pettopet anymore as
> mritopet is more robust - hence the reason why do_mritopet needs
> revamping.
>
> Yorick's days are counted and it will be retired in 2008 so I suspect I
> will be tempted at some point to do the work, same goes for dot ... but
> time is a luxury I don't have anymore since I'm a fulltime sys admin.
>
> As for PET motion correction, another option might be available, ie using
> Anthonin Reilhac's Dynamic PET motion correction method. It would have to
> be adapted for static PET images by pooling together a 12-(static)-scan
> study for example and then considering individual scan as time frames. I
> gave that a try last year but the results weren't very good and I failed
> to find time to get back to it. Anthonin seemed confident that it could
> work so there's still some hope.
>
> BUT concerning Ji Hyum KO's data - it is Dynamic PET, so Anthonin's method
> should be preferred ! Under BIC linux systems, you will find
> /usr/local/bin/do_PET_frame_realignment to do the job.
>
> As for Keith's fmristat (for PET), I never got around to using/testing it.
> It uses a different approach to estimate the variance - Keith calls it a
> "local form of pooling" and he posted something on the bic-users mailing
> list many years ago ... here it is:
>
> >       Well I must admit PET scanners have changed in the last 10 years
> > and the assumption of equal sd probably needs to be checked. In the mean
> > time, fmristat's multistat program does (almost) everything that DOT's
> > statistical analysis does, but better. Instead of pooling the sd, it
> > smoothes it, i.e.
> > a sort of local pooling. We usually choose the amount of smoothing so
> > that the resulting df is large, say 100. If you set the FWHM of the
> > smoother very large (say 100mm), you get the pooled sd (almost); if you
> > set it to 0 you get the voxel sd.
> > I would suggest you look into this - the help of multistat (look under
> > INPUT_FILES_SDEFFECT) tells you how to run it for PET data - essentially
> > all you do is leave the input sd files blank -
> >
> > Keith Worsley
> > Department of Mathematics and Statistics, McGill University
> > 805 ouest, rue Sherbrooke, Montreal, Quebec, Canada H3A 2K6
> > tel: (514) 398-3842, fax: (514) 398-3899
> > e-mail: keith.worsley at mcgill.ca, web: http://www.math.mcgill.ca/keith
>
> HTH,
>
> S
>
> On Mon, 5 May 2008, EJ Nikelski wrote:
>
> > Hi all,
> >
> >    Reading this e-mail reminded me that I could use some advise on a
> > related issue.  Pls forgive me if its a wee bit tangential to the
> > subject line.
> >
> >   Specifically, given that Keith's fmristat (for PET) assumes that
> > the input volumes have already been spatially normalized, do we have
> > any tools to help with this task, short of doing the minctracc (or
> > mritoself, mritotal) calls manually?   In the days of 'dot' (ah, the
> > good old days), Greg Ward's scripts (do_mritopet,  do_mritotal,
> > do_pettopet) were nicely able to generate the required xfms  --
> > however, while still available on Yorick, they do not appear to be
> > migrating to the Linux systems.  I suppose that one could use
> > fmr_preprocess to do PET motion correction (with some fiddling),
> > however, the version of this script that I have seen is buggy (at
> > least the version that I found has bugs), and it does not appear to be
> > quality controlled (i.e. no official release).
> >
> >   So in sum, the questions are (1) are the old PET preprocessing
> > tools (Greg's stuff)  unsupported and therefore not
> > being migrated off of Yorick, (2) and what are other BIC PET
> > researchers using to do motion correction, cross-modality alignment,
> > and stereotactic transformation? Ideas and suggestions?
> >
> > Thanks,
> >
> >
> > -Jim
> >
> >
> >
> > On Mon, May 5, 2008 at 6:58 PM, Andrew Janke <a.janke at gmail.com> wrote:
> >> Hi Ji,
> >>
> >>  I was hoping Sylvain would answer this one as I am not that familiar
> >>  with the stats associated with PET but in any case here goes...
> >>
> >>
> >>  2008/5/1 Ji Hyum KO <kojinet at bic.mni.mcgill.ca>:
> >> >  As far as I understand, I should calculate the t threshold based on
> >> >  Worsely et al., Human Brain Mapping, 1996.
> >> >  I am really sure that it is very well-written famous paper, but I
> >> >  couldn't figure out how to calculate the t-threshold in the given
> >> >  conditions.
> >>
> >>  Correct, to calculate this I would suggest that you use Keith Worsleys
> >>  MATLAB package (called fmristat) to do this.
> >>
> >>    http://www.math.mcgill.ca/keith/fmristat/
> >>
> >> >  Is there any easy way to calculate t threshold for p<0.05 (corrected)?
> >>
> >>  This will depend on the number of subjects, (and thus Degrees of
> >>  Freedom), the number of voxels you are considering and so forth.
> >>
> >> >  And, is it going to be the same even if I consider the whole brain rather
> >> >  than just striatum, e.g., fallypride study?
> >>
> >>  It will be different, but again this will depend on the method you use
> >>  to calculate the t-value. Certainly it will change if you calculate
> >>  pooled variance across you data (or mask).
> >>
> >>  Again though I would suggest that you spend some time getting
> >>  acquainted with the fmristat package. Keith has a number of examples
> >>  on his webpages that should help you get going.
> >>
> >>
> >>  a
> >>
> >>  --
> >>  Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/)
> >>  Canberra->Australia +61 (402) 700 883
> >>  _______________________________________________
> >>  MINC-users at bic.mni.mcgill.ca
> >>  http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>
> >
> >
> >
> > --
> > =================================
> > Jim Nikelski, Ph.D.
> > Postdoctoral Research Fellow
> > Bloomfield Centre for Research in Aging
> > Lady Davis Institute for Medical Research
> > Sir Mortimer B. Davis - Jewish General Hospital
> > McGill University
> > Tel: (514) 340-8222 x 2298
> > Fax: (514) 340-8295
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
>
> ---
> Sylvain Milot (sylvain at bic.mni.mcgill.ca)
>                (bicadmin at bic.mni.mcgill.ca)
> Brain Imaging Centre
> Montreal Neurological Institute
> 3801 University Street
> Webster 2B, Room 212
> Montreal, Qc., Canada, H3A 2B4
> Phone  : (514) 398-4965, Fax: 398-8948
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>           Montreal, Qc., H2W 1S4
> _______________________________________________
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>