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

[EJ Nikelski]

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