BTW: I also meant to mention that I don't see how using the "Threshold
stats images as well as masking" option can solve this problem, because
if the stats image has both positive and negative values, then there is
no "threshold" that will allow all legitimate values while excluding
just the voxels whose values are exactly zero.
cheers,
-MH
On Thu, 2010-06-17 at 08:58 -0500, Michael Harms wrote:
> Hi Steve,
> If you search the featquery web page
> (http://www.fmrib.ox.ac.uk/fsl/feat5/featquery.html) for "zero" you find
> the following statements:
>
> ---
> Featquery will calculate various quantities within the selected mask,
> for example, the number of non-zero voxels within the mask, the mean and
> max values of the stats image within the mask, and the co-ordinates of
> the max image value within the mask.
>
> Featquery saves the mask, once transformed into the native space of the
> selected FEAT directory, inside the Featquery output directory, called
> "mask" (even if this only contains a single non-zero voxel, in the case
> of selecting a co-ordinate).
>
> If you turn on Do not binarise mask (allow weighting) then if your mask
> is non-binary, its non-zero values will weight all Featquery output
> values rather than treating the mask as binary.
>
> The first column in the main table shows the "stats image", i.e. lists
> the different FEAT stats images that you asked Featquery to report on;
> each of these is also a link to a raw text file giving the data
> timeseries plot at the position of the maximum image value within the
> mask. The next column tells you the number of non-zero voxels within the
> mask.
> ---
>
> So, the web page clearly indicates (1st and 4th statements above) that
> the number of voxels output measure is the number of non-zero voxels
> (consistent with the -V flag in the featquery script). And on careful
> reading, the 2nd and 3rd statements above deal with the mask itself,
> rather than the values underlying the mask in the statistic of interest.
> But overall, the frequent mention of "non-zero" gives the
> impression/expectation that ALL featquery output would be based on the
> non-zero values in the STATISTIC image, especially since that is the way
> the number of voxels output is itself treated. Indeed, that was exactly
> the expectation that someone here had, but I upon seeing 0 as the output
> for the median and 10% values, I realized that it couldn't be the case
> that zero values in the statistic image under the mask were being
> excluded.
>
> Since exact 0's are almost always doing to reflect an absence of data at
> that voxel, why is the default behavior to include those 0's as part of
> the mean/median/percentile statistics?
>
> That said, if those stat values are going to include the 0's, then I
> would suggest that you make this explicitly clear on both the web page,
> and within the text of featquery's html report. Based on our
> experience, I'm rather confident in speculating that we are certainly
> not the only ones that assumed that the mean/median/percentile
> statistics excluded 0's under the mask from the calculation. In our
> particular case, in which we had some masks that ended up including a
> fair number of zero values in the statistic images of interest, the
> featquery statistics are meaningless.
>
> Best,
> -MH
>
>
> On Thu, 2010-06-17 at 07:59 +0100, Stephen Smith wrote:
> > Hi - which part of the manual are you thinking of? I think the
> > script is correct - the intention is to estimate the statistics across
> > all voxels inside the mask, unless you turn on the thresholding
> > option?
> >
> >
> > Cheers.
> >
> >
> >
> > On 15 Jun 2010, at 03:57, Michael Harms wrote:
> >
> > > Hello,
> > > Re-posting this since the original post coincided with HDBM.
> > >
> > > Best,
> > > -MH
> > >
> > > ---------------------------- Original Message
> > > ----------------------------
> > > Subject: [FSL] bug in featquery's treatment of zeros?
> > > From: "Michael Harms" <[log in to unmask]>
> > > Date: Thu, June 10, 2010 4:58 pm
> > > To: [log in to unmask]
> > > --------------------------------------------------------------------------
> > >
> > > Hello FSL developers,
> > > Is Featquery supposed to include only non-zero voxels for all
> > > calculated
> > > statistics included in its output (i.e., report.txt)? That at least
> > > seems to be the implied behavior according to the Featquery web
> > > page.
> > >
> > > However, if that is the intent, it doesn't appear to be happening.
> > > For brevity I'll just cut to what I think is the relevant line in
> > > the
> > > featquery script:
> > >
> > > catch { exec sh -c "${FSLDIR}/bin/fslstats ${fqroot}/tmp -k
> > > ${fqroot}/tmpmask -m -R -V -p 10 -p 50 -p 90 -x -s" } thevals
> > >
> > > Shouldn't the flags be "-M -R -V -P 10 -P 50 -P 90 -x -S" if the
> > > intent
> > > is to include only non-zero voxels in the calculations?
> > >
> > > thanks,
> > > -Mike H.
> > >
> > >
> > > --
> > > Michael Harms, Ph.D.
> > > --------------------------------------------------------------------
> > > Conte Center for the Neuroscience of Mental Disorders
> > > Washington University School of Medicine
> > > Department of Psychiatry, Box 8134
> > > Renard Hospital, Room 6604 Tel: 314-747-6173
> > > 660 South Euclid Ave. Fax: 314-747-2182
> > > St. Louis, MO 63110 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
> > ---------------------------------------------------------------------------
> >
> >
> >
> >
> >
> >
> >
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