Hi Ilana,
I'll let the first question to the FS experts to answer. For the second:
1. Is it legitimate toconclude from this that the regressor's overall effect is
that it's associated with a thinner cortex (e.g., older subjects have a thinner
cortex), eventhough most of the cortex does not survive FDR or multiple
comparison correction?
Even if the effect exists, your experiment wasn't able to detect it as
significant, since nothing survived the multiple testing correction you
used. Most scientific journals wouldn't accept conclusions based on
non-significant results, despite how compelling the hypothesis might be.
2. If yes, is there a way of exporting the distribution, or getting some
numerical representation of the negative and positive values across the cortex,
or within aparc annotations.
The p-values are in the files sig.mgh, in subdirectories of the qdec
directory where the results of the analyses were stored. There are
multiple ways to open and a suggestion is to convert to ASCII using the
-c option of mris_convert, then open in Octave/Matlab with dlmread.
3. Is there a way to set FDR separately for positive and negative values?
The plain answer is no, because for the FDR procedure to work, it's
necessary that the p-values under the null are uniformly distributed
between 0 and 1 (from the definition of p-values). If you drop part of
your distribution, then the p-values are no longer distributed like
that. It turns out, however, that in some particular cases, part of the
distribution does not actually exist (see Self& Liang, J Am. Stat
Assoc, 1987 for some cases, particularly the Cases 5 and 7). A
workaround is to divide the q by a constant that depends on the fraction
of the distribution that known to be missing (e.g., for Case 5, instead
of q=0.05, one could use q=0.025 to obtain the same 5% of false
discoveries). However, these particular cases I believe don't apply to
your scenario, so please, refrain from applying FDR separately only on
positives or negatives.
There is also a second reason for not applying FDR separately: for each
set (positive and negative), the number of tests would be reduced, on
average, by half, alleviating the multiple testing problem and making,
on average, twice as easy for results to survive the threshold,
inflating the amount of false discoveries, something undesired.
Hope this helps!
All the best,
Anderson
On 05/16/2011 09:53 AM, Ilana Hairston wrote:
Hi there,
First the simple question - is there a way to run mris_anatomical_stats on all
my subjects at once generating a single output file?
Second - actually comprised from several questions: when looking a the
unthresholded group analysis on cortical thickness (in the averaged space), the
distribution of negative and positive z values is not necessarily normal.
i.e., the range of negative values maybe be 0 to -5, and the range of positive
values 0 to +3.
1. Is it legitimate toconclude from this that the regressor's overall effect is
that it's associated with a thinner cortex (e.g., older subjects have a thinner
cortex), eventhough most of the cortex does not survive FDR or multiple
comparison correction?
2. If yes, is there a way of exporting the distribution, or getting some
numerical representation of the negative and positive values across the cortex,
or within aparc annotations.
3. Is there a way to set FDR separately for positive and negative values?
thanks
ilana
Ilana Hairston
hairstons...@gmail.com
*************************
Our ignorance is not so vast as our failure to use what we know.
—M. King Hubbert, peak oil prophet
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