Hi Darren,
the -log10(p) transform simply means you're looking at the exponent, with
increasing values meaning more significant. For example, if your threshold
were set to:
fthresh = 1
fmid = 2
fslope = 1
nothing with p>1e-1 would be colored, the mid point of the color scale
would be p=1e-2 and the full saturation would be fmid+1/fslope=1e-3.
If fslope is too confusing (which it is to most people) you can set fmax
instead.
Note that in your example you should be using log10 not log:
-log10(0.05)
ans =
1.3010
so setting fthresh = 1.3 would give you an effective threshold of .05
(instead of .1 in the example above).
cheers,
Bruce
--------------------------------------------------------
Bruce Fischl email: [EMAIL PROTECTED]
Mass. General Hosp. NMR Center. tel:(617)-726-4897
Rm. 2328, Building 149, 13th Street fax:(617)-726-7422
Charlestown, MA 02129 USA
On Wed, 30 Oct 2002, Darren Weber wrote:
>
> Dear Doug et al,
>
> I've completed mris_surfglm on the cortical thickness, comparing two groups.
> For a linear regression, I would normally check the assumptions of
> linearity, homoscedasticity and normality in the residuals, but for 250,000
> analyses, it's a daunting, if not impossible, task! So, lets assume the
> linear model applies.
>
> I need to confirm and clarify a few points on how to display/threshold the
> stats.
>
> Firstly, I followed the --help option examples and saved the output stats
> using:
>
> --sigt ./glm/group-sigt-rh.w paint
>
> I can now load these values as an overlay on the target subject surface of
> choice, great. Now the questions arise as to what quantity this is and how
> to use the overlay threshold GUI.
>
> Firstly, what quantity is it? According to the --help option:
>
> #Save the signficance (p-value) of the t-ratio of the contrast. The
> #value is actually the -log10 of the significance with the same
> #sign as the t-ratio from which it was computed. The significance
> #is computed from a double-sided t-test and is NOT corrected for
> #multiple comparisons across space. fmt is the format (see OUTPUT
> #FORMATS).
>
> So, the output values are not t or p, but -log10(p). Why is this so? I
> don't understand the advantage of doing this transform on the p-values.
>
> If so, and this should be simple, do we calculate a threshold of p = .05 as:
>
> >> p = .05;
> >> thresh = -log(p)
>
> thresh = 2.9957
>
> This would be a 2-tail threshold for any value of p. How would you obtain a
> 1-tailed threshold? Perhaps multiply p by 2, ie:
>
> >> thresh = -log(p*2)
>
> thresh = 2.3026
>
>
> OK, so we get a threshold value somehow. I'm not sure how to use the
> overlay threshold GUI, which has three slides and a slope value. The
> tksurfer manual does not describe the threshold controls, it only contains
> the following description:
>
> Overlay File Display Options
> To select which overlay to show, use the View->Overlay Layer submenu. The
> field names are automatically set to the file name loaded. You can change
> this name by typing a new one into the information area in the Tool window.
> The display for the current overlay can be configured in the
> View->Configure->Configure Overlay
> Display dialog. You can select the color scale to use with the radio buttons
> in the top area of the dialog. The Truncate option can be checked to turn
> off the display of negative values. Check the Reverse option to reverse the
> sign of the values as they are drawn in the color scale. View-> Inverse and
> Complex are reserved for future upgrades.
>
> What does each slider do and how would you best set these so that the above
> threshold values will be applied accurately?
>
> Thanks very much, Darren
>
>
>
> --
> Darren Weber, PhD Student
> Cognitive Neuroscience, School of Psychology
> Flinders University of SA, GPO Box 2100, Adelaide, SA 5001, Aust.
> Ph: (61 8) 8201 3889, Fax: (61 8) 8201 3877
> http://203.3.164.46/~dlw/homepages/index.html
>
>
