doug-

thanks for all the help on this. another quick question:

when choosing the simulation type does the ending have to match the sim sign? for instance i see examples with

--sim mc-z 10000 3 mc-z.pos.3 --sim sign pos

or

--sim mc-z 10000 3 mc-z.neg.3 --sim sign neg

I guess what i am asking is what does the first sign (in the mc-z.(SIGN).3 mean?

michael

On Wed, Jun 13, 2012 at 2:26 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:

If you run it with --help, you will see this. let me know if this is not clear.

6. Select the threshold sign (--sim-sign). This is the sign of the threshold used to create the clusters for cluster-wise correction of multiple comparisons. Options are abs (unsigned), pos (positive), and neg (negative). If you have an a priori hypothesis (eg, group1 > group2), then choose positive. If you don not know the sign, then use abs. Choosing a sign will yield stronger results (ie, smaller p-values), but you will lose the other sign.

The FWHM is obtained from the data (glmdir/fwhm.dat)

doug

On 06/13/2012 02:04 PM, mdkruepke@uwalumni.com wrote:

...

Freesurfers-

When correcting for multiple comparisons using: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --sim mc-z 5 4 mc-z.negative \ --sim-sign neg --cwpvalthresh 0.4\ --overwrite What does the sign mean (ie - the neg, pos, abs). Also for the mc-z simulation type do we no longer need to include the smoothness of our data (FWMH)?

Michael D. Kruepke PhD - University of Illinois at Urbana-Champaign BA - Psych - University of Wisconsin-Madison mdkruepke@gmail.com mailto:mdkruepke@gmail.com (262)-483-7449

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