Hi all, just following up on my previous question. For the purposes of showing uncorrected p-values <0.005 as well as the corrected results (via mri_glmfit-sim) I would like to get the table of uncorrected p-values. I have tried using mri_glmfit-sim --glmdir results.glmdir --cache 2.3 abs --cwp 1 --2spaces and it does output p-values, but there has gone through the simulations. I would like the raw p-values from this step: mri_glmfit --y rh.noreg.thickness.08B.mgh --fsgd file.fsgd dods --C diff_noreg.mtx --surf fsaverage rh --cortex --glmdir rh.thick.noreg.sm08.glmdir

What command would I use?

Thanks

Corinna

On Wed, Sep 21, 2016 at 4:31 PM, Corinna Bauer <corinnab83@gmail.com> wrote:

Hello all,

I would like to get a table of the uncorrected p-values to compare with the corrected ones obtained using mri_glmfit-sim. I tried the following, which outputs a table of clusters and their vertices, but it does not include p-values. Is there a flag that I shoudl include to output the p-values?

mri_surfcluster --in sig.mgh --sign abs --subject fsaverage --hemi lh --surf white --annot aparc --no-adjust --bonferroni 2 --no-fixmni --ocn cache.uncorr.abs.sig.ocn.mgh --oannot cache.uncorr.abs.sig.ocn.annot --cwsig cache.uncorr.abs.sig.cluster.mgh --thmin 2.3 --sum cache.uncorr.abs.sig.ocn.dat

Thanks

corinna