In the table produced by glmfit-sim, the maximum vertex-wise uncorrected
-log10(p) is given. Is that enough?


On 10/03/2016 02:55 PM, Corinna Bauer wrote:
> 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
> <mailto: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
>
>
>
>
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