That is a slight bug in that there is no default (you have to specify). Below is the text from running it with --help. If you have an apriori hypothesis that group1 > group2, then choose positive. If you don't know the sign, then use abs. Choosing a sign will yield stronger results (ie, smaller p-values), but you will lose the other sign.

doug

This is the sign of the threshold used to create the clusters for cluster-wise correction of multiple comparisons.

Antonella Kis wrote:

Dear Doug,

Thank you so much for your help. I still have one more question please: WHEN i WAS TRYING TO RUN THE:

mri_glmfit-sim \ --glmdir Group_Analysis.glmdir \ --sim neg perm 10000 3 permcsd\ --cwpvalthresh .05

as you recommended me so withouth --sim-sign I got the error that I must specify the sign so I choose neg. I believe the default should be abs but can you please shortly explain what exactly the --sim-sign means?

Thank you very much. Antonella

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*From:* Douglas N Greve greve@nmr.mgh.harvard.edu *To:* Antonella Kis atorok9@yahoo.com *Cc:* "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Sent:* Tuesday, January 31, 2012 12:39 PM *Subject:* Re: [Freesurfer] re-running mri_glmfit-sim

You have to re-run doug

Antonella Kis wrote:

...

dear All,

I would like to know if I am running the mri_glmfit-sim \ --glmdir Group_Analysis.glmdir \ --sim perm 10000 3 permcsd \ --sim-sign neg \ --cwpvalthresh .05

and I want to change the --sim-sign from neg to positive if I need

to run again the whole simulation or I can just run:

...

mri_glmfit-sim --glmdir Group_Analysis.glmdir \ --no-sim --sim-sign

pos or how exactly to edit the mri_glmfit in this case?

...

Also if I need to add one more subject do I need to re-run the whole

simulation or for multiple comparison I can just use the --no-sim option?

...

Thank you very much! Antonella

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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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