again, FDR should have nothing to do with it. If you want a voxel-wise threshold at 2, just set that threshold when you run mri_glmfit-sim with "--cache 2 sign" where sign is pos, neg, or abs doug
Antonella Kis wrote:
Hi Doug,
Thanks again for helping. I am trying to use QDEC but there are no clusters surviving after FDR (it says statics cannot be done so gives me error by running FDR). So I am trying to get the thickness values only for the clusters that are formed in QDEC after setting up a threshold = 2 (before running FDR). In order to do this you suggested me to run mri_glmfit-sim on the QDEC results. The only problem is that I cannot run the -sim if there is no FDR data (stats) so I cannot cache the clusters formed only by thresh 2 in QDEC. Is theer a way to do it?
Many thanks, AK
*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:* Wednesday, September 28, 2011 12:06 PM *Subject:* Re: [Freesurfer] Error with mri_glmfit-sim
What does FDR have to do with it? FDR should not come into play in this. doug
Antonella Kis wrote:
Good morning Doug,
I tried running the -sim on my QDEC output (as you recommended me last days) but for some data the FDR gives me error (cannot calculate clusters statistics) so mri_glmfit-sim is not working either since the corrections by multiple comparisons is not working. What should I do in this case so I can get as output my cortical thickness values for the formed clusters at threshold 2, before multiple comparison?
Many thanks, AK
-- 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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