It should be the sig.mgh file in your contrast directory.
doug
ps. Please post to the list and not me directly. thanks!

On 07/18/2012 11:56 AM, Antonella Kis wrote:
> Hi Doug,
>
> Many thanks for your prompt response and your help. I have one more question please. I searched for mri_surfcluster command and I am not sure what should be my input file.
>
> Can you please clarify this for me? Should this be  L-frontal.fsgd since I have more subjects?
>
>
> Thank you.
> Antonella
>
> ------------------------------------------------------------------------
> *From:* Douglas N Greve <greve@nmr.mgh.harvard.edu>
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Sent:* Wednesday, July 18, 2012 11:39 AM
> *Subject:* Re: [Freesurfer] FDR versus mri_glmfit-sim with --cache option
>
> Hi Antonella, first of all, FDR and clusterwise correction are doing
> different things. Technically, you don't get clusters from FDR. FDR will
> choose a voxel-wise threshold for you, and any voxel above threshold can
> be interpreted as surviving FDR (but you should know how to interpret it
> -- see Tom Nichols' paper). Of course, many of the voxels may appear as
> clusters. In your case, FDR found a voxel-wise threshold of 3.8
> (meaning  p<1.5849e-04). The fastest way to get the values you want is
> to go outside of QDEC. First, run mri_surfcluster using a threshold of
> 3.8 (--thmin 3.8). Specify an output cluster number map (--ocn ocn.mgh)
> and a summary file (--sum sum.dat). This will produce a lot of
> "clusters", two of which should be the ones below (you can prune the
> list by specifying that the clusters need to be a certain size
> (--minarea). Once you have the ocn file, you can run mri_segstats,
> something like
>    mri_segstats --seg ocn.mgh --i y.mgh --avgwf avgwf.dat  --excludeid 0
> y.mgh is the glmfit input file created by qdec. This will produce
> avgwf.dat which will have a column for each cluster, the order will be
> the same as that in sum.dat.
>
> douig
>
> On 07/18/2012 11:25 AM, Antonella Kis wrote:
> > Dear FS team,
> >
> >
> >
> > I am doing a cortical thickness study using QDEC. I used FDR and got
> > the following clusters:
> >
> > Generating cluster stats using min threshold of 3.8...
> > Found 2 clusters
> > Contrast: 'lh-Diff-Class1-Class2-Intercept-thickness', 15fwhm, DOF: 69
> > ClusterNo  Max  VtxMax  Size(mm2)  TalX  TalY  TalZ NVtxs Annotation
> > ---------  ---  ------  ---------  ----  ----  ---- ----- ----------
> >      1  -3.8743  18231      4.55  -39.8    1.5  14.1  14  precentral
> >      2  -3.8065  47386      2.66    -8.2  33.1  33.9    4  superiorfrontal
> > ============================================================
> >  I need to get the cortical thickness values from each subject within
> > this clusters so I am trying to use
> > mri_glmfit-sim with --cache option and I wonder what value should I
> > choose in this case for cache (2, 3.3 or 4)
> > and what --cwpvalthresh 0.05 or .025  to get the same results as FDR's
> > results.
> >
> > I tried:
> > mri_glmfit-sim \
> > --glmdir lh.L_frontal.glmdir \
> > --cache 3 neg \
> > --cwpvalthresh .05 \
> > --overwrite
> >
> > # ClusterNo  Max  VtxMax  Size(mm^2)  MNIX  MNIY  MNIZ    CWP
> > CWPLow    CWPHi  NVtxs  Annot
> >    1      -3.874  18231    320.36    -39.8    1.5  14.1  0.02610
> > 0.02410  0.02820  949  precentral
> >    2      -3.807  47386    700.61    -8.2  33.1  33.9  0.00020
> > 0.00000  0.00040  1053  superiorfrontal
> >
> > so as you can see the clusters are the same but their Size and NVtxs
> > is so different. What is wrong?
> >
> > Thank you for your time and help.
> > 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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-- Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html