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
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
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