Thanks Doug,
So I suppose should be the sig.mgh from running mri_glmfit:
mri_glmfit \
--y lh.L_frontal.15.mgh \
--fsgd L_frontal.fsgd dods\
--C lh-Avg-thickness-Cor.mtx \
--surf fsaverage lh \
--cortex \
--glmdir lh.L_frontal.glmdir
Is this right?
Thank you.
Antonella
________________________________
From: Douglas N Greve <gr...@nmr.mgh.harvard.edu>
To: Antonella Kis <ator...@yahoo.com>; "Freesurfer@nmr.mgh.harvard.edu"
<Freesurfer@nmr.mgh.harvard.edu>
Sent: Wednesday, July 18, 2012 12:03 PM
Subject: Re: [Freesurfer] FDR versus mri_glmfit-sim with --cache option
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 <gr...@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
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
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> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> -- Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>
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>
>
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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
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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