On Tue, Jun 4, 2013 at 11:25 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

--no-sim takes an argument. Run mri_glmfit-sim with --help to get more info
doug

On 06/04/2013 09:11 AM, Glen Lee wrote:

Hi Doug,
I tried as you suggested, but i've got the following error: e.g.,cannot find any csd files.
However, I can see them stored in csd folder as shown below:

/2D/results/LH/GLM/csd> ls
mc-z.negative.j001-osgm.csd perm.abs.2.j001-osgm.csd

I'm guessing that I need to define the path for this csd folder?

Here is the command line that I typed in:
mri_glmfit-sim --cwpvalthresh 0.99 --glmdir GLM --no-sim --overwrite

-Glen

On Mon, Jun 3, 2013 at 11:03 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

hi Glen, no cluster will show up if the p-value for all clusters
is above .05. You can change this with --cwpvalthresh to something
like .99. That should give you all the clusters. Also, you don't
have to run the full simulation again; you can use the --no-sim
option and it will use the simulation that you already did.
doug

On 6/3/13 9:45 PM, Glen Lee wrote:

Indeed, I initially tried 10,000 iterations and got nothing.
What else then could have gone wrong?

FYI, I use v5.1.0.

On Mon, Jun 3, 2013 at 5:32 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

You will need more like 10000 iterations instead of 100.
doug

On 06/03/2013 04:49 PM, Glen Lee wrote:
> Hello Freesurfer experts--
>
> I ran mri_glmfit-sim to validate the group level GLM result
(which was
> already done using mri_glmfit), but I was not able to get
any result
> out of it.
>
> Even with a quite liberal threshold (2), no vertices came
out (below
> is what I typed in for the random permutation).
>
> mri_glmfit-sim --glmdir GLM --sim perm 100 2 perm.abs.2
--sim-sign
> abs --overwrite
>
> What is strange is that I was clearly see a number of
clusters when I
> overlaid sig.mgh at a matched threshold (e.g., p>2), but no
cluster
> shows up in perm.abs.2.sig.cluster.mgh.
> I should be able to see the identical map between those right?
>
> FYI, I also pasted the content in
perm.abs.2.sig.cluster.summary below.
> As can be seen, nothing is listed in the stats table.
>
> Any of your help would be greatly appreciated.
> -Glen
>
>
>
>
>
>
> # Cluster Growing Summary (mri_surfcluster)
> # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36
greve Exp $
> # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
> # CreationTime 2013/06/03-20:19:31-GMT
> # cmdline mri_surfcluster --in GLM/osgm/sig.mgh --csd
> GLM/csd/perm.abs.2.j001-osgm.csd --mask GLM/mask.mgh --cwsig
> GLM/osgm/perm.abs.2.sig.cluster.mgh --vwsig
> GLM/osgm/perm.abs.2.sig.voxel.mgh --sum
> GLM/osgm/perm.abs.2.sig.cluster.summary --ocn
> GLM/osgm/perm.abs.2.sig.ocn.mgh --oannot
> GLM/osgm/perm.abs.2.sig.ocn.annot --annot aparc --csdpdf
> GLM/osgm/perm.abs.2.pdf.dat --cwpvalthresh .05 --o
> GLM/osgm/perm.abs.2.sig.masked.mgh --no-fixmni --surf white
> # cwd /glen/2D/results/LH
> # sysname Linux
> # hostname sumo.uphs.upenn.edu <http://sumo.uphs.upenn.edu>
<http://sumo.uphs.upenn.edu>
> # machine x86_64
> # FixVertexAreaFlag 1
> # FixSurfClusterArea 1
> #
> # Input GLM/osgm/sig.mgh
> # Frame Number 0
> # srcsubj fsaverage_sym
> # hemi lh
> # surface white
> # annot aparc
> # SUBJECTS_DIR /usr/local/freesurfer5-1/subjects
> # SearchSpace_mm2 59961.4
> # SearchSpace_vtx 82070
> # Bonferroni 0
> # Minimum Threshold 2
> # Maximum Threshold infinity
> # Threshold Sign abs
> # AdjustThreshWhenOneTail 1
> # CW PValue Threshold: 0.05
> # Area Threshold 0 mm^2
> # CSD thresh 2.000000
> # CSD nreps 100
> # CSD simtype perm
> # CSD contrast osgm
> # CSD confint 90.000000
> # Overall max 3.495 at vertex 61659
> # Overall min -4.18843 at vertex 73402
> # NClusters 0
> # Total Cortical Surface Area 59961.4 (mm^2)
> # FixMNI = 0
> #
> # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP
> CWPLow CWPHi NVtxs Annot
>
>
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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 <tel:617-724-2358>
Fax: 617-726-7422 <tel:617-726-7422>

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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