Hi Joshua, there are several issues. First, you are using a threshold of p<.0001 which is pretty severe. It works for the tutorial, but you need to understand what this threshold is and pick one appropriate for your data. Second, you are only doing 5 iterations. You need to be doing something like 10000. If you are doing a whole cortex analysis, you can use the cached table instead of doing a simulation (with --qache). Running your own simulation will take a long time. The smoothing level is a little high, I usually run at 10 or 15. There's nothing wrong, it is just a little high. doug

On 05/05/2013 03:39 AM, Joshua deSouza wrote:

Hi Doug,

The image has undergone fwhm 20 smoothing.

The final glmdir file is given in the attachments. RC.txt was the contrast name and folder in which the cluster correction files are kept.

The glmdir creation command line : mri_glmfir --y lh.thomasR.20.mgh --fsgd R.txt dods --C RC.txt --surf fsaverage lh --cortex --glmdir lh.thomasR.glmdir

The glmfit-sim command line is : mri_glmfit-sim --glmdir lh.thomasR.glmdir --sim mc-z 5 4 mc-z.negative --sim-sign neg --cwpvalthresh 0.999 --overwrite

The command line to view the image is : tksurfer fsaverage lh inflated -annot lh.thomasR.glmdir/RC.txt/mz-z.negative.sig.ocn.annot fthresh 1 -curv -gray

The version of freesufrer i'm using is 1.379.2.17

Thank you helping me out with this.

On Sat, May 4, 2013 at 12:12 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

Can you send the command line and terminal output and the version
of FS
you are using?
doug
On 05/03/2013 09:01 AM, Joshua deSouza wrote:
> Hello all,
>
> I am facing a problem whereby after running GLMfit and cluserwise
> correction for multiple comparisons using the monte-carlo method, I
> was unable to generate any clusters. I do have significant images
> produced for the glmfit.
>
> All procedures were done according to the tutorial to match the
> effects under FSGD.
>
> There are no clusters available even when I set the cwpvalthresh to
> .999 which is supposed to show all clusters. What is the cluster
> generation dependent upon? As my glmfit does show significant areas.
>
> Please advise
>
>
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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>

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