There should be an ocn.dat file that corresponds to the CSD base name that you passed to mri_glmfit-sim. The cache just uses a pre-computed table. The computations are pretty simple. It synthesizes white gaussian noise on the surface, smooths it by a certain amount, then finds clusters at various thresholds and signs. It tabulates how likely a cluster of a given size is given the smoothing level, threshold, and sign. doug

On 04/16/2012 09:10 PM, zhang mingxia wrote:

Hi Doug,

Thanks. I have done Clusterwise Correction for Multiple Comparisons, so there is some file like mc-z.positive.y.ocn.dat. I have seen the column.

By the way, I just know the clusterwise correction(which I get the mc-z. files) use the permutation method. What about the "--cache" one? Is there any introduction on website? I have not seen any.

Thanks again.

Mingxia

On Thu, Apr 12, 2012 at 10:33 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

Hi Zhang, there should be a file named something like
"cache.th13.abs.y.ocn.dat" that is output as part of the
correction for
multiple comparisons. This will have a column for each significant
cluster in the order that the clusters are in. Each row is a
subject. So
you can take the mean over the subjects to get the number you want.
doug


On 04/10/2012 08:01 PM, zhang mingxia wrote:
> Dear Freesurfer experts,
>
> I have done the whole brain analysis and get some significant
> clusters. How can I get the mean thickness of these clusters of
every
> subject?
>
> Thank you very much.
>
> Mingxia Zhang
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
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>
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the
sender and properly
dispose of the e-mail.