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.