The threshold is a significance threshold, ie, -log10(p), so sig=2.3 -> p < 10^-2.3 = .005. This will not work for fsaverage5. You can try generating a new set of tables for fsaverage5 with mri_mcsim. doug
Xinian Zuo wrote: > Thank you, Doug! Found the CSD file. Just want to make sure that I > picked up the correct one: > mult-comp-cor/fsaverage/lh/cortex/fwhm08/abs/th23/mc-z.csd > corresponding to a FWHM=8, voxel-wise z-thr=2.3, the sign is both pos > and neg? Actually, the zstats were converted from pearson > correlations, which I want to see both pos and neg relationships. > Another point: is the CSD file designed for fsaverage specifically? I > did analysis on fsaverage5, can I just use this file or have to > resample the surface to fsaverage space? > > Xi-Nian > > On Tue, Dec 13, 2011 at 5:43 AM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu> wrote: > >> If you have a full-width half-max (FWHM) for your analysis, you can convert >> your z into a sig (-log10(p)*sign(z)), then run mri_surfcluster. You should >> give it a CSD file that corresponds to your FWHM, the sign of the contrast >> you are interested in, and the voxel-wise threshold. The CSD files are >> located here $FREESURFER_HOME/average/mult-comp-cor >> doug >> >> >> Xinian Zuo wrote: >> >>> Hi List, I have a question on how to write out the matlab vector >>> containing the Z-statistics and perform subsequent multiple >>> corrections. I already read some functions and know how to write it to >>> a mgh surface file. Here, my question is 'is there any specific things >>> on the header of the surface file, which allows me to do cluster-wise >>> correction (see corrected p-value < 0.025) if there is such a command >>> for that?'. Thanks! >>> >>> >>> >> -- >> 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 >> >> >> >> 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. >> >> > > > > -- 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
