It is more straightforward if you use -log10(p). If you want to do an unsigned test, then run it twice, once with pos and once with neg, then multiply the resulting cluster-wise p-values by 2. doug
On 10/21/2014 02:11 AM, Joo Tan wrote: > > Hi > > > I have a few questions regarding the use of “mri_volcluster” for > clusterwise thresholding. Essentially, we have a volume of pvalues > obtained from a two tailed t-test comparing beta values from condition > A vs condition B. > > When I ran this command: > > mri_volcluster --intransformedP.nii --sum cwthres_sum.txt --sign abs > --fwhm 6--mask avgmas.nii --cwpvalthresh 0.05--thmin 2.3 --cwsig > cwthresclusters.cwsig.nii > > I got this error message: > > ERROR: you must specify a pos or neg sign with --fwhm > > Input was –log10(p-value) > > Thmin was –log10(primary p threshold) > > Is there a way to perform clusterwise thresholding on results from two > tailed tests? Is it essential to use –log10(p) values as input? Can I > use raw t-values or any other values as input and thmin instead? > > Finally, are there any papers/references which this command is based on? > > > Many thanks! > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list 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.
