Hi Doug, Thank you for the custom permutation script; it is very helpful.
However, it is still not clear how to use mri_mcsim to create tables with different thresholds. I understand how to use it to restrict the search space and how to use it on different subjects, but I don't see any option for specifying different thresholds. Is there a specific option in mri_mcsim for doing this? Thank you, -Andy ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve <gr...@nmr.mgh.harvard.edu> Sent: Thursday, September 7, 2017 5:55:30 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cluster-Defining Threshold of p=0.025 If you want to use that threshold, you will have to create tables for that threshold using mri_mcsim. See https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo Alternatively, I have a version of mri_glmfit-sim that will run permutation with non-orthogonal designs. https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_glmfit-sim This is the direction I'm pushing people in. To run it, use the normal permutation options and add --perm-resid This uses the ter Braak method. Run mri_glmfit-sim --help to get more info On 09/07/2017 11:05 AM, Jahn, Andrew wrote: > Hello, > > Is it possible to use cluster-defining thresholds such as p = 0.025 > with mri_glmfit-sim? (This would roughly correspond to a negative log > value of 1.6.) My design doesn't allow the use of permutations for > simulating cluster sizes, so I have to use the mczsim option; however, > from what I can tell it doesn't allow using any non-cached options. > > > Thanks, > > -Andy > > > > _______________________________________________ > 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<http://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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=DwIBAg&c=cjytLXgP8ixuoHflwc-poQ&r=h-S9eBUOU6jgx_fyX6Af8TeTt7dGNPjG7qjp2Qe-zMs&m=7dwQJDogv4w-2-MgP5exf4vmnDjsQooz0tQsUyZRkFk&s=8S0l8EjW9GU0a0bo8j1jLq0yijKG3KYh7lr-RArddLQ&e= . 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.
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