Hi Doug, thank you very much! I have two follow-up questions for your two suggestions: 1) If I want to use mri_glmfit-sim but my conjunctions are not from contrasts that are all from the same GLM, I guess I can still do what you suggested but I will have to come up with a fwhm.dat for the conjunction, correct? Is there a way to compute this from the conjunction sig map, or should I use the average or the max or the min of the contrasts that go into the conjunction? This is for functional data.
2) It seems that there is a version of mri_mcsim that allows one to specify a range of FWHM with the flag --fwhm-max; however, version 1.17 that comes with the 5.1 and 5.3 releases does bot have that option. Is the version of mri_mcsim that understands --fwhm-max available? Thanks again, Caspar 2013/10/24 Douglas N Greve <gr...@nmr.mgh.harvard.edu> > > Hi Caspar, there are a couple of things you can do: > > 1. Go into the mri_glmfit folder used to create the input contrasts to > the conjunction. Create a subfolder. Save the conjunction as sig.mgz and > create a file called "C.dat" (it can be empty) in this folder. Then run > mri_glmfit-sim specifying to do the simulation rather than using cached > data. > > 2. Create cached data by running mri_mcsim. This may take longer than > #1, but once you have the cached data you do not need to run it again, > which could be useful if you are going to do more analyses with this > template > > doug > > > On 10/23/2013 02:55 PM, Caspar M. Schwiedrzik wrote: > > Hi, > > I have a question regarding cluster size thresholding using > > mri_glmfit-sim. Namely, I have a sig.nii conjunction map that I made > > with mri_concat. > > The analyses that serve as input to the conjunction map are done on a > > custom surface template. > > If I want to run mri_glmfit-sim, how would that work? I obviously do > > not have precached data. > > Thanks, Caspar > > > > > > > > > > _______________________________________________ > > 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. > >
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