I don't know of a tool that would do it. I could imagine measuring the spatial autocorrelation function, then running the MC simulation using that instead of a gaussian (AFNI added this, but it only runs in the volume). Getting a particular ACF on the surface would be hard.
On 05/16/2017 08:00 PM, Kevin Aquino wrote: > Hi Doug, > > Thanks for that! with regards to your last point > > Unfortunately, it does not help much. Much was made of the bug > that Eklund, et al, found in the alphasim program (the AFNI mc > simulator), but even after fixing it, the volume-based analyses > still had very high false positive rates. This is because the > problem is that the smoothness in the data is not Gaussian, so any > method that assumes Gaussianity will be inaccurate. > > > From what I read, the MC simulations on the surface uses this Gaussian > assumption. Do you have any ideas (or something in the works) on how > to handle these issues on a single subject level? - since the > permutation test won't be applicable. > > > Cheers, > > > *Dr Kevin Aquino* > Research fellow, > Sir Peter Mansfield Magnetic Resonance Center, The University of > Nottingham. > > Honorary Research Fellow > School of Physics, Faculty of Science, University of Sydney > > *E* kevin.aqu...@nottingham.ac.uk > <mailto:kevin.aqu...@nottingham.ac.uk>, aqu...@physics.usyd.edu.au > <mailto:aqu...@physics.usyd.edu.au> | *W* *MailScanner has detected a > possible fraud attempt from "www.physics.usyd.edu.au" claiming to be* > https://kevinaquino.github.io <http://www.physics.usyd.edu.au/%7Eaquino/> > > ---------------------------------------------- > > The brain is a wonderful organ. It starts working the moment you get > up and does not stop until you get into the office. > - > Robert Frost > > CRICOS 00026A > This email plus any attachments to it are confidential. Any > unauthorised use is strictly prohibited. If you receive this email in > error, please delete it and any attachments. > > Please think of our environment and only print this e-mail if necessary. > > > On Wed, May 17, 2017 at 1:18 AM, Douglas Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > On 5/15/17 10:34 PM, Kevin Aquino wrote: >> Hi all, >> >> First of all, Freesurfer V6 is working like a dream, my 0.7 mm >> segmentations are running really well and in comparisons to >> hi-resrecon in 5.3 and early beta, I'm having to do fewer manual >> corrections! >> >> >> Now for my questions, >> >> 1. I'm running mri_mcsim in order to correct for multiple >> comparisons via the FS-FAST stream. I'm wondering how many >> iterations are advised, and how can one check for convergence in >> an automatic fashion. >> >> I've run the simulations with 1000 and 10,000 iterations on a 1mm >> segmentation with the FWHM simulations at 8mm. (i.e. >> using mri_mcsim --o . --base mc-z --save-iter --surf subject >> lh/rh --nreps 10000 --fwhm 8) and I can't see many differences >> between the two when correcting for multiple comparisons (i.e. >> using cluster-sess -analysis myanalysis -thresh 3 -cwp .05 -s >> SESSION -sign pos). > For the tables hat we distribute I ran it to 10,000, but there > will probably not be much difference with 1000. If you look in the > cluster summary file, it will actually give the 95% confidence > intervals on the cluster p-values. If the worst is ok, then you > don't really need to run it more. >> >> 2. I'm trying to find some references that detail the simulations >> and form the corrections, does anyone have advice which list I >> can read/start off with, as well as some key papers that use it >> (esp on a single subject level). > You can check out "Smoothing and cluster thresholding for cortical > surface-based group analysis of fMRI data" by Don Hagler >> I really like this approach and It does look to circumvent (I >> think...) a lot of the problems of cluster-wise corrections >> described with Eklund et al. (Cluster failure paper). > Unfortunately, it does not help much. Much was made of the bug > that Eklund, et al, found in the alphasim program (the AFNI mc > simulator), but even after fixing it, the volume-based analyses > still had very high false positive rates. This is because the > problem is that the smoothness in the data is not Gaussian, so any > method that assumes Gaussianity will be inaccurate. > doug >> >> Cheers, >> >> >> *Dr Kevin Aquino* >> Research fellow, >> Sir Peter Mansfield Magnetic Resonance Center, The University of >> Nottingham. >> >> Honorary Research Fellow >> School of Physics, Faculty of Science, University of Sydney >> >> *E* kevin.aqu...@nottingham.ac.uk >> <mailto:kevin.aqu...@nottingham.ac.uk>, >> aqu...@physics.usyd.edu.au <mailto:aqu...@physics.usyd.edu.au> | >> *W* *MailScanner has detected a possible fraud attempt from >> "www.physics.usyd.edu.au" claiming to be* >> https://kevinaquino.github.io >> <http://www.physics.usyd.edu.au/%7Eaquino/> >> >> ---------------------------------------------- >> >> The brain is a wonderful organ. It starts working the moment you >> get up and does not stop until you get into the office. >> - >> Robert Frost >> >> CRICOS 00026A >> This email plus any attachments to it are confidential. Any >> unauthorised use is strictly prohibited. If you receive this >> email in error, please delete it and any attachments. >> >> Please think of our environment and only print this e-mail if >> necessary. >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > _______________________________________________ Freesurfer mailing > list Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <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. > > _______________________________________________ > 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
