Actually, would would be preferable would be running a permutations test something that you describe in:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg49846.html is there an easy to run mri_glmfit-sim's permutation simulations on a single subject? I've run through the FS-FAST pipeline mkanalysis-sess -fsd bold -surface self rh -fwhm 4.5 -event-related -paradigm attn.par -nconditions 4 -spmhrf 0 -TR 1.9 -analysis myanalysis -per-session -refeventdur 450 -force -nuisreg moco.txt -1 -polyfit 0 mkcontrast-sess -analysis myanalysis -contrast attn -c 1 -a 2 -a 3 -c 4 selxavg3-sess -s SESSION -analysis self_attn_sm_reg.rh -no-preproc -fwhm But mri_glmfit-sim is expecting the output from mri_glmfit mri_glmfit-sim --glmdir . --perm 1000 3 pos --log ./selxavg3.log >> ERROR: cannot find ./mri_glmfit.log should I just run mri_glmfit with the appropriate flags, or is there a mri_glmfit-sim version for data that has passed through selxavg3 ? 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, aqu...@physics.usyd.edu.au | *W* https://kevinaquino.github.io <http://www.physics.usyd.edu.au/~aquino/> ---------------------------------------------- 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 Tue, May 16, 2017 at 12:34 PM, Kevin Aquino <aqu...@physics.usyd.edu.au> 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). > > 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). 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). > > 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, 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/~aquino/> > > ---------------------------------------------- > > 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 > 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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