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.aquino@nottingham.ac.uk, aquino@physics.usyd.edu.au | *W* https://kevinaquino.github.io http://www.physics.usyd.edu.au/~aquino/
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On Tue, May 16, 2017 at 12:34 PM, Kevin Aquino aquino@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,
- 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).
- 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.aquino@nottingham.ac.uk, aquino@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
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