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 MailScanner has detected a possible fraud attempt from "www.physics.usyd.edu.au" claiming to be https://kevinaquino.github.io

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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,

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.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

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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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