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*
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