you can't really do permutation at the first level because the temporal
autocorrelation and non-orthogonal design matrix violate the permutation
assumptions.
On 5/15/17 11:23 PM, Kevin Aquino wrote:
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
<mailto:kevin.aqu...@nottingham.ac.uk>, aqu...@physics.usyd.edu.au
<mailto:aqu...@physics.usyd.edu.au> | *W* *MailScanner has detected a
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On Tue, May 16, 2017 at 12:34 PM, Kevin Aquino
<aqu...@physics.usyd.edu.au <mailto: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
<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
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