On 10/17/16 2:16 AM, Ajay Kurani wrote:
Hi Doug,
I had some additional questions regarding multiple comparisons in
Freesurfer.
1) Do you correct the left and right hemispheres separately or combine
both together for muliple comparison correction?
We correct each hemi independently and then bonferroni correct both. Eg,
if you have a cluster in the left hemi that has a pvalue = .01, then we
would multiply the pvalue by 2 to account for both hemis. When you run
mri_glmfit-sim with --2space, it will do this for you automatically.
2) Say you are testing multiple contrasts in your model: A > B, A< B
etc. Do you correct for multiple contrasts and if not, is there any
particular reason why not.
I think you should, but most people probably don't. This is an unsigned
test. In FS, you would specify "abs" as the sign (absolute, vs pos
(positive) or neg), and FS will do the right correction. In other
packages, eg, FSL, you must specify an F-test (even then it might not do
the right thing).
Thanks,
Ajay
On Wed, Aug 3, 2016 at 2:45 AM, Ajay Kurani <dr.ajay.kur...@gmail.com
<mailto:dr.ajay.kur...@gmail.com>> wrote:
Hi Doug,
Thank you very much for your update regarding this issue.
1)Just curious, will LGI be included in this report as this is
another analysis of interest?
2)As for the cortical thickness I originally used 15mm in the
analysis so based on your email I think using 5-10mm may be more
prudent in order to minimize FPR. From your email, I understand
that mris_surf2surf (command I use to convert individual subject
to fsaverage or template and smooth to 10-15mm) assumes an ACF
estimation of smoothness which DOES NOT take into account the long
tail distribution. Does this mean that when using mri_mcsim on my
own template, the cluster extents for a given smoothness will be
undersampled due to the fact that the "true" smoothness is more
than what is estimated in the simulation, correct? For instance,
when I select 15mm in qdec, it would point to the 21mm folder
(fwhm.dat=20.8mm estimate), and I would select a given cluster
extent for p=0.05. However, in this case, 15mm may translate to a
larger FWHM than the estimated 21mm, correct?
3)You mentioned that I can use mri_glmfit-sim which is permutation
testing based. I am struggling a bit in understanding how this
differs from the simulation ran with mri_mcsim/qdec? Does qdec
monte carlo simulation option run mri_glmfit-sim in the background
to estimate the smoothness which looks up the cluster extent
within the mri_mcsim based on the estimated FWHM? If so, is this
estimate incorrect due to the fact that the long tails are not
taken into account?
Thanks,
Ajay
On Mon, Aug 1, 2016 at 11:43 PM, Ajay Kurani
<dr.ajay.kur...@gmail.com <mailto:dr.ajay.kur...@gmail.com>> wrote:
Hello Freesurfer Experts,
Recently there were two article published regarding
clusterwise simulations for volumetric fmri analyses and
potential errors for underestimating clusterwise extent
thresholds.
1)
http://www.pnas.org/content/113/28/7900.full.pdf?with-ds=yes
<http://www.pnas.org/content/113/28/7900.full.pdf?with-ds=yes>
2) biorxiv.org/content/early/2016/07/26/065862
<http://biorxiv.org/content/early/2016/07/26/065862>
One issue pointed out from these articles seems software
specific, however the second issue is determining the proper
clustersize. The heavy-tail nature of spatial smoothness seems
to be ignored and a gaussian shape is generally assumed,
leading to an underestimation of the spatial smoothness which
can affect cluster size calculations. The issues are
highlighted in the second article above.
I created my own monte carlo simulation in Freesurfer for a
specific brain template and I wanted to find out if these
concerns also apply to my surface based simulations? I am not
sure if it does since the monte carlo tool is a GRF simulation
as opposed to an analytic equation, however given that these
articles were highlighted very recently, I wanted to ensure I
am running things appropriately for surface based cortical
thickness/dti analyses.
Thanks,
Ajay
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