It sounds like you have reported everything correctly. The clusterwise
p-value corresponds to a critical cluster size at the given cluster
forming threshold (4), sign (neg), and fwhm (fwhm.dat in the glmdir). So
the answer to the reviewer is "yes". If you want to report the critical
size, then look in (if fwhm=10)
$FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex/fwhm10/neg/th40/mc-z.cdf
The MaxClustCDF column gives the the clusterwise p-value and the
MaxClustBin gives the size of the cluster needed to achieve that
p-value. Eg, a p-value of .05 would require a cluster of about 35 mm2.
On 08/08/2017 01:30 PM, Martin Juneja wrote:
> Hi,
>
> One of my papers is under review showing significant differences in
> cortical surface area between healthy controls and patients.
>
> In this paper, regarding statistical results, for multiple comparison
> correction, I ran Monte Carlo simulations using following command:
> mri_glmfit-sim \
>
>--cache 4 neg \
>--cwp 0.05\
> --2spaces
> In the paper, I reported that multiple comparisons were corrected at p
> < 0.05 using Monte Carlo simulations. I also reported cluster sizes
> (number of voxels) of all clusters which survived multiple comparison
> correction.
>
> I checked literature and found that that's how people report cluster
> results after running analysis in FreeSurfer.
>
> One of the reviewers asked- Did you consider any constraints on
> findings (specifically cluster size) before considering the finding
> significant?
>
> Could you please help me in understanding this question and how can
> this be answered?
>
> In this paper:
> http://onlinelibrary.wiley.com/store/10.1002/pbc.25386/asset/pbc25386.pdf?v=1&t=j63uanho&s=7c11176285c624160ccde7b1d93e759e20bc13a9,
>
> authors reported that -
> "The data were tested against an empirical null distribution of
> maximum cluster size across 10,000 iterations using Z Monte Carlo
> simulations as implemented in FreeSurfer [31,32] synthesized with a
> cluster-forming threshold of P < 0.05 (two-sided), yielding clusters
> fully corrected for multiple comparisons across the surfaces.
> Clusterwise corrected P < 0.05 (two-sided) was regarded significant."
>
> I assume that that's what reviewer is demanding me to report in my paper.
>
> I would really appreciate any help.
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
