Thank you!
Date: Mon, 21 Sep 2015 23:43:39 -0400
From: gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Question about the multiple comparison correction in
FreeSurfer
On 9/21/15 9:15 PM, chenhf_uestc wrote:
Hi, Douglas
Thanks for your reply. I have two further questions here.
First, I know that
--grf is gaussian random fields for the volume (not surface). Could
the Monte Carlo simulation such as "--cache 4 neg" be used for
correction on volume? Because the manual introduces this method
for the correction on surface, and thus I do not whether this
method could be used on volume.
Yes, I think that should work. If you are going to run simulations
on the surface, see
https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo
Second, in the Monte Carlo simulation on surface
"--cache 4 neg", I can specify the sign (neg for negative, pos,
or abs). However, in the grf correction, there are "--grf 3 pos or neg
". Could I
specify the sign "abs" such as "--grf
3 abs".
No, sorry
Best,
Feng
发件人：Douglas N Greve
<gr...@nmr.mgh.harvard.edu>
发送时间：2015-09-22 05:35
主题：Re: [Freesurfer] Question about the
multiple comparison correction in FreeSurfer
收件人："freesurfer"<freesurfer@nmr.mgh.harvard.edu>
抄送：
--grf is gaussian random fields for the volume (not surface).
Re: --2spaces, your understanding is correct.
FDR: you can do it in matlab, something like
sig = MRIread('sig.mgh');
p = 10.^-abs(sig.vol)
pthresh = fast_fdrthresh(p,fdr);
ind = find(p < pthresh);
sig.vol(ind) = 0;
MRIwrite(sig,'sig.fdr.mgh')
It is also possible with mri_surfcluster
On 09/20/2015 12:47 PM, chenhf_uestc wrote:
> Dear Freesurfer experts,
> I have some questions about the multiple comparison correction
method
> for group analysis in Freesurfer. The manual stated that we could
use
> the commands as follows:
> mri_glmfit-sim \
> --glmdir lh.gender_age.glmdir \
> --cache 4 neg \
> --cwp 0.05\
> --2spaces
> This is the alphasim correction, right? When I write this command
in
> terminal, there are detailed explanations about this command. In
the
> above-mentioned command, I used parameter "--cache threshold sign".
In
> this way, a precomputed Z Monte Carlo simulation (--cache) was
used.
> Also, I can run my own simulation by using "--sim mc-z
> iterations threshold".
> However, I find an interesting parameter "--grf threshold sign". I
> would like to know whether this parameter could give me another
> correction method rather than alphasim, i.e. the gaussian random
field
> correction method? In other words, if I add the parameter "grf",
then
> the mri_glmfit-sim performs the GRF correction; if I do not add
this
> parameter, then mri_glmfit-sim performs alphasim correction, right?
> Another question is about the parameter "--2spaces: adjust p-values
> for two hemispheres", I give an example here. I want to perform
> cluster-level correction of *p<0.05* based on vertex-wise thershold
of
> 4 (p < .0001) for the left hemisphere; and perform the same
correction
> for the right hemisphere. So, I should add the parameter
"--2spaces".
> Is this equal to perform cluster-level correction of *p<0.025
(0.05/2,
> if I also want to examine the subcortical diferences, then the
cluster
> p value should be 0.05/3)* based on vertex-wise thershold of 4 (p <
> .0001). Have I understood correctly?
> The third question is that could I perform False discovery rate
(FDR)
> using commands rather than GUI? If not, could I load the sig.mgh
file
> into MatLab and then perform FDR correction manually?
> In addition to the aforementioned multiple comparison correction
> method, is there other correction method in Freesurfer?
> Best,
> Feng
>
>
> _______________________________________________
> 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/
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The information in this e-mail is intended only for the person to whom it is
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