Dear Douglas,
Thank you for your reply. I read the related FDR paper given in the “mri_fdr –help”.
Please tell me if the FDR correction in FreeSurfer do like the below.
For the V vertices being tested, the general procedure is as follows:
(1) Select a desired FDR bound q between 0 and 1. This is the maximum FDR that the researcher is willing to tolerate on average and we select q=0.05.
(2) Order the P values from smallest to largest: P(1) ≤P(2) ≤• •≤P(v). Let v(i) be the vertex corresponding to P value P(i).
(3) Let r be the largest i for which: P(i) ≤i/V*q/c(V), where c(V) is a predetermined constant.
(4) Declare the voxels v(1), . . . ,v(r) active, or in other words, threshold the image of test statistics at the value corresponding to the P value P(r).
If I response like this, is it right?
Thank you very much, and looking forward to reply.
Kind regards,
Livia
You should read the FDR paper for more detail. But the FDR is the number of false positives relative to the total number of positives. The way it is interpreted is that when you look at an image, 5% of the voxels above threshold are false. You don't know which 5%. If the 5% came out of a big blob, probably you would not change your conclusion about that blob. If there were a few single voxels that were above threshold, you probably don't want to write your paper around it.
On 4/16/18 11:42 PM, Livia Liu wrote:
Dear Douglas,
Thank you for your reply. I run “mri_fdr –help” to get docs that include some information for how to use this command. However, I still don’t know how FDR was used to correct for multiple comparisons.
This question is an opinion given by one reviewer, and I really don’t know how to reply.
For the description "To correct for multiple comparisons, the thresholds of the P maps were set to yield an expected false discovery rate (FDR) of 0.05." The reviewer said “Would help to provide more details as to how FDR was used to correct for multiple?”
Would you please give me some help to response the question? Thank you very much.
Kind regards,
Livia
2018-04-17 0:40 GMT+08:00 Douglas N. Greve <dgreve@mgh.harvard.edu>:
You can also use mri_fdr Run it with --help to get docs
> ______________________________
On 04/16/2018 10:23 AM, Livia Liu wrote:
>
> Dear FS experts,
>
> I'd like to know that how FDR was used to correct for multiple
> comparisons. I do FDR correction in two way in FreeSurfer.
>
> 1, Do the FDR correction in the qdec tool. And the page of “False
> Discovery Rate” in the page “Multiple-Comparisons Correction in Qdec”
> was lost.
>
> 2, Use “lme_mass_FDR.m” to do the FDR correction in LME model, which
> was based on Tom's FDR.m in the github, however the page was also lost.
>
> Would help to provide more details as to how FDR in the two way was
> used to correct for multiple comparisons?
>
>
> Thank you very much, and looking forward to reply.
>
> Kind regards,
>
> Livia
>
>
>
>
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