Not sure what Tom would do, but in
https://github.com/CPernet/spmup/blob/master/plot/gp_event_plot.m
<https://github.com/CPernet/spmup/blob/master/plot/gp_event_plot.m>
I compute and plot the 95% CI of the mean parameter estimates inside
blobs - if that helps
> Hi Jeff,
>
> Now is time to phone a friend. Tom, how do you appease editors here?
>
> Best regards,
> Guillaume.
>
>
> On 09/02/2021 17:55, Jeff Browndyke wrote:
>> Hi, Guillaume.
>>
>> We ran a standard GLM with a peak voxel threshold of p<0.001 and cluster threshold of pFWE<0.01 in CONN looking for group differences in one of the whole brain voxel-wise functional connectivity metrics. The journal is is requesting CI for any stated p-values, so in this case I took it to mean the CI for p-values reported for cluster extent significance (e.g., cluster A extent k=459, p-FWE=0.003).
>>
>> Warm regards,
>> Jeff
>>
>>
>>> On Feb 9, 2021, at 12:26 PM, Guillaume Flandin <[log in to unmask]> wrote:
>>>
>>> Dear Jeff,
>>>
>>> It seems that for the script you are mentioning, one could nowadays
>>> directly call spm_graph.m. Concerning confidence intervals for
>>> cluster-level inference, are you looking for CI on the cluster extent?
>>> If so, it might not be easy, but see e.g. this:
>>> https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.sciencedirect.com%2Fscience%2Farticle%2Fpii%2FS1053811919307785&data=04%7C01%7C%7C8c0049706e0e4903b55108d8cd23dc46%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637484901195944274%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=E1rfGwfXALm2YZo0wjvRLMi263FH0jZ1WKNingaso%2F8%3D&reserved=0
>>> When you say "thresholded @ p-FWE<0.01", what was the cluster-forming
>>> threshold?
>>>
>>> Best regards,
>>> Guillaume.
>>>
>>>
>>> On 09/02/2021 13:38, Jeffrey Browndyke wrote:
>>>> SPMers,
>>>>
>>>> I have used the following scripts in the past to derive std err and
>>>> confidence intervals for peak voxel results:
>>>>
>>>> https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fimaging.mrc-cbu.cam.ac.uk%2Fimaging%2FExtracting_beta%252C_standard_error_and_confidence_interval_for_a_coordinate&data=04%7C01%7C%7C8c0049706e0e4903b55108d8cd23dc46%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637484901195944274%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=WEym1XB3tW3D5DlvaRSeohBgNrSHR5VnU0Fc31%2BP6K8%3D&reserved=0
>>>> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fimaging.mrc-cbu.cam.ac.uk%2Fimaging%2FExtracting_beta%252C_standard_error_and_confidence_interval_for_a_coordinate&data=04%7C01%7C%7C8c0049706e0e4903b55108d8cd23dc46%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637484901195944274%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=WEym1XB3tW3D5DlvaRSeohBgNrSHR5VnU0Fc31%2BP6K8%3D&reserved=0>
>>>>
>>>> But, we are being asked to provide confidence intervals for the
>>>> cluster-level significance for blobs in one of our analyses (thresholded
>>>> @ p-FWE<0.01).
>>>>
>>>> Any pointers or guidance on where to find or how to derive this info?
>>>>
>>>> Thanks,
>>>> Jeff Browndyke
>>>>
>>>> Sent from my iPhone
>>> --
>>> Guillaume Flandin, PhD
>>> Wellcome Centre for Human Neuroimaging
>>> UCL Queen Square Institute of Neurology
>>> London WC1N 3BG
--
Dr Cyril Pernet,
Centre for Clinical Brain Sciences (CCBS)
Neuroimaging Sciences
[log in to unmask]
https://cpernet.github.io/
|