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Nirstorm / nirstorm

Brainstorm plugin for fNIRS data analysis
GNU General Public License v3.0
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GLMs on the different level #133

Closed GuyRens closed 4 years ago

GuyRens commented 4 years ago

Hi,

I was wondering whether someone could help me with getting started on performing GLM's on fnirs data as I have little experience with neuroimaging in general.

I already noticed that there is a tutorial on this, although it is still in progress. https://github.com/Nirstorm/nirstorm/wiki/%5BWIP%5D-GLM

Also, I found a training a few months back at the developers' university. I was wondering whether there are slides of the GLM's which could be shared? https://www.concordia.ca/research/perform/research/events/nirstorm-training-20200129.html

In sum, the questions I have is: Could someone briefly explain me how to get started on the different GLM's that are accessible in the Nirstorm menu of the pipeline editor?

Many thanks in advance

Guy

GuyRens commented 4 years ago

Dear all,

I found out how to do so based on the mini courses (2018 and 2020). But I had one more question: In the mini course of 2020 (https://github.com/Nirstorm/nirstorm/wiki/NIRSTORM-Mini-Course-2020-%28PERFORM-Center%29) it is stated about the group GLM

Note: In this process, we assume that the montage is consistent across the subject. (eg the montage is the same for each subject). This process will only keep the non-bad channel from all the subjects. If you are using a different montage for each subject or have missing channels, we recommend you to project the concentration variation on the cortex before doing the GLM.

My question is: How can you perform the GLM on the projected concentration variation? And if you can calculate the GLM this way, does this mean you can do significance plotting in the 'brain space' and not signal space?

Edouard2laire commented 4 years ago

Hi. Sorry, I am currently rushing for OHBM poster deadline in two days :)

My question is: How can you perform the GLM on the projected concentration variation? And if you can calculate the GLM this way, does this mean you can do significance plotting in the 'brain space' and not signal space?

The main idea is to reconstruct the time course along the cortical surface using MNE. Then you can use GLM normally on the map obtained. The only difference is that you definitely have to correct for multiple comparison when performing the Student t-test. Bonferoni might be too strict as it assume all test are independent. FDR seems good option here.

GuyRens commented 4 years ago

thanks for the help! I made it work