SNR of specific ROIs

[Dmitriy Desser]

Dear all,

i have calculated SNR/tSNR of my fMRI data (resting state) with MRIQC. Now I have to calculate SNR and tSNR values of some specific ROIs related to my study.

Does anybody have an idea how to do it?

Best,

Dima

[oest...@stanford.edu]

Hi Dima,

That is a long-lasting open issue in our road map (https://github.com/poldracklab/mriqc/issues/375 and https://github.com/poldracklab/mriqc/issues/710).

We would very happily accept help to implement it. If you are going to calculate it anyways, why not contributing to MRIQC? I'd assist you through the process.

Cheers,

Oscar

[Dmitriy Desser]

Hi Oscar,

thank you very much! 

is there any possibility to extract mean images and devitation images from mriqc html results report? I want to calculate tSNR maps first, then match them to ROI masks and calculate the mean values with fslmaths. 

Do you maybe have any other ideas on how to do that?

Cheers,

Dima

[Dmitriy Desser]

Hi Oscar,

i have calculated ROI tSNR values for specific ROIs using Harvard-Oxford-Atlas. I have preprocessed my data with fmriprep first. The biggest issue was, that the preprocessed images of fmriprep output are in different space (NI152NLin2009cAsym) as Atlas and images are not skullstripped. So I have coregistered the scull-stripped T1w image to the space of atlas, and then coregistered the functional data using the same matrix. After this it is possible to calculate ROI specific tSNR values with a simple function. 

Could you maybe take a look on my code?

What do you think, if it is a good way to do it? 

Thank you very much!

Cheers,

Dima

[jamy andy]

Hi Dima et al.,

Has there been some updates on this topic? 

I am also interested in extracting various quality metrics from specific ROIs.

Thanks,

Best wishes

J.A.