help > Change confounds from batch script
Showing 1-5 of 5 posts
Display:
Results per page:
Aug 14, 2019  12:08 PM | Georgia Gopinath
Change confounds from batch script
Hi conn community,

I am wondering if anyone knows how to change which confounds are used when running your analysis with a batch script. I tried setting batch.Denoising.confounds={} but that has not worked.

Thank you in advance!

Georgia
Aug 15, 2019  01:08 PM | Stephen L. - Coma Science Group, GIGA-Consciousness, Hospital & University of Liege
Change confounds from batch script
> Dear Georgia,
>

I recently implemented setting additional denoising confounds in my own
script, you can maybe get inspiration from that:

https://github.com/lrq3000/csg_mri_pipel...


Hope this helps,

Best regards,
Stephen Karl Larroque

Aug 16, 2019  12:08 PM | Georgia Gopinath
RE: Change confounds from batch script
Hi Stephen,

Thank you!

I tried using CONN_x.Denoising.confounds.names = [{'Effect of rest'}, CONN_x.Setup.rois.names] to only regress 1 confound (I am working with rsfMRI data), however I am finding that no matter what is included in the parentheses, White matter +CSF + effect of rest are regressed. Do you have any experience with this?

Thank you,

Georgia
Aug 19, 2019  01:08 AM | Stephen L. - Coma Science Group, GIGA-Consciousness, Hospital & University of Liege
RE: Change confounds from batch script
Dear Georgia,

Did you check what is in CONN_x.Setup.rois.names ? Because it might contain the names of the white matter and CSF, if maybe you try to remove that, this might fix the issue.

Also make sure to set the following:

CONN_x.Setup.rois.add = 0;

If this does not fix the issue, then it might be that the WM and CSF denoising confounds might be hardcoded.

Hope this helps,
Best regards,
Stephen
9 hours ago | Georgia Gopinath
RE: Change confounds from batch script
Hi Stephen,

Thank you again! I realized that the GUI displays white matter, CSF, and effect of rest as the confounds even when they are set differently in the batch script (the actual confounds used are shown in project/results/preprocessing/_list_BETA_denoising.txt). The lines used in your script work perfectly!

Best,

Georgia