Can you run RABIES preprocessing with only BOLD images and without T2 scans?

[geowk]

Hello,

1. Is it possible to run RABIES preprocessing without T2 scans for a group of subjects. This involves mouse data, but a general question for rat data as well. We have the Allen Brain template, but no T2 structural images in native space.

2. In another scenario we have 10 mice to preprocess, and for 1 of the mice, the T2 has an artifact and can't be used for preprocessing. Is there a way account for this one missing T2 scan with regard to the co-registration and normalizing to the Allen Brain template to still include that dataset for group analysis?

Thanks.

g.

[Gab-D-G]

Hi,

1. it is possible to use RABIES without anatomical images by using the --bold_only option https://rabies.readthedocs.io/en/latest/preprocessing.html#adapted-workflow-without-structural-scans-i-e-bold-only . You can also use T1 scans instead of T2.
2. Unfortunately, RABIES currently assumes that all images preprocessed at once have an anatomical scan (unless using --bold_only). This scan without a T2 could be processed seperately from the rest of the images, but it would not be possible to use the built-in analysis options in RABIES (e.g. group ICA), although you could pull together all the outputs after the confound correction stage to conduct your own analysis. If you do, you will want to make sure that the same commonspace target was specified for all scans (e.g. specify the Allen brain template both for the execution with T2s and without T2s using --bold_only).

I hope this helps,
Gabriel DG

[geowk]

Great, Gabriel.

Thank you for the suggestions.

-g.