Individual preprocess steps?

[colon-perez]

I am working on preprocessing my data and wanted to know if there is a way to select certain options for specific datasets and others for the rest. I am struggling with two data sets for the BOLD. I figured out the parameters for the anat file, and they all look pretty good in my opinion (result of anat inho cor)

Then, most of the bold inho cor look like this (pretty good in my opinion)

But one keeps coming back like this (pretty bad)

This affects the RAS_autobox_inho_cor_registration

and the registration between bold and anat (all others look good)

I am trying to find a set of parameters that would work, but to no avail. This dataset has been dealt with in the same way as the others, and one run did well for this dataset but did not work for another. I re-ran it, and it won't work. So, any potential insights will be greatly appreciated. I have tried auto-box, using all different registration steps. I am currently trying affine since that one worked once before, but it does not seem to work anymore.

[Gab-D-G]

Hello, have you tried the --bold_robust_inho_cor option? I believe it is most likely to help your case. Note that this increases computational time, as an additional data driven template is generated from the BOLD images.

[colon-perez]

Thanks! I ended up figuring it out. It took just a few iterations to fix it, but yes, the bold_robust_inho_cor option fixed it, along with other minor changes. That was one of my first attempts, and it still failed, so I never tried it again. Now, I'm working on finalizing the analysis.

[Gab-D-G]

Amazing, glad to hear you found a way!