Extracting ROIS in fsl after Mumford workaround of fmriprep

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Hi all,
I would like to ask a similar question to this old thread, as I am running with exactly the same problem: FSL featquery with fmriprep'd data - #2 by gspitz

I have preprocessed my data with fmriprep and did the Mumford workaround for the sake of group analysis. Now I want to extract ROIS. However, the files needed for that were erased as part of the workaround. This results in the following error: “Error - transform to take mask into space of example_func does not exist in the FEAT directory - run FEAT registration”

In this thread, it says that if I run “updatefeatreg script” after the workaround, I can generate the required files.
Does anyone knows what is this script and where can I find it?

Thank you very much,
Lior

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It looks like updatefeatreg is a utility in your FSL installation already, so you should be able to run it on your data by invoking updatefeatreg <inputdir> -options (see FEAT/FAQ - FslWiki)

1 Like
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Thank you! it worked and I managed to extract the ROI.

But now I have a follow-up question:

After regenerating the example_functostandard.nii.gz file, the mean_func files in the stats folder and the reg_standard folder are not the same anymore. This is in contrast to Janet Mumford’s explicit warning that after the workaround, we should triple check that these files are the same (I used the fslhd to check it).

So, is it valid to do the whole-brain group analysis with the mumford workaround, and then to extract ROIs with different mean_func files? can we say that the whole-brain analysis and the ROI analysis are comparable in such a case?

Thank you,
Lior