Weird brain mask in FMRIPREP report

fmriprep

#1

Dear Experts

I got strange brain mask in ROIs in BOLD space part of the report. There are several different tasks for this subject, and only the 2 runs of one particular task in this subject shown very strange red contour pattern on the right-uppermost of the figures. Attached is one of them.

Any advice or possible influence of this on the confounds and AROMA procedure?

Thank you very much!

Best regards,
Chen-Chia


#2

By the way, I am running with version 1.0.15.
These strange shaped red contours were also shown in other subjects as well. These contours are not shown in the corresponding brainmask.nii.gz.

Thank you very much!


#3

Hi! Thanks for the report. Our current hypothesis is that it’s just a plotting issue. Your confirmation that it does not appear in the brainmask.nii.gz itself is consistent with this.

So I don’t think you need to worry about this, for the time being, but we’ll still be fixing it when we can. If you’re interested in trying your hand at a fix, we would welcome a pull request! (This particular code will be in niworkflows.)


#4

I had this issue too, and not just with the brain mask but also with the T1 segmentation (and no sign of it in the actual image). Thanks for the clarification! Had me worried for a while.