fMRIPREP registration issue for single run


Upon inspection, registration between the functional and anatomical image seems to be failing for 1 run (of 12). The BOLD data looks shifted/cut off when overlaid (see attached photo). This is only occurring for 1 run, and the raw data for the run looks normal.

Has anyone encountered this issue? If so, do you recommend re-running everything again, or is there a specific step I should target?


Can you upload the co-registration reportlet as generated by fMRIPrep?


Do you mean the .html visual report? If not, where should I look for this? Thank you!


Either the .html report (with the figures folder with is located at sub-<id>/figures/) or the figure about coregistration (you’ll find a link to it in the html report under the figure).


Hi Oscar,

I put the zipped files on google drive- let me know if you have any problems accessing them:

The run in question is Session 3, Run 1. Thanks!!



Okay, you can see the same problem in the reports for task-HSR_run-01 so we can rule out a visualization issue.

Could you check for differences in the headers of run-01 and run-02 of that task?


The only difference in the nifti headers between runs is in the minimum and maximum display range of the image intensity. This differs between all runs though, and doesn’t seem a likely culprit.

The orientation and the translation are the same across runs.


I redownloaded the data from flywheel, double checked all the json files and verified BIDS formatting, ran again last night-- same outcome. Let me know if you have any thoughts on how to troubleshoot this!

Thank you so much!


Yes, I’m not surprised by that.

Could you 0) backup your data; and 1) copy the nifti header from a functioning file?

We’ll probably want to add a check on the field causing this behavior.


I’ve uploaded a single volume from the problematic run, and one from a run that looks normal:

Let me know if you need anything else, and what I can do from here. Thank you!


Just fetched the data. Will look into this tomorrow. Sorry for the slow response.