fMRIPREP registration issue for single run

fmriprep
#1

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?

#2

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

#3

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

#4

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).

#5

Hi Oscar,

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

https://drive.google.com/file/d/1lGQi5ChKdgjQv56n1RlMdnx-MkdaqfJ8/view?usp=sharing

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

Corey

#6

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?

#7

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.

#8

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!

#9

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.

#10

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

https://drive.google.com/open?id=1H7v4I_x3UwifKrvixL6yzuzzTCwrIiwR

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

#11

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