Fmriprep output badly misaligned?

1

Hi, I had fmriprep run on a single session dataset (1st time): a T1 and 6 functional scans (each the identical protocol/task). I’ve looked at this data with other tools before, it seemed pretty normal (meaning, I could plot the same post-registration voxel over six scans and see a similar retinotopy stimulus-evoked time course).

This was the command:

fmriprep-docker /Volumes/vision/Data/BIDS/bidsout /Volumes/vision/Data/new_pype/output participant --participant-label sub-01

looking at the html summary output, I see that the first of 6 EPIs is extremely badly misaligned, like nonsense (turned sidewise, rotated 90deg, etc). On that scan I got the message " bbregister refinement rejected". It was rejected also on another scan, which is also poorly aligned but at least in the right universe.

Of the other 4 (bbregister succeeded), three look perfect but one is rather off.

How can I investigate where this went wrong? I used dcm2bids to convert the data this time, could it go wrong there (formatting problem?)?

thanks
-andrew

edit for more detail

What I had done previously that got nice results was a patched-together notebook from this nipype tutorial:

https://miykael.github.io/nipype_tutorial/notebooks/example_preprocessing.html

And the inputs to that were niftis that had been converted using the MATLAB dcm2nii function:

So I thought that since the underlying stuff was mostly the same, the dcm2bids → fmriprep would give similar results.

2

Some more info:
The affine matrices in the (input) niftis all are the same.

These are relatively narrow-angle scans (back of the head).
So I guess that makes the alignment harder.

Here are means of the raw (pre-fmriprep) images:

rawbids
rawbids888×550 322 KB

Here they are after:

preprocd
preprocd1000×622 274 KB

To my eye 3 of those are perfect, two are poor and one (the top left) is very bad. How do I track down the problem?

3

Partial FOV registration is challenging. Which fmriprep version are you using?

You may have a look at this topic and issue therein:

If you are already using the latest fmriprep version, could you try the option --bold2t1w-init header to see if you get some improvement?

1 Like
4

Thanks! I will try it.

The initial alignment is not too far off, I only wish I could tell the registration not to stray too far from the initial affine. But I understand part of the principle of fmriprep is not setting special variables…

Using version v21.0.2.

5

It worked! Maybe it was just luck, but all scans now seem sensibly aligned. Thanks again!

1 Like