I got what I believe are reasonable results from susceptibility distortion correction with fMRIprep version 21.0.2. Here is a snapshot of the fieldmap from the output report with v21.0.2:
And here is a snapshot of the sdc results from the report with v21.0.2:
I got different/unusual results when using v23.0.2 to process the same data. Here is a snapshot of the fieldmap from the output report for v23.0.2:
And here are the sdc results with v23.0.2:
I used singularity containers for both versions of fMRIprep and, other than changing the container/version, I ran the same command to process the same data each time. I was also sure to use a clean working directory with each run.
Does anyone have an idea what might be causing the different results?
May 15, 2023, 3:56pm
In short, SDCflows (the SDC software fMRIPrep uses) has been undergoing some major revisions. You can see the change log here. Without knowing more about your fieldmaps, hard to say much more.
Thanks. We have two magnitude images (one for each echo) and a single phase difference image. It’s odd that the revisions to SDCflows would introduce what look like errors. Hopefully someone else may have encountered a similar issue and can weigh in. I’m also happy to provide any additional information that would be helpful.
May 15, 2023, 7:00pm
This adds to the usual suspect cases of SDC with the phase difference method.
Similar issues were reported here:
@jsein Thank you so much again for your time and the detailed guidance.
I have applied SDC using fMRIPrep LTS v20.2.7 as suggested, the output looks pretty reasonable.
I checked the fieldmap less SDC by including --use-syn-sdc flag with both v23.0.1 and v20.2.7_LTS. It did work fine to some extent for v.20.2.7 but not good for v23.0.1. The outputs are as follows:
synsdc with LTS v20.2.7
synsdc with v23.0.1
I started skullstripping t…
Summary of what happened:
Dear fMRIprep experts,
I previously used the --use-syn-sdc for two sets of data using version 22.0.2 then re-ran the pre-processing after deleting all the output files using the latest version 23.0.1 and noticed that the images are more distorted compared to that using the older version (see attached screenshots below; subject 1 and 2 are from a different group than subject 3 and 4).
Not sure if this is relevant but I previously did not include the --cifti-output fl…
@jsein, it turns out changing only the fMRIPrep version to 20.2.7 led to WAY better distortion correction:
In light of this, I’ll be interested to hear what developers think about next steps.
Thanks for pointing me to the previous threads! This is very helpful.