I am using fMRIPrep with fieldmap-based susceptibility distortion correction. I’m wondering if you could provide some insight into the output for one subject. Screenshots can be found here
I’m having trouble telling if the SDC around the OFC/midline looks correct, as well as the BOLD mask at x=0. For the mask, is the deviation of the red line into the brain at x=0 an issue, or does it look the way it does because it is the midline? I’ve included the alignment image for additional reference.
Any insight would be appreciated.
What version fMRIPrep are you using? I think in recent versions there should be a red outline in the reports which show brain boundaries based on the T1. SDCflows was also revamped in v21+.
Thanks for the response. This dataset was processed using version 20.2.3. Do you know whether the FreeSurfer outputs could be reused if I update versions and re-process?
For v21, yes, but v22 uses FreeeSurfer 7.2 (not freesurfer 6 like previous versions). Perhaps try v21.0.2?
Recently, I ran the newest version of the fMRIprep (22.0.0) on the data which was previously preprocessed with 20.2.6. With the older version, the output looked perfectly fine. However, with the newest version the “corrected” data after the distortion correction looks much worse than the original input. The shapes are stretched out (please find attached the example of my output below). The number of motion outliers is very little so it’s unlikely that these effects are due to the excessive movement of the subject.
The command I use is: datalad containers-run -m “run fmriprep on sub-002” -i “BIDS/sub-002/" -o "derivatives/fmriprep/sub-002” -n pipeline/fmriprep BIDS derivatives participant --participant-label 002 --fs-no-reconall --fd-spike-threshold 0.9 --dvars-spike-threshold 2 --verbose --output-spaces MNI152NLin2009cAsym:res-2 --ignore fieldmaps --use-syn-sdc
Moreover, it takes multiple hours to finish running the fMRIprep for one subject, whereas before it used to be 1h.
Could please please advise how can I solve the issue of the distortion correction not working well? Is it correct that the newest version takes so long?
Thank you for your help!
Here’s the version after distortion correction