I’m trying to use fieldmap-free distortion correction in fmriprep, via the --use-syn-sdc flag, but it doesn’t seem to be working.
Has anyone come across a similar error? fmriprep output doesn’t raise any type of warning or error, as far as I can tell (the output is quite verbose, so I search for ‘distortion’ and ‘B0’ to check, but I also don’t get any other warnings or errors related to this issue).
I’m using fmriprep version 22.0.2 via singularity on a cluster.
Thanks for the quick reply, Steven! My answers to your questions below…
Does fMRIPrep finish?
Yes, it finishes and does not report any errors. It does not mention the SYN SDC method in the method section. It explicitly states no SDC was applied in the preprocessing for each functional run.
v23 stable release behavior
Wouldn’t know, we only have the 22.0.2 .sif container file available to us at my institution
phase encoding direction
In case it helps, data were converted using dcm2bids
completely BIDS valid
I’ll triple check this, but yes, they are.
I didn’t mention this before but it’s worth bringing up now, I guess – I do have fieldmaps for this dataset. fMRIPrep would process the field maps (indicated in the HTML output) but not use them for SDC. I have the ‘intended for’ field in their .json files filled out (tried it a couple different ways based on publicly available examples and other posts in this forum), but it still wasn’t working. So I’m trying to switch over to the SYN method.
It appears you have singularity installed, is there any reason you cannot install your own container with singularity build fmriprep_23.1.4.sig docker://nipreps/fmriprep:23.1.4?
In the JSON is it explicitly defined under the field called PhaseEncodingDirection? This would really be more of a factor of the dcm2niix version, not dcm2bids (although I imagine any version of dcm2niix released in the past 5 years shouldn’t be messing this simple field up). dcm2niix, especially older versions, can be weird on GE scanners - does that apply to you?
I believe IntendedFor errors are included in the BIDS validation report, so sharing that report would be helpful. If fieldmaps are present, they will be favored ahead of SDC unless if --force-syn is on. So I wonder if fMRIPrep wants to use the fieldmaps, for some reason can’t, so is instead not doing any SDC.
Are your fieldmaps GRE or SE? GRE fieldmaps have been a bit hit-or-miss since v21, but work well in the long-term support branch (20.2.7). SE should work fine (in fact, better), on v23.
It’s not obvious why that’s needed for SyN-SDC, which calculates displacements directly, but the reason is that we go a step further and estimate the fieldmap from the displacments, which requires a readout vector. We could just make up a number, but then we would need to be sure to be able to determine what that number was when applying the fieldmap.
Assuming this is the problem, you can just stick in a fake TotalReadoutTime. 0.03125 is a power of two that’s conveniently close to a plausible readout time. But you should definitely make a note somewhere that this is fake and no algorithms that require a true value should rely on this.