Matt Cieslak

@smeisler are you using the pyAFQ recon workflow in qsiprep on your HCP data? Or standalone PyAFQ? If it's through the recon workflow there may be a y-flip in the...

Hi @pmd84, are your run-1 and run-2 scanned with the same PhaseEncodingDirection and TotalReadoutTime? If not, they are in different distortion groups and will be processed differently. Also, you'd officially...

aha! The fieldmap file can have `"IntendedFor": ["dwi/run-1.nii.gz", "dwi/run-2.nii.gz"]` with the actual file names. This will result in both runs being distortion corrected and possible concatenated

Happy new year to you too! The first place I usually check is whether the `bids-validator` works. If so, I wonder if your epi fieldmap has the same phase encoding...

Hi @araikes, DWI masking has been a tricky problem. The final mask that gets written out is a combination of the T1w mask and the DWI mask qsiprep calculates. In...

It does, but you have to specify that pybids shouldn't try to validate the file names

I'm not sure what's happening here exactly, but it may help to use a new working directory with `-w` just in case there are some stale or missing files from...

are you running this on a system with memory limits? Is it in a docker or singularity container?

@julfou81 are you sure that the `IntendedFor` fields in your fieldmap BIDS are pointing to the correct image? I think you are running into a separate problem

@julfou81 just so you're aware the bug reported by @lucindasisk is still not fixed in the current release. It is lower on the priority list of bugs to fix because...