> > Also, a low resolution T2w image is problematic (minimum tested is 1mm > isotropic and we know some things don’t work well when it gets worse than > 1mm though that is probably not the source of the current issue). > can you elaborate on what things may not work well? this is a different topic though. Note that we have started acquiring the higher res T2 from the time when I decided to use the HCP pipelines.
> > It is possible that because this data doesn’t meet the minimum > acquisition requirements (at least 1mm isotropic T1w and T2w, field map, > fMRI—if using MB then saving SBRef) you’ll have to hack the pipelines > somehow to get them to work more robustly. You’ll need to look into what > is happening in the EPI to T1w registration, focusing on the files output > by this module: > Point taken for the SBRef. Our MB images look fairly good (eyeballing them, and compared to HCP unprocessed data) so I thought it'd be ok without the SBRef. Going forward we'll definitely include the SBRef acquisition in our data. > > > https://github.com/Washington-University/Pipelines/blob/master/fMRIVolume/scripts/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased.sh > > Especially focusing on line 255 (check that the inputs to epi_reg look > okay and the outputs). epi_reg is an FSL script, but you might have to > either hack it or improve its inputs to get it to work. These days, we > recommend using spin echo phase reversed images that match your fMRI > acquisition’s geometry and echo spacing to compute field maps (they are > faster to acquire) and you don’t have to rely as much on epi_reg to handle > everything in a black box. > The output of epi_reg is indeed flipped. I'll dig into it and see how I can fix that. > > Of course, we definitely recommend users ask about their MRI protocols > on the HCP Users list before acquiring them, so we can prevent these kind > of issues ahead of time. > Thanks for this recommendation. This data was acquired prior to the release of the HCP preprocessing pipelines. I realize that not all of the optimizations that you have implemented will work well with this data, however I do like the innovation of the CIFTI format (in most cases, people who work with surface data completely ignore subcortical structures, and I want to work with both) and running the HCP preprocessing pipelines seemed like the easiest way to go to end up with that format. Thanks for all the good work and responsiveness. - Julien _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
