Dear HCP users, It's exciting to see the second data release out today. I had a little trouble implementing the fMRIvolume pipeline in Glaser et al and wondered if anyone here could help based on their experience with it:
- The paper describes echo-spacing, but I am not confident in my conversion to readout time, and I could not find readout time in appendix 1. My best guess is echo-spacing of 0.58ms * 72 x-axis slices (phase-encode steps) / multiband factor of 3 = 13.92 ms. Is that correct? - When supplied with the sets of L->R and R->L phase encoded images, topup's iout output looks terrific. However, I can't apply the correction to other scans. When I issue the command: applytopup --imain=SBRef_RL_grad --datain=refblip.txt --inindex=1 --topup=my_field --out=SBRef_RL_grad_corrected -v --method=jac I get the output "libc++abi.dylib: terminate called throwing an exception". Can anyone see something wrong with my command (refblip.txt is a file with the characters -1 0 0)? I have checked all the relevant filepaths. - As a workaround, I took the fout result from topup and used it as a fieldmap. It reduces distortion, but not quite to the standard of the iout output of topup. Perhaps I am using the wrong readout time, which affects the Hz values; or perhaps it's just better to work with applytopup? Cheers, Jordan ____________________ Jordan Poppenk, Ph.D. Post-doctoral Research Fellow Princeton Neuroscience Institute [email protected] _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
