I am trying to run
-continue option. It seems to be skipping the
dirstat command and failing (screenshot below) on the
len(shell_bvalues)==len(shell_asymmetries) + 1 check (line 297 of
dwifslpreproc) even though that condition would be met if the dirstat command was run. Is there an option to make sure
dirstat command runs through even when using the
A little bit of context on why I need to use the
-continueoption. I am using local condor setup to launch a batch of jobs running
topup/applytopupportion seems to use less memory and only a single cpu while
eddy_openmpcan use multiple cpus and needs more memory. If I request cpus and memory sufficient for
eddy_opempupfront then I am not able to get optimal throughput. My strategy is to first request only a single CPU and small amount of memory to get as many
topupsrunning at the same time as possible and let the
dwifslpreprocfail on out-of-memory error. Then re-launch
-continue scratch eddy_in.niioption requesting more cpus and memory. I did use
-nocleanupoption for the first launch.
Your help and advice on getting the
-continue option working properly or any other way of getting maximal throughput using
dwifslpreproc (because of the inherent differences in the throughputs of
eddy_openmp) would be greatly appreciated! I am currently not able to share the sample data since that would require me to include only skull-stripped data and organize about 8 Gb of data. But if that’s something you would need to help me, I will work on making that available. Please let me know.
Thanks in advance for your help!