I have been trying to run dwifslpreproc with default settings on my virtual machine: Ubuntu 20.04, 4 cores 32GB RAM
I have b0 images from AP and PA directions so I used the -rpe_pair option. Specifically, here is the command I used: dwifslpreproc dwi_den.mif dwi_den_preproc.mif -pe_dir AP -rpe_pair -se_epi b0_pair.mif -eddy_options " --slm=linear --data_is_shelled"
Then it quits at topup:
dwifslpreproc: [ERROR] topup --imain=topup_in.nii --datain=topup_datain.txt --out=field --fout=field_map.nii.gz --config=/usr/local/fsl/etc/flirtsch/b02b0.cnf --verbose (dwifslpreproc:793)
dwifslpreproc: [ERROR] Failed command did not provide any output information
It looks like topup might have crashed straight away, but it’s hard to tell from that output… Can I just check first what version of MRtrix you’re using (dwifslpreproc -version)? Assuming it’s recent, you should find a temporary folder in the folder where you ran that command called something like dwifslpreproc-tmp-****** (you should see it mentioned in the output of dwifslpreproc, it normally leaves this temporary folder around if there’s an error). If you look inside that folder, there should be a topup_output.txt in there, which may contain more information.
You could try running that topup command directly from within the temporary folder, see what happens.
Hi! So sorry for my late reply!
The version I’m using is 3.0.2. There is no topup_output.txt inside that folder too…
I ran the topup command inside the folder and it crashed right away. Kernel messages showed traps: topup[16850] trap invalid opcode ip:7fe44eee4404 sp:7ffc097c2298 error:0 in libopenblas.so.0[7fe44e4d2000+22cc000]
