Fmriprep autorecon31 error using Docker

Hi everyone,

Very new to fmriprep and fmri so apologies if I miss any details.

I have just run fmriprep 1.4.1 using Docker on my Windows computer (also using fs and aroma) and up until this point it was running fine with no errors but I’ve just run a participant and come across a autorecon31 error in the html file. I had a browse on the forum and accordingly looked for an inactive version of freesurfer in my .bashrc file but was not able to find this.

Does anyone have any other ideas as to why this is happening or what I can do to resolve this error?

Many thanks in advance!

Hi @aysham,

Can you provide your full command, and any details of your error? If it’s this issue, it may be that rerunning will resolve it.


Hi Chris,

Thanks for responding! The command I put in was

fmriprep-docker C:\Users\am\Documents\fMRIExp\Pre-Processing\bids C:\Users\am\Documents\fMRIExp\fmriprep2 --fs-license-file C:\Users\am\Documents\license.txt --participant-label en04a --use-aroma

and the error was this:

I’m now re-running it for the 3rd time but the error has consistently come up the last two times so my guess is it likely to come up again (but maybe I’ll get lucky!)

Thank you again,

You should be able to find more details of the error in C:\Users\am\Documents\fMRIExp\fmriprep2\freesurfer\sub-en04a\scripts\recon-all.log.

So at the bottom of the file it writes:

Started at Mon Aug 19 20:05:57 UTC 2019
Ended at Mon Aug 19 20:39:01 UTC 2019
#@#%# recon-all-run-time-hours 0.551
recon-all -s sub-en04a finished without error at Mon Aug 19 20:39:02 UTC 2019

And no other errors pop up in the log file but it does in the html. I have just checked the other run and the log file states the same (pasted below)

Started at Tue Aug 20 02:51:33 UTC 2019
Ended at Tue Aug 20 03:24:48 UTC 2019
#@#%# recon-all-run-time-hours 0.554
recon-all -s sub-en04a finished without error at Tue Aug 20 03:24:48 UTC 2019

Any idea what might be causing this?

Many thanks again,

Hmm. Well, perhaps there’s a recon-all-lh.log (or similar) and another one for rh. Those might have the information you’re looking for.