I'm running recon-all by wrapping it in a Nipype workflow.

(cmdline:

recon-all -all -i {data/T1_files(iterfield)} -openmp 64 -sd . -s seg )

The workflow(p1.py) executes smoothly without errors. But it doesn't save the final output files. There is no 'fsaverage' directory created either.

'Runtime_info.txt' shows no errors either, it shows that the files are being created successfully too.

I decided to then run a pipeline(p2.py) with recon-all node as an input to the bbregister node. Looks like it fails after the recon-all node. I've attached the recon-all.log file as well, it exits the command after the mri_nu_correct step without further information.

Please help, as all my future work is contingent on recon-all running smoothly.

Thank,

Pratik Kashyap