[RESOLVED] Error in ‘hcp_diffusion’

Use Questions
1

Hi,
I’m trying to use qunex for preprocessing with T1, T2, rs-fMRI, and DWI data. An error occurred during the run_eddy step in hcp_diffusion . I later attempted using nogpu , but encountered the same error. Below is my log file.
with GPU:
runlog:
Log-hcp_diffusion-2025-07-27_16.05.03.308169.log (3.0 KB)
comlog:
error_hcp_diffusion_STG001_2025-07-27_16.05.03.328768.log (112.1 KB)

NoGPU:
runlog:
Log-hcp_diffusion-2025-08-06_10.37.22.468589.log (2.8 KB)
comlog:
error_hcp_diffusion_STG001_2025-08-06_10.37.22.492763.log (112.5 KB)

Thanks a lot!

Best,
Kelly

2

Hi,

The error is:

EDDY::ECScanManager::GetShellIndicies: Data not shelled

If data is shelled but eddy is acting up, try adding:

--hcp_dwi_extraeddyarg="--data_is_shelled"

To your command call.

Let me know how it goes.

Best, Jure

3

Hi, Jure
After investigation, we found that there was a problem with the data. It was not fully scanned during data collection.
Thank you for your reply.

4

Yes, it is either a data issue or eddy is for some reason detecting that it is not shelled even if it is.

Glad we solved it.

Best, Jure