Setting up Diffusion MRI analysis

Use Questions
1

Hi all,

When I tried running the “hcp_diffusion” command (without GPU), an error occurred. Could you please help me figure out why this error happened?

Here is my command:

qunex_container hcp_diffusion \
    --sessionsfolder="${STUDY_FOLDER}/sessions" \
    --batchfile="${STUDY_FOLDER}/processing/batch.txt" \
    --overwrite="no" \
    --hcp_nogpu \
    --container="${QUNEX_CONTAINER}"

and my error log is attached as below:
error_hcp_diffusion_HCPA001_2025-03-07_09.39.59.692004.log (78.0 KB)

Thanks for the help!

Best,
Acacius

2

Hi Acacius,

Based on your log, I assume that your processing ran out of resources (most likely memory). As you can see in the log, there is a word Killed in there. This usually happens when the system does not have enough resources to execute something, so the operating system kills the process. Diffusion is computationally extremely heavy, per my experience, you need about 32 GB of memory for hcp_diffusion and even more for some of the steps that can follow. For, example for dense tractography, you often need 64 GB.

Best, Jure

3

Got it. Many thanks to your kindly help!

Best,
Acacius