Very long running time qsiprep processing DSI data

Software Support
,
1

Summary of what happened:

Hi, I am new to qsiprep, and I am using it to preprocess my DSI data. I have chosen the SHOREline for motion correction. The problem is, it took about 16 hours to complete one subject’s preprocessing. I wonder if this amount of time is normal and if there is any way to reduce the processing time? And I used 4 cores for this program’s execution to protect the computer from crashing. Thank you very much.

Command used :

for subj in $(seq -w 001 060); do
    docker run --rm -it \
        --cpus="4" \
        -v /path/output:/data:ro \
        -v /path/output:/out \
        -v /path/freesurfer/license.txt:/opt/freesurfer/license.txt:ro \
        pennbbl/qsiprep:latest \
       /data /out participant \
       --participant-label $subj \
       --hmc_model 3dSHORE \
       --output-resolution 2 \
       --fs-license-file /opt/freesurfer/license.txt
done

Version:

0.20.1

Environment (Docker, Singularity / Apptainer, custom installation):

docker

Data formatted according to a validatable standard? Please provide the output of the validator:

PASTE VALIDATOR OUTPUT HERE

Relevant log outputs (up to 20 lines):

N/A (code completed)

Screenshots / relevant information:

2

Hi @ruoxi and welcome to neurostars!

It is hard to know what is typical because it varies depending on how much data is being processed (number of images, number of directions per image). But in general, QSIPrep is a process that should last on the order of hours. But you can try allowing more than 4 cores (if your system has more available) which should speed it up.

Best,
Steven

2 Likes
3

Hi Steven, thanks for your prompt reply!