Diffusion preprocessing for multiple subjects

Use Questions
1

Hi,

We have recently started running the diffusion preprocessing pipeline (without GPU).

It ran successfully with the following command, for subject 10001:

\qunex_container hcp_diffusion \
\ "sessions="${SESSIONS}-- \
\ "mappingfile="${INPUT_MAPPING_FILE}-- \
\ "container="${QUNEX_CONTAINER}-- \
\"dockeropt="-v ${BIND_FOLDER}:${BIND_FOLDER}-- \
\ "sessionsfolder="${STUDY_FOLDER}/sessions-- \
\ "batchfile="${STUDY_FOLDER}/processing/batch.txt-- \
\ parsessions=3-- \
\ "hcp_dwi_negdata="10001_DWI_dir6_PA.nii.gz-- \
\ "hcp_dwi_posdata="10001_DWI_dir185_AP.nii.gz-- \
\ hcp_dwi_combinedata=2-- \
\ hcp_dwi_selectbestb-- \
\ hcp_nogpu-- \
\ extra-eddy-arg=--niter=8-- \
extra-eddy-arg=--fwhm=10,8,6,4,2,0,0,0 0--

We wish to run this command on several participants at the same time. How should we modify the command so instead of the hard-coded subject number, we can use a variable that changes to the relevant subject number on every run?

Many thanks!

Yael

2

Hi Yael,

if your batch file is correctly prepared and it includes parameters on top, followed by the data about all sessions and their images, then you can simply skip the --sessions="${SESSIONS}" parameter and QuNex will run the processing over all sessions inside the batch file. As you have parsessions set to 3, it will process 3 sessions in parallel. Once one of the three finishes, it will automatically pick the next one. Also, the hardcoded negdata and posdata can be skipped in this case, as QuNex will automatically pull it for each session from the batch file.

Let me know if this works. You can also upload your batch file here so I can check it looks good.

Best, Jure