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DCAN-Labs / abcd-hcp-pipeline

bids application for processing functional MRI data, robust to scanner, acquisition and age variability.
https://hub.docker.com/r/dcanumn/abcd-hcp-pipeline
BSD 3-Clause "New" or "Revised" License
49 stars 19 forks source link

Exact Container Call and Version for ABCC BIDS Derivatives #46

Closed tjhendrickson closed 2 years ago

tjhendrickson commented 2 years ago

I'm sorry I know I asked this a while ago, but I think I forgot to save it. What was the exact call and container version for the abcd-hcp-pipeline when processing the ABCC BIDS derivatives? A colleague is looking to replicate results.

Additionally, if you have the configuration file used for DCANBoldPreProc that would be helpful!

arueter1 commented 2 years ago

Great question, Tim! I've assigned Fez to this. I know we are a bit swamped right now, but hopefully we can address this by next week Friday.

tjhendrickson commented 2 years ago

Just checking in on this!

ericfeczko commented 2 years ago

Sorry, I forgot to answer this until now!

0.03 for the docker container and 2.0.0 for the code base itself.

I can't put an exact usage, since I don't remember the bandstop we used. @perronea can you provide an example with the correct band stop filter numbers? Thanks!

tjhendrickson commented 2 years ago

Here is an example usage with docker as it was run to generate ABCC outputs.

sudo /opt/acc/sbin/exadocker run --name=basename ${TempSubjectDir} --rm -v ${TempSubjectDir}/BIDS_unprocessed:/bids_input:ro -v ${TempSubjectDir}/BIDS_processed:/output -v ${TempSubjectDir}/cleaning.json:/cleaning.json -v ${TempSubjectDir}/license.txt:/opt/freesurfer/license.txt dcanlabs/abcd-hcp-pipeline:dev /bids_input /output --freesurfer-license=/opt/freesurfer/license.txt --participant-label=${participant} --ncpus=${CPU_CORES} --bandstop 18.582 25.7263 --custom-clean /cleaning.json