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QSIprep Mac - nothing happens
Dear @mattcieslak
I'm trying to run QSIprep with Mac OS High Sierra. It seems that not is happening after running the code. I have started almost 6 hours ago and there's not going on the terminal and there's no output file. I think I'm doing right based on data preprocessed with QSIprep in my Ubuntu notebook.
QSIprep generated only tmp files in my Ubuntu and I got an memory failure. For this reason I'm trying with more RAM.
Follow the code an an image of the terminal after running:
docker run -ti --rm -v /Users/brainsmclab/freesurfer/license.txt:/fslicense.txt:ro -v /Users/brainsmclab/Documents/Eduardo/qsiprep:/data:ro -v /Users/brainsmclab/Documents/Eduardo/qsiprep/outputs:/out pennbbl/qsiprep:latest /data /out participant --output-resolution 1.2 --fs-license-file /fslicense.txt -w /out/tmp
Sincerely, Eduardo
Hi Eduardo,
I'm sure Matt will have better suggestions, but you may want to try the --low-mem option if the RAM is still an issue.
Some issues that resemble memory failures can occur if files are not found in the directories where they are expected. If I understand correctly, the command was intended to run the QSIprep preprocessing routine. Is /Users/brainsmclab/Documents/Eduardo/qsiprep/ the root BIDS directory for this dataset (i.e. contains original converted NIFTIs for sub-ID/ses-ID/dwi anat fmap) or the outputs of a prior preprocessing run? This may not be the source of the issue, but I keep the root BIDS directory labeled bids and place the qsiprep outputs in bids/derivatives/qsiprep; mounting bids to /data and bids/derivatives/qsiprep to /out.
Cheers, Paul
Dear @pcamach2 and @mattcieslak I'm so sorry for the late reply. I will be back to the data in the next week and I will let you know if the suggestions will be successful.
The command is intended to run QSIprep preprocessing. I'm using the root BIDS directory, I just named it in a confusing way. Sorry about that.
Best, Eduardo
you can also see a lot more printed out if you add -v flags. I usually run it with -v -v