dkp

I'd love to see an example of a proper docker command for the cleanup as well. I've had no success guessing how this should be done.

@PeerHerholz and @jinseo0904 here's what I tried: ``` docker run -ti --rm \ -v ${PWD}/inputs:/bids_dataset:ro \ -v ${PWD}/outputs:/output_directory \ -v ${PWD}/working:/tmp \ -v ${PWD}/inputs/code/freesurfer_license_file.txt:/opt/freesurfer-6.0.0/license.txt \ micalab/micapipe:latest \ -bids /bids_dataset \...

Sorry to take so long to get back to you. The first command correctly put me inside the container...but there, it seems the micapipe_cleanup script cannot be found: ```bash root@3c84af9079b8:/home/mica#...

@PeerHerholz Thank you for the suggestion, unfortunately running the startup script does not seem to find micapipe_cleanup. I'm happy to try other suggestions and I appreciate your time. -Dianne ```bash...

Follow up: I ran run-01 first and then renamed the func directory, then I ran run2. I guess this works.

Another data point: I tried adding --writable-tmpfs to qsirecon mrtrix_multishell_msmt_ACT-hsvs reconstruction on our HPC and it generated a nice report! export RECON_SPEC=mrtrix_multishell_msmt_ACT-hsvs apptainer run --cleanenv --writable-tmpfs \ --bind ${DATA}:/data:ro \...

Unfortunately, I did not have the same luck with dipy_mapmri. This created some files and then crashed after 48 minutes [slurm-1615412_mapmri_crash.txt](https://github.com/PennLINC/qsiprep/files/12504960/slurm-1615412_mapmri_crash.txt) using --writable-tmpfs and allowing the odf reports. However, this...

This continues to happen even though Obsidian Sync is set to sync themes and snippets on all machines. Is there somewhere else I could put my theme (I have a...

We routinely collect multi-PLD PASL sequences and we are very disappointed that this has been labeled low priority ; ( We would love to be able to use ASLprep.

Thanks so much: Here's a dataset converted to BIDS with multi-PLD ASL data. I'm happy to share the DICOMS if you need, but this passes bids validation with only a...