I am unable to run fmriprep without it stalling. I have checked my memory in docker and it should be fine (12GB). There is no error log and my BIDS files have been validated. They were covered from .IMA on a linux and then copied over the a MacOS where I am running fmriprep. I am not using a conda environment. For this run I asked for no recon-all but previously with recon-all it still doesnt work. I also have already run recon-all in freesurfer for all my subjects.
This is the line where it stalled: [Node] Executing "norm <niworkflows.interfaces.fixes.FixHeaderRegistration>
I am using a docker wrapper. This is my code to run
#!/bin/zsh
#Define veriables
bids_root_dir="/Users/andreaellsay/Desktop/bids"
subj=“P001”
nthreads=“4”
mem_mb=“8000”
#Check if Docker is available
if [ -x “$(command -v docker)” ]; then
fmriprep-docker $bids_root_dir $bids_root_dir/derivatives
participant
–participant-label $subj
–skip-bids-validation
–md-only-boilerplate
–fs-license-file $HOME/Downloads/license.txt
–fs-no-reconall
–output-spaces MNI152NLin2009cAsym:res-2
–nthreads $nthreads
–stop-on-first-crash
–mem_mb $mem_mb
-w $HOME
else
echo “Docker is not installed.”
fi
fmriprep-docker is installed correctly.