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.
Command used (and if a helper script was used, a link to the helper script or the command generated):
chmod +x fmriprep.sh
source ~/.zprofile
zsh fmriprep.sh
#!/bin/zsh
# Define variables
bids_root_dir="/Users/andreaellsay/Desktop/bids"
subj="P001"
nthreads="4"
mem_mb="12000"
# 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 \
--output-spaces MNI152NLin2009cAsym:res-2 \
--nthreads $nthreads \
--stop-on-first-crash \
--mem_mb $mem_mb \
-w $HOME
else
echo "Docker is not installed."
fi
We prefer if you keep your software support posts in compliance with the template, so I added it back in for you. You can see some information, importantly the BIDS validation output and fMRIPrep version, are missing. You can edit your post to add it back in.
Looks good! In the future, outputs of the tree command are better at listing files than screenshots, as text can be parsed more easily. Similarly, better to copy and paste code output from the terminal into the text editor, using the </> button to format code easier to read.
A computing cluster is a large computational resource, usually associated with a research center or institution, that one can use to submit intensive computational jobs. Most of them are linux-based, which is why I asked. On computing clusters, most non-root users (that is, not admins) do not have permission to run Docker. Instead, use Apptainer/Singularity:
First build the container:
cd /where/you/want/image/to/be
singularity build fmriprep_23.1.3.img docker://nipreps/fmriprep:23.1.3
I have been trying to download Singularity but I run into this error. Go has been correctly installed into my /usr/local and the path has been added to ~/.bashrc
(base) andrea@winstonlab-2:~/singularity$ ./mconfig
make -C builddir
sudo make -C builddir install
Configuring for project `singularity-ce' with languages: C, Golang
=> running pre-basechecks project specific checks ...
=> running base system checks ...
checking: host C compiler... cc
checking: host C++ compiler... c++
checking: host Go compiler (at least version 1.17)... not found!
mconfig: could not complete configuration
make: Entering directory '/home/andrea/singularity/builddir'
make: *** No targets specified and no makefile found. Stop.
make: Leaving directory '/home/andrea/singularity/builddir'
make: Entering directory '/home/andrea/singularity/builddir'
make: *** No rule to make target 'install'. Stop.
make: Leaving directory '/home/andrea/singularity/builddir'
You should go to your server admin for this kind of question, but often times singularity is available as a module. E.g., it would be among the options in module avail, which you can then load with module load NAMEOFMODULE.
