We’ve painstakingly processed a huge dataset through Freesurfer including manual edits. I’d like to use those FreeSurfer outputs, but I am unsure where to specify the SUBJECTS_DIR in the in CPAC 1.85 config files. I could assume that it takes it from the environmental variable, but since I’m in Docker, that probably isn’t going to be right. do I specify it in the docker command via the cpac wrapper?
I am not a CPAC person, but have you tried experimenting with the
--env-file arguments for
I have not, but thank you for the suggestion.
It looks like the syntax hasn’t made its way into the user guide yet, but I believe the only way to do it currently is with a data config file with
freesurfer_dir subkeys under the
anat key like
(of course filling in the relevant paths and strings for your subjects).
Then you’ll also need a pipeline config to specify that you want to ingress FreeSurfer outputs and not re-run recon-all like
plus whatever other options you want to configure under
surface_analysis (see Default pipeline configuration YAML file - C-PAC 1.8.5 Beta documentation for an annotated example pipeline config)
I’ll try to track down the instructions and get them added to the user docs (and post them here).