Ali Khan
Ali Khan
Also I think --sdm apptainer isn't any different from --use-singularity (or --use-apptainer), just updated cli naming scheme.
> Ya I noticed the issue that we can't seem to use the hippunfold_deps singularity container when running hippunfold in conda, even if we're not enabling ---use-conda (which seems like...
this is no longer required
Looks like you are passing it a nifti when you need to pass it the subject directory (sub-01) that contains anat/sub-01_T1w.nii
@jordandekraker forgot to bring up in the meeting whether we can just drop 18K as an output density-- thoughts? I think the 8k surface has sufficient resolution..
Sounds good, I'll make a PR to change the default. There are a couple other minor things to address there too (missing coords metrics, and removing space wildcard from the...
if you want to do a wet-run test, you could use, e.g. sub-bbhist: ``` datalad install https://gin.g-node.org/hippunfold/multihist7 datalad get -d multihist7 multihist7/sub-bbhist/anat/*desc-tissue_dseg.nii.gz ``` Upon writing this I realize now we...
a more direct approach could just use synthseg (and use the hipp label).. if there is a conda env for synthseg would be something we could incorporate into dev-v2.0.0
Looks lile the problem is in how you have setup your wrapper. By running multiple runs at once in the same folder you are creating conflicts. Hippunfold supports all the...
Technically if you are running the docker/singularity container to run hippunfold, then you may need to also incorporate some workarounds to ensure the job running on the compute node is...