TemplateFlow

https://www.templateflow.org/ is a repository of neuroimaging templates (eg. MNI) and a python library to pragmatically download them. You can find these on rhea:/opt/ni_tools/templateflow/

• on Rhea (linux server) the environment variable TEMPLATEFLOW_HOME is set to /opt/ni_tools/templateflow/ – a shared location for all templates.
  • ~/.cache/templateflow can be a symbolic link to /opt/ni_tools/templateflow/
• when using Docker or singularity, consider bind mounting your $TEMPLATEFLOW_HOME to that used in the container -v /opt/ni_tools/templateflow/:/root/.cache/templateflow. This will avoid downloading large files every time the container is run

templateflow uses Git annex to only copy files when requested. Until templateflow.api.get is run a template will only be a stand in empty file. Here's an example of grabbing left and right for all the 32k versions of fsLR

# export HTTPS_PROXY=socks5h://localhost:12345  # deal with rhea python certs issue / man-in-the-middle from upmc
python -c "import templateflow; templateflow.api.get('fsLR', space=None, hemi=['L','R'],density='32k', suffix=['veryinflated','inflated','midthickness','sphere'])"

The results is den-32k files with some size, and the rest still with size 0 (empty).

 du -h /opt/ni_tools/templateflow/tpl-fsLR/*hemi-L* |sort -hr
712K    /opt/ni_tools/templateflow/tpl-fsLR/tpl-fsLR_den-32k_hemi-L_veryinflated.surf.gii
712K    /opt/ni_tools/templateflow/tpl-fsLR/tpl-fsLR_den-32k_hemi-L_midthickness.surf.gii
712K    /opt/ni_tools/templateflow/tpl-fsLR/tpl-fsLR_den-32k_hemi-L_inflated.surf.gii
704K    /opt/ni_tools/templateflow/tpl-fsLR/tpl-fsLR_space-fsaverage_hemi-L_den-32k_sphere.surf.gii
552K    /opt/ni_tools/templateflow/tpl-fsLR/tpl-fsLR_hemi-L_den-32k_sphere.surf.gii
148K    /opt/ni_tools/templateflow/tpl-fsLR/tpl-fsLR_hemi-L_den-32k_desc-vaavg_midthickness.shape.gii
0       /opt/ni_tools/templateflow/tpl-fsLR/tpl-fsLR_space-fsaverage_hemi-L_den-59k_sphere.surf.gii
0       /opt/ni_tools/templateflow/tpl-fsLR/tpl-fsLR_space-fsaverage_hemi-L_den-164k_sphere.surf.gii
0       /opt/ni_tools/templateflow/tpl-fsLR/tpl-fsLR_hemi-L_den-59k_sphere.surf.gii
0       /opt/ni_tools/templateflow/tpl-fsLR/tpl-fsLR_hemi-L_den-59k_desc-vaavg_midthickness.shape.gii

 ls /opt/ni_tools/templateflow

tpl-dhcpAsym             tpl-MNI152NLin2009bSym   tpl-NKI
tpl-dhcpSym              tpl-MNI152NLin2009cAsym  tpl-NMT31Sym
tpl-dhcpVol              tpl-MNI152NLin2009cSym   tpl-OASIS30ANTs
tpl-Fischer344           tpl-MNI152NLin6Asym      tpl-onavg
tpl-fsaverage            tpl-MNI152NLin6Sym       tpl-PNC
tpl-fsLR                 tpl-MNI305               tpl-RESILIENT
tpl-MNI152Lin            tpl-MNIColin27           tpl-UNCInfant
tpl-MNI152NLin2009aAsym  tpl-MNIInfant            tpl-VALiDATe29
tpl-MNI152NLin2009aSym   tpl-MNIPediatricAsym     tpl-WHS
tpl-MNI152NLin2009bAsym  tpl-MouseIn