TemplateFlow

https://www.templateflow.org/ is a repository of neuroimaging templates (eg. MNI, fsLR) and a python library to pragmatically download them.

This includes volumetric as well as Surface-based Analysis (cifti).

You can find template flow atlases on rhea in /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

Fetching

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

UPMC Certificates can cause problems, especially in docker. Look there if you get SSL errors. 

# export HTTPS_PROXY=socks5h://localhost:12345  # deal with rhea python certs issue / man-in-the-middle from upmc
# export REQUESTS_CA_BUNDLE=/etc/ssl/certs/ca-certificates.crt
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

Templates

 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