====== TemplateFlow ======

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

This includes volumetric as well as [[:tools:cifti_surfaces]].

You can find template flow atlases on [[:admin:it:rhea|rhea]] in ''/opt/ni_tools/templateflow/''

  * on [[:admin:it:rhea]] <del>the environment variable ''TEMPLATEFLOW_HOME'' is set to ''/opt/ni_tools/templateflow/''</del> -- a shared location for all templates.
    * ''~/.cache/templateflow'' **can be** a symbolic link to ''/opt/ni_tools/templateflow/''
  * when using [[:tools:docker]] or [[:tools: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 ''[[:tools: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''

<wrap alert> [[tools:certificates]] can cause problems, especially in docker. Look there if you get SSL errors. </wrap>
<code>
# 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'])"
</code>

The results is ''den-32k'' files with some size, and the rest still with size 0 (empty).
<code>
 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
</code>
===== Templates =====

<code=bash>
 ls /opt/ni_tools/templateflow
</code>
<code example>
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

</code>