Quick test

Download datasets

$ cd /path/to/data

$ curl https://amubox.univ-amu.fr/public.php/dav/files/7tf4ooJsyjHfSbG --output skullTo3d_CI_v2.zip

$ unzip -o skullTo3d_CI_v2.zip -d skullTo3d_CI_v2

Testing depending on the installation

Testing from Singularity image

$ singularity run -B /path/to/data:/data /path/to/containers/skullto3d_v0.1.sif segment_skull -data /data/skullTo3d_CI_v2/cerimed_marmo -out /data/skullTo3d_CI_v2/cerimed_marmo/results -soft ANTS_skull_robustreg -species marmo -sub Tresor -ses 01 -brain_dt T1 T2 -skull_dt T1 petra CT -deriv -padback

Testing from docker image

For testing the docker installation, the beginning of the commands should be replaced by docker run -v /path/to/data:/data macatools/macapype:v0.3.1, e.g.

$ docker run -v /path/to/data:/data macatools/skullto3d:v0.1 segment_skull -data /data/skullTo3d_CI_v2/cerimed_marmo -out /data/skullTo3d_CI_v2/cerimed_marmo/results -soft ANTS_skull_robustreg -species marmo -sub Tresor -ses 01 -brain_dt T1 T2 -skull_dt T1 petra CT -deriv -padback

Testing from python package install

From pip install

$ segment_skull -data /path/to/data/skullTo3d_CI_v2/cerimed_marmo -out /path/to/data/skullTo3d_CI_v2/cerimed_marmo/results -soft ANTS_skull_robustreg -species marmo -sub Tresor -ses 01 -brain_dt T1 T2 -skull_dt T1 petra CT -deriv -padback

From github install

$ python workflows/segment_skull.py -data /path/to/data/skullTo3d_CI_v2/cerimed_marmo -out /path/to/data/skullTo3d_CI_v2/cerimed_marmo/results -soft ANTS_skull_robustreg -species marmo -sub Tresor -ses 01  -brain_dt T1 T2 -skull_dt T1 petra CT -deriv -padback

Note the /path/to/data instead of /data (as in the container install) in the arguments

Testing the macaque datasets with CT and petra

Two other dataset, corresponding to one macaque and one baboon, are available in the test dataset. Please not that due to higher image resolution, the preprocessing will take a longer time.

Testing from Singularity image

Macaque CT petra

$ singularity run -B /path/to/data/:/data /path/to/containers/skullto3d_v0.1.sif segment_skull  -data /data/skullTo3d_CI_v2/cerimed_macaque -out /data/skullTo3d_CI_v2/cerimed_macaque/results -soft ANTS_skull_robustreg -species macaque -sub Stevie -ses 01 -brain_dt T1 T2 -skull_dt CT petra t1 -deriv -padback

See Commands for more info on robustreg in soft