Add containers for ABCD apps

[yarikoptic]

the ones behind https://brainlife.io/apps to go under https://github.com/ReproNim/containers/tree/master/images/abcd

• figure out where API endpoint for listing them is (@soichih?)
• while adding containers add metadata annotation for them (may be at git-annex level for now). I guess should be described somewhere within https://github.com/brainlife/abcd-spec

[yarikoptic]

Some notes from a chat with @soichih

• The "entry point" for the ABCD app is not a "container" but rather the app itself which underneath might use container or multiple
• the same container could be reused across multiple apps
• brainlife CLI could be used to get information about apps (npm install brainlife ; bl login ; bl app query --json; didn't try -- need to recall login)
• There is https://brainlife.io/api/warehouse/app/query endpoint .

We get 495 apps ATM

❯ curl --silent https://brainlife.io/api/warehouse/app/query | jq '.[].name' | nl | tail
   486	"Compute summary statistics of diffusion measures mapped to cortical surface - Freesurfer stats - Deprecated Surface"
   487	"app-anatomy"
   488	"app-time-frequency"
   489	"app-maxwell-filtering"
   490	"app-filter"
   491	"FSL Top-up & Eddy Correct"
   492	"Extract individual tractograms for each segmented white matter tract"
   493	"Freesurfer 7.3.2"
   494	"Compute Backbone Network"
   495	"app-events"

- app record points in "github" to github user/repo.

here is selection of freesurfer apps with github repos for them

❯ cat /tmp/apps.json | jq '.[]| [.name, .github ] | @sh' | grep -i freesurfer | nl
     1	"'Freesurfer' 'brainlife/app-freesurfer'"
     2	"'Freesurfer on OSG (fsurf)' 'brainlife/app-freesurfer-osg'"
     3	"'Freesurfer Deface' 'brainlife/app-deface'"
     4	"'Freesurfer Labels to 3D Surfaces' 'kitchell/app-3Dfreesurfs'"
     5	"'HCP Pipeline (PreFreeSurfer)' 'brainlife/app-hcp-prefreesurfer'"
     6	"'HCP Pipeline (FreeSurfer)' 'brainlife/app-hcp-freesurfer'"
     7	"'HCP Pipeline (PostFreeSurfer)' 'soichih/app-hcp-postfreesurfer'"
     8	"'Convert Pial (Cortical) and White Matter Surfaces from Freesurfer' 'kitchell/app-3DPialWM_freesurfer'"
     9	"'Freesurfer Group Analysis' 'brainlife/app-freesurfer-agg'"
    10	"'Freesurfer on OSG' 'brainlife/app-freesurfer-osg'"
    11	"'Freesurfer Statistics' 'brainlife/app-freesurfer-stats'"
    12	"'Make white matter mask in dwi space from Freesurfer' 'brainlife/app-make-white-matter-mask-freesurfer'"
    13	"'Make white matter mask in dwi space from Freesurfer (dtiinit)' 'brainlife/app-make-white-matter-mask-freesurfer'"
    14	"'Parcellation Statistics - Deprecated' 'brainlife/app-freesurfer-stats'"
    15	"'Compute summary statistics of diffusion measures from subcortical segmentation' 'brainlife/app-freesurfer-stats'"
    16	"'Temp extract warp freesurferpost HCP' 'brainlife/app-extract-warp-temp'"
    17	"'Generate ROIs for Visual White Matter Analysis in Freesurfer Space (Benson pRF)' 'brainlife/app-roiGenerator'"
    18	"'Generate Visual Regions of Interest Binned by Eccentricity Estimates (Benson Atlas) - Freesurfer Space' 'brainlife/app-roiGenerator'"
    19	"'Parcellation Statistics' 'brainlife/app-freesurfer-stats'"
    20	"'Freesurfer 7.1.1' 'brainlife/app-freesurfer'"
    21	"'Parcellation Statistics - Volume' 'brainlife/app-freesurfer-stats'"
    22	"'Parcellation Statistics - Surface - Deprecated Datatype' 'brainlife/app-freesurfer-stats'"
    23	"'Parcellation Statistics - Surface' 'brainlife/app-freesurfer-stats'"
    24	"'Compute summary statistics of diffusion measures from Parcellation (volume)' 'brainlife/app-freesurfer-stats'"
    25	"'Compute summary statistics of diffusion measures from Freesurfer Parcellation (volume)' 'brainlife/app-freesurfer-stats'"
    26	"'Freesurfer 7.1.1 Longitudinal (Step1/2)' 'brainlife/app-freesurfer-longitudinal'"
    27	"'Freesurfer 7.1.1 Longitudinal (Step 2/2)' 'brainlife/app-freesurfer-longitudinal'"
    28	"'Freesurfer 7.1.1 - Multiple T1w Inputs' 'bacaron/app-freesurfer'"
    29	"'Freesurfer Longitudinal Statistics' 'brainlife/app-freesurfer-longitudinal-statistics'"
    30	"'Compute summary statistics of diffusion measures mapped to cortical surface - Freesurfer computations' 'brainlife/app-cortex-tissue-mapping-stats'"
    31	"'Compute summary statistics of diffusion measures mapped to cortical surface - Freesurfer stats - Deprecated Surface' 'brainlife/app-cortex-tissue-mapping-stats'"
    32	"'Freesurfer 7.3.2' 'brainlife/app-freesurfer'"

so the official seems to be the https://github.com/brainlife/app-freesurfer , and looking at https://github.com/brainlife/app-freesurfer/blob/master/main#L11 we see that execution happens via "straight" singularity exec ... docker://brainlife/freesurfer:7.3.2 ...

• there is brainlife/ on standard docker hub, e.g. https://hub.docker.com/r/brainlife/freesurfer so in principle we could have archived all those images (script to mirror all versions of containers from docker hub #48) and/or convert them to singularity but unless we come up with non-ad-hoc way to make use our singularity images instead of keeping converting from docker - benefit is unclear

With all that in mind, we might want

• a dedicated "subdataset" for abcd apps which would then contain individual apps as subdatasets as well.
• within in an archive of docker images from various locations accompanied with converted singularity images
• ... yet to analyze/figure out how we could "inject" ourselfves into main of the apps if at all

[yarikoptic]

just confirming on a sample one that no name of the image is stored anywhere in the metadata

❯ pwd
/tmp/app-dtiinit
❯ git grep neurodebian
main:singularity exec docker://brainlife/mcr:neurodebian1604-r2017a ./compiled/dtiinit
❯ curl --silent https://brainlife.io/api/warehouse/app/query | jq . | grep neurodebian1604-r2017a

so we would indeed need to have archive of all images. Ideally in OCI form from which we could then produce also singularity images or use directly with podman/docker