bids-apps/aa

BIDS App containing an instance of the Automatic Analysis

aa's Issues

Failed to instantiate MATLAB

when I ran this docker command:
sudo docker run -i --rm
-v ~/bids/dataset/:/bids_dataset
-v ~/outputs:/outputs
bids/aa
/bids_dataset /outputs participant --participant_label 01
--fs-license-file /outputs/fs_license.txt

I got this error:
LD_LIBRARY_PATH is .:/opt/mcr/v94/runtime/glnxa64:/opt/mcr/v94/bin/glnxa64:/opt/mcr/v94/sys/os/glnxa64:/opt/mcr/v94/sys/opengl/lib/glnxa64
Failed to initialize MATLAB Runtime Instance: The specified component has expired.

Invalid argument order

A valid BIDS App takes the following positional arguments

1. Position 1: input bids directory
2. Position 2: output directory
3. Position 3: analysis level

However, aa currently takes:

1. Position 1: input bids directory
2. Position 2: XML config file
3. Position 3: XML config file2
4. Position 4: output directory
5. Position 5: analysis level

making it incompatible with the framework. The extra XML files would have to be moved to positions 4 and 5.

TODO

• sub-pipeline selection from a limited set of predefined pipelines
• config file (m-file) to customize the pipeline

Lack of documentation about the compulsory XML config files

It's hard to use the app not knowing that it would expect.

Unknown digests on Docker Hub

heyo!

I'm not sure if this tool (and bids app) is still alive, but most of the tags / digests on Docker Hub are unknown, possibly could be that they were purged for some reason?

https://hub.docker.com/r/bids/aa/tags

invalid freesurfer license in circle ci

https://app.circleci.com/pipelines/github/bids-apps/aa/32/workflows/44b8665c-0b59-4bd3-890e-e95b65f3ae0b/jobs/228/parallel-runs/0/steps/0-104

cannot run latest image in CI

see #11

test example take too long to run on default circle ci

https://app.circleci.com/pipelines/github/bids-apps/aa/31/workflows/ca78bfaf-0639-4d5f-9637-9e38c7f3c3df/jobs/224/parallel-runs/0/steps/0-106

circle.yml missing

Please add circle.yml file (see https://github.com/BIDS-Apps/example/blob/master/circle.yml)