bids-apps / broccoli Goto Github PK

Container fails to build:

https://circleci.com/gh/BIDS-Apps/BROCCOLI/87?utm_campaign=build-failed&utm_medium=email&utm_source=notification

Trying to run BROCCOLI docker on a BIDS dataset with multiple runs creates the condition *.txt files and then I assume it tries to do something (no logs during that time) and then crashed with:

/Downloads/BROCCOLI/code/bids/broccolipipeline.sh: line 4: 323 Segmentation fault FirstLevelAnalysis -runs ${num_runs} ${bold_files} ${output_dir}/${subject}/${subject}_T1w_brain.nii.gz /usr/local/fsl/data/standard/MNI152_T1_2mm_brain.nii.gz ${regressor_files} ${output_dir}/${subject}/${task_name}/contrasts.txt -output ${output_dir}/${subject}/${task_name}/${subject} -device 0 -savemnimask -saveallaligned -savedesignmatrix -saveoriginaldesignmatrix -regressmotion

I used BIDS dataset ds001 (I downloaded it from https://drive.google.com/drive/folders/0B2JWN60ZLkgkMGlUY3B4MXZIZW8)

This issue happens with both bids/broccoli:v1.0.0 and bids/broccoli:latest (which I believe should be v1.0.1)

after running this docker command:
sudo docker run -i --rm
-v ~/bids/dataset/:/bids_dataset
-v ~/outputs:/outputs
bids/broccoli
/bids_dataset /outputs participant --participant_label 01

I get this error:
Initialization error is "Unable to create an OpenCL context for the selected device."
OpenCL error is "CL_DEVICE_NOT_AVAILABLE"
OpenCL initialization failed, aborting!
See buildInfo* for output of OpenCL compilation!

A single paragraph describing the scope of the App would be enough.

How can we include the contrast.txt file in the docker command?