Segmentation fault - Multiple runs per participant still not fixed

[S-Gur]

Notice this is the same issue I opened for BIDS-Apps/BROCCOLI (issue #10); I don't think the problem is specific to the Docker version, but please update Docker as well after this issue is resolved:

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)