process_folder crashes when launched via Niftyweb submission

[jcohenadad]

When I submit scans via the Niftyweb interface, the Daemon launches WMGM, which then launches process_folder.py, however it crashes. See log-WMGM.txt:

[26-10-2018 22:11:01] Start: 11029-WMGM-parameters.txt
Evaluating: execute_command_or_else_stop (/home/niftyweb_sct/gm_challenge/WMGM 11029 /home/niftyweb_sct/data_tmp/11029-0_0-data1.nii.gz /home/niftyweb_sct/data_tmp/11029-0_1-data2.nii.gz /home/niftyweb_sct/data_tmp/11029-0_2-9418-0_2-UCLqsmsc_2Dffe_20180416.pdf -field 1.5T -coil PRODUCT -sequence PRODUCT -data 2018102622.09)
The command (/home/niftyweb_sct/gm_challenge/WMGM 11029 /home/niftyweb_sct/data_tmp/11029-0_0-data1.nii.gz /home/niftyweb_sct/data_tmp/11029-0_1-data2.nii.gz /home/niftyweb_sct/data_tmp/11029-0_2-9418-0_2-UCLqsmsc_2Dffe_20180416.pdf -field 1.5T -coil PRODUCT -sequence PRODUCT -data 2018102622.09) failed. 1
[26-10-2018 22:11:02] Finish: 11029-WMGM-parameters.txt
[26-10-2018 22:11:02] Error computing results: 11029-WMGM-parameters.txt

However, when I run the process directly on ferguson, it succeeds in running process_folder.py:

ferguson:~ $ sct/python/bin/python gm_challenge/NiftyWeb_setup/daemon_SOFTWEB_2files.py WMGM 11029 /home/niftyweb_sct/data_tmp/11029-0_0-data1.nii.gz /home/niftyweb_sct/data_tmp/11029-0_1-data2.nii.gz /home/niftyweb_sct/data_tmp/11029-0_2-9418-0_2-UCLqsmsc_2Dffe_20180416.pdf -field 1.5T -coil PRODUCT -sequence PRODUCT -data 2018102622.09
Program: WMGM
lock_file: /home/niftyweb_sct/data_tmp/lock-WMGM
Check if a queue of this program already exists...
--> Nope!
List of files to process:
['11029-WMGM-parameters.txt']
[26-10-2018 22:13:45] Start: 11029-WMGM-parameters.txt
Evaluating: execute_command_or_else_stop (/home/niftyweb_sct/gm_challenge/WMGM 11029 /home/niftyweb_sct/data_tmp/11029-0_0-data1.nii.gz /home/niftyweb_sct/data_tmp/11029-0_1-data2.nii.gz /home/niftyweb_sct/data_tmp/11029-0_2-9418-0_2-UCLqsmsc_2Dffe_20180416.pdf -field 1.5T -coil PRODUCT -sequence PRODUCT -data 2018102622.09)
Copy data...
Segment spinal cord...
Segment gray matter...
Crop data (for faster processing)...
Generate white matter segmentation...
Erode white matter mask...
Register data2 to data1...
Compute contrast...
Compute SNR_single...
Compute SNR_diff...
--> created file: results.csv

[26-10-2018 22:14:40] Finish: 11029-WMGM-parameters.txt
[26-10-2018 22:14:40] Upload fails, no such file:/home/niftyweb_sct/data_tmp/11029_WMGM.zip
[26-10-2018 22:14:40] Error uploading results: 11029-WMGM-parameters.txt
You have new mail in /var/mail/niftyweb_sct

@fprados any idea what could go wrong?