Error in 'test_MBM_and_MAGeT.py '

[fire9291]

Hi, I want to test pydpiper on Zebrafish data. But when I run the test code: python pydpiper_testing/test_MBM_and_MAGeT.py test-data/ I got an error :MBM.py: error: unrecognized arguments: --time-to-seppuku=1

I am not particularly clear about the operation mechanism of pydpiper, so I just deleted the line 'time-to-seppuku 1' in sample.cfg. But got another error as following:

_File "/home/yang/anaconda3/envs/atlas/bin/MBM.py", line 4, in import('pkg_resources').run_script('pydpiper==2.0.15', 'MBM.py') File "/home/yang/anaconda3/envs/atlas/lib/python3.7/site-packages/pkg_resources/init.py", line 651, in run_script self.require(requires)[0].run_script(script_name, ns) File "/home/yang/anaconda3/envs/atlas/lib/python3.7/site-packages/pkg_resources/init.py", line 1448, in run_script exec(code, namespace, namespace) File "/home/yang/anaconda3/envs/atlas/lib/python3.7/site-packages/pydpiper-2.0.15-py3.7.egg/EGG-INFO/scripts/MBM.py", line 548, in mbm_application() File "/home/yang/anaconda3/envs/atlas/lib/python3.7/site-packages/pydpiper-2.0.15-py3.7.egg/pydpiper/execution/application.py", line 206, in f execute(pipeline(options).stages, options) File "/home/yang/anaconda3/envs/atlas/lib/python3.7/site-packages/pydpiper-2.0.15-py3.7.egg/pydpiper/execution/application.py", line 156, in execute ensure_commands_exist(stages) File "/home/yang/anaconda3/envs/atlas/lib/python3.7/site-packages/pydpiper-2.0.15-py3.7.egg/pydpiper/execution/application.py", line 124, in ensure_commands_exist raise ValueError("Missing executables: %s" % bad_cmds) ValueError: Missing executables: ['convert', 'montage', 'minc_displacement', 'lin_from_nlin', 'xfmavgscipy.py', 'ANTS']

Does it mean that my packages were not installed properly? I installed minc-toolkit-v2 from conda, I've been struggling with this for days, can anyone help me?

[fire9291]

By the way, I tried to download Pydpiper VM, but the the url cannot be connected http://repo.phenogenomics.ca/repo/MICe-software. Where can I download from?

[gdevenyi]

pydpiper is installed in MINC-VM, https://github.com/CoBrALab/MINC-VM

[gdevenyi]

Same error previously reported, https://github.com/Mouse-Imaging-Centre/pydpiper/issues/424

[fire9291]

pydpiper is installed in MINC-VM, https://github.com/CoBrALab/MINC-VM @gdevenyi Thanks very much! I installed MINC-VM successfully. But I still got an error when trying to test pydpiper_testing/test_MBM_and_MAGeT.py test-data/ in VM. Can you help me deal with this? By the way, where can I find the latest updated test code? After all, I need to successfully execute the test program to help me understand its execution process.

[fire9291]

Same error previously reported, #424

I found #424, but it can not help me deal with the Err ValueError: Missing executables: ['convert', 'montage', 'minc_displacement', 'lin_from_nlin', 'xfmavg_scipy.py', 'ANTS']