Issue while executing DMRIprep

[aleramp88]

Hello, I have tried using dmriplaygroundlab but I get this error when executing the protocol:

Error during running Traceback (most recent call last): File "/home/rampininia94/anaconda3/envs/dtienv-py310/lib/python3.10/site-packages/dtiplayground/api/dmriprep.py", line 77, in _execute_dmriprep res= self.run(req) File "/home/rampininia94/anaconda3/envs/dtienv-py310/lib/python3.10/site-packages/dtiplayground/api/dmriprep.py", line 279, in run raise Exception("Error during running") Exception: Error during running Any ideas what this could be due to? (tried with conda and with pip, same error)

[styner]

Not sure, the error message is not very helpful, unfortunately. A few questions: which version are you running? what command line generates this error?

[aleramp88]

Hi! thank you for the speedy reply :) It's version 0.5.7. So, running it from the GUI I get that nonspecific error. I went back and tried running it from terminal using the command suggested in the GUI itself, after I generated the protocol. Here below is the output. Further detail: I just wanted to give it a first try with just one subject, this might be an incomplete protocol but it was just to see if it runs correctly. I attach the protocol too. protocols.json

(base) rampininia94@pars:~$ dmriprep run-dir /home/rampininia94
[2024-03-14-11-19-40]   VERSION : 0.5.7
[2024-03-14-11-19-40]   application: dmriprep
[2024-03-14-11-19-40]   application_dir: /home/rampininia94/.niral-dti/dmriprep-0.5.7
[2024-03-14-11-19-40]   config_dir: /home/rampininia94/.niral-dti
[2024-03-14-11-19-40]   execution_id: 8477d99c-fcfa-429c-957b-fae4529a8011
[2024-03-14-11-19-40]   log: /home/rampininia94/.niral-dti/dmriprep-0.5.7/log.txt
[2024-03-14-11-19-40]   no_log_timestamp: false
[2024-03-14-11-19-40]   no_verbosity: false
[2024-03-14-11-19-40]   parameters:
[2024-03-14-11-19-40]     dtiplayground-tools:
[2024-03-14-11-19-40]       info:
[2024-03-14-11-19-40]         version: 0.0.1
[2024-03-14-11-19-40]       path: /home/rampininia94/.niral-dti/dtiplayground-tools
[2024-03-14-11-19-40]     fsl:
[2024-03-14-11-19-40]       info:
[2024-03-14-11-19-40]         name: fsl
[2024-03-14-11-19-40]         verson: 6.0.5.1:57b01774
[2024-03-14-11-19-40]       path: /usr/local/fsl
[2024-03-14-11-19-40]   version: 0.5.7
[2024-03-14-11-19-40]   
[2024-03-14-11-19-40]   Configuration directory is not found or some files are missing, commencing initialization ...
[2024-03-14-11-19-40]   Looking up DTIPLAYGROUNDTOOLS environment variable...
[2024-03-14-11-19-40]   Found DTIPLAYGROUNDTOOLS: /home/rampininia94/.niral-dti/dtiplayground-tools/
[2024-03-14-11-19-40]   Use the installed DTIPlaygroundTools? [Y/n]
y
[2024-03-14-11-19-50]   Looking up FSLDIR environment variable...
[2024-03-14-11-19-50]   Found FSLDIR: /usr/local/fsl
[2024-03-14-11-19-50]   Config file written to : /home/rampininia94/.niral-dti/dmriprep-0.5.7/config.yml
[2024-03-14-11-19-50]   DTI playground tools are found in /home/rampininia94/.niral-dti/dtiplayground-tools
[2024-03-14-11-19-50]   FSL directory is found at /usr/local/fsl
[2024-03-14-11-19-50]   Software path file is written to : /home/rampininia94/.niral-dti/dmriprep-0.5.7/software_paths.yml
[2024-03-14-11-19-50]   [_load_modules] begins ... 
[2024-03-14-11-19-50]   Loading modules from /home/rampininia94/anaconda3/lib/python3.10/site-packages/dtiplayground/dmri/preprocessing/modules 
[2024-03-14-11-19-50]   Loading module : BASELINE_Average
/home/rampininia94/anaconda3/lib/python3.10/site-packages/pandas/core/arrays/masked.py:60: UserWarning: Pandas requires version '1.3.6' or newer of 'bottleneck' (version '1.3.5' currently installed).
  from pandas.core import (
[2024-03-14-11-19-51]   Loading module : BRAIN_Mask
[2024-03-14-11-19-51]   Loading module : BRAIN_Tractography
[2024-03-14-11-19-51]   Traceback (most recent call last):
[2024-03-14-11-19-51]     File "/home/rampininia94/anaconda3/bin/dmriprep.py", line 237, in <module>
[2024-03-14-11-19-51]       result=args.func(args)
[2024-03-14-11-19-51]     File "/home/rampininia94/anaconda3/bin/dmriprep.py", line 127, in command_run_dir
[2024-03-14-11-19-51]       app.run(options)
[2024-03-14-11-19-51]     File "/home/rampininia94/anaconda3/lib/python3.10/site-packages/dtiplayground/dmri/common/appbase.py", line 413, in run
[2024-03-14-11-19-51]       return self.runImpl(options)
[2024-03-14-11-19-51]     File "/home/rampininia94/anaconda3/lib/python3.10/site-packages/dtiplayground/dmri/preprocessing/app.py", line 64, in runImpl
[2024-03-14-11-19-51]       return self.runQC(_options)
[2024-03-14-11-19-51]     File "/home/rampininia94/anaconda3/lib/python3.10/site-packages/dtiplayground/dmri/preprocessing/app.py", line 127, in runQC
[2024-03-14-11-19-51]       return _run(_options)
[2024-03-14-11-19-51]     File "/home/rampininia94/anaconda3/lib/python3.10/site-packages/dtiplayground/dmri/common/appbase.py", line 434, in wrapper
[2024-03-14-11-19-51]       self.initialize(args)
[2024-03-14-11-19-51]     File "/home/rampininia94/anaconda3/lib/python3.10/site-packages/dtiplayground/dmri/common/appbase.py", line 241, in initialize
[2024-03-14-11-19-51]       self.initializeImpl(options)
[2024-03-14-11-19-51]     File "/home/rampininia94/anaconda3/lib/python3.10/site-packages/dtiplayground/dmri/preprocessing/app.py", line 53, in initializeImpl
[2024-03-14-11-19-51]       modules=module.load_modules(system_module_paths = system_module_paths, user_module_paths=config['user_module_directories'])
[2024-03-14-11-19-51]     File "/home/rampininia94/anaconda3/lib/python3.10/site-packages/dtiplayground/dmri/common/__init__.py", line 83, in wrapper
[2024-03-14-11-19-51]       res=func(*args,**kwargs)
[2024-03-14-11-19-51]     File "/home/rampininia94/anaconda3/lib/python3.10/site-packages/dtiplayground/dmri/common/module.py", line 18, in _load_modules
[2024-03-14-11-19-51]       modules=_load_default_modules(system_module_paths, module_names, **options)
[2024-03-14-11-19-51]     File "/home/rampininia94/anaconda3/lib/python3.10/site-packages/dtiplayground/dmri/common/module.py", line 25, in _load_default_modules
[2024-03-14-11-19-51]       return _load_modules_from_paths(system_module_paths,module_names, **options)
[2024-03-14-11-19-51]     File "/home/rampininia94/anaconda3/lib/python3.10/site-packages/dtiplayground/dmri/common/module.py", line 47, in _load_modules_from_paths
[2024-03-14-11-19-51]       mods.append(p.module_finder.find_module(p.name).load_module(p.name))
[2024-03-14-11-19-51]     File "<frozen importlib._bootstrap_external>", line 548, in _check_name_wrapper
[2024-03-14-11-19-51]     File "<frozen importlib._bootstrap_external>", line 1063, in load_module
[2024-03-14-11-19-51]     File "<frozen importlib._bootstrap_external>", line 888, in load_module
[2024-03-14-11-19-51]     File "<frozen importlib._bootstrap>", line 290, in _load_module_shim
[2024-03-14-11-19-51]     File "<frozen importlib._bootstrap>", line 719, in _load
[2024-03-14-11-19-51]     File "<frozen importlib._bootstrap>", line 688, in _load_unlocked
[2024-03-14-11-19-51]     File "<frozen importlib._bootstrap_external>", line 883, in exec_module
[2024-03-14-11-19-51]     File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
[2024-03-14-11-19-51]     File "/home/rampininia94/anaconda3/lib/python3.10/site-packages/dtiplayground/dmri/preprocessing/modules/BRAIN_Tractography/BRAIN_Tractography.py", line 9, in <module>
[2024-03-14-11-19-51]       from dipy.tracking.benchmarks.bench_streamline import length
[2024-03-14-11-19-51]   ModuleNotFoundError: No module named 'dipy.tracking.benchmarks'
[2024-03-14-11-19-51]

[styner]

Thanks. So, there are two things at play here. The initial error was due an incomplete init/setup. It looks like it needs to be run at least once via the command line (the way you just did it) rather than via the UI. Then the second error was raised 1-2 weeks ago (https://github.com/NIRALUser/DTIPlayground/issues/56) and is related to an API change in dipy. I assume you are using dipy 1.7 or 1.8, version 0.5.7 only supports dipy 1.6. Two possibilities: 1) downgrade your dipy to 1.6 , 2) upgrade dtiplayground to 0.5.8b6 ( pip install --upgrade dtiplayground==0.5.8b6 ), this is a beta release version with new functionality (fiber profile extraction has been added) and thus is not as stable but should work.