search

gsanroma / bullseye_pipeline

pipeline for creating bullseye parcellation of cerebral white matter from part of the FreeSurfer outputs and commands
BSD 3-Clause "New" or "Revised" License
5 stars 2 forks source link

Problem Installing #1

Open JoanBalado opened 3 years ago

JoanBalado commented 3 years ago

Hi,

Thank you for this repo Gerdard.

I am having one issue installing the pipeline. After installing it from source (and double-checking that all dependencies are working), I get this error message when I invoke run_bullseye_pipeline from the terminal (I am working in a Ubuntu 20 OS):

Traceback (most recent call last): File "/usr/local/bin/run_bullseye_pipeline", line 11, in load_entry_point('bullseye-pipeline==1.0.0', 'console_scripts', 'run_bullseye_pipeline')() File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 490, in load_entry_point return get_distribution(dist).load_entry_point(group, name) File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 2854, in load_entry_point return ep.load() File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 2445, in load return self.resolve() File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 2451, in resolve module = import(self.module_name, fromlist=['name'], level=0) File "/usr/local/lib/python3.8/dist-packages/bullseye_pipeline-1.0.0-py3.8.egg/bullseye_pipeline/run_bullseye_pipeline.py", line 6, in from bullseye_pipeline import create_bullseye_pipeline ImportError: cannot import name 'create_bullseye_pipeline' from 'bullseye_pipeline' (/usr/local/lib/python3.8/dist-packages/bullseye_pipeline-1.0.0-py3.8.egg/bullseye_pipeline/init.py)

I went to the bullseye directory and I didn't see any "create_bullseye_pipeline.py" script (I don't know if this is the problem).

Thank you for your help. P.d.: Additionally, is it possible to use python 3 instead of python 2.7?

LuuuXG commented 4 months ago

I met the same issue. Two modifications:

1) add from .bullseye_pipeline import create_bullseye_pipeline into __init__.py 2) change from utils import * to from .utils import * in bullseye_pipeline.py

can solve this problem.

But I have a problem running this package with Freesurfer 7+ version, don't know if it is related to the freesurfer version.

report Error since this node:

[Node] Error on "bullseye.filter_lobes" (/mnt/f/Public_dataset/ADNI_test/derivatives/bullseye/output/bullseye/_subject_ids_cvs_avg35_inMNI152/filter_lobes)