connectomicslab/connectomemapper3

BUG: CMP3 does not work with new nibabel `4.0.0`

sebastientourbier opened this issue · 0 comments

It has been reported in #199 the following error:

py37cmp-gui) mn@mn-HP-Z840-Workstation:~$ cmpbidsappmanager
Traceback (most recent call last):
File "/home/mn/miniconda3/envs/py37cmp-gui/bin/cmpbidsappmanager", line 5, in
from cmp.cli.cmpbidsappmanager import main
File "/home/mn/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/cmp/cli/cmpbidsappmanager.py", line 30, in
import cmp.bidsappmanager.gui.principal
File "/home/mn/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/cmp/bidsappmanager/gui/principal.py", line 21, in
import cmp.project
File "/home/mn/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/cmp/project.py", line 23, in
from cmp.pipelines.diffusion import diffusion as Diffusion_pipeline
File "/home/mn/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/cmp/pipelines/diffusion/diffusion.py", line 22, in
from cmp.stages.diffusion.diffusion import DiffusionStage
File "/home/mn/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/cmp/stages/diffusion/diffusion.py", line 18, in
from .reconstruction import *
File "/home/mn/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/cmp/stages/diffusion/reconstruction.py", line 33, in
from cmtklib.diffusion import FlipTable, FlipBvec
File "/home/mn/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/cmtklib/diffusion.py", line 14, in
import nibabel.trackvis as tv
ModuleNotFoundError: No module named 'nibabel.trackvis'

Based on https://nipy.org/nibabel/changelog.html#api-changes-and-deprecations, a number of elements in the API were removed in the latest 4.0.0 version released on Saturday 18 June 2022. This includes nibabel.trackvis.

Code should be modify to incorporate those changes.