Import Error

[MRPM12]

Hi experts.

I started to use TractSeg but am facing the following error. Is there a solution?
$ TractSeg -i Diffusion.nii.gz -o tractseg_output --raw_diffusion_input --output_type tract_segmentation
Traceback (most recent call last):
File "/home/brain/.local/bin/TractSeg", line 20, in
from tractseg.libs import plot_utils
File "/home/brain/.local/lib/python3.8/site-packages/tractseg/libs/plot_utils.py", line 11, in
from nibabel import trackvis
ImportError: cannot import name 'trackvis' from 'nibabel' (/home/brain/.local/lib/python3.8/site-packages/nibabel/init.py)

[wasserth]

Which version of nibabel are you using and which version of TractSeg?

[MRPM12]

Thank you for your reply.
The version of nibabel is 4.0.2 and the version of TractSeg seems to be 2.4. pip install TractSeg showed the following.

Requirement already satisfied: TractSeg in /home/brain/.local/lib/python3.8/site-packages (2.4)
Requirement already satisfied: nibabel>=2.3.0 in /home/brain/.local/lib/python3.8/site-packages (from TractSeg) (4.0.2)

[wasserth]

Trackvis is no longer supported by nibabel. So you can not use the output format trk_legacy. The other output formats should work.
Otherwise you can try doing
pip install --upgrade nibabel==3.2.1
This will downgrade nibabel.

[MRPM12]

Thank you for your suggestion. I tried to change to the recommended version of nibabel and conducted TractSeg module. Then the below showed.

$ TractSeg -i Diffusion.nii.gz -o tractseg_output --raw_diffusion_input --output_type tract_segmentation
Traceback (most recent call last):
File "/home/brain/.local/bin/TractSeg", line 20, in
from tractseg.libs import plot_utils
File "/home/brain/.local/lib/python3.8/site-packages/tractseg/libs/plot_utils.py", line 22, in
from tractseg.libs import fiber_utils
File "/home/brain/.local/lib/python3.8/site-packages/tractseg/libs/fiber_utils.py", line 10, in
from dipy.tracking.streamline import compress_streamlines as compress_streamlines_dipy
ImportError: cannot import name 'compress_streamlines' from 'dipy.tracking.streamline' (/home/brain/.local/lib/python3.8/site-packages/dipy/tracking/streamline.py)

Is there more appropriate way to use TractSeg?

[wasserth]

It seems that dipy does not work well with the older nibabel. I would recommend to not use trk_legacy output format, but trk or tck.

[yizhwan]

Hi, I am also getting the same error with trackvis. Can I just confirm, in order to not use: trk_legacy output format, but trk or tck, should we modify your plot_utils script to do this? If so how should we go about doing this? I have tried adding the option in my command as below in a bash script:

    TractSeg -i "${wkdir}/input/preproc/ses-${Sessionnum}/TractSeg/S${sub_number}/TractSeg_input/Diffusion.nii.gz" \
    -o my/output/directory \
    --bvals "${wkdir}/input/preproc/ses-${Sessionnum}/TractSeg/S${sub_number}/TractSeg_input/Diffusion.bvals" \
    --bvecs "${wkdir}/input/preproc/ses-${Sessionnum}/TractSeg/S${sub_number}/TractSeg_input/Diffusion.bvecs" \
    --tracking_format tck \
    --raw_diffusion_input

But it still generates the error:

Traceback (most recent call last):
File "/home/anaconda3/envs/yh/bin/TractSeg", line 20, in
from tractseg.libs import plot_utils
File "/home/anaconda3/envs/yh/lib/python3.9/site-packages/tractseg/libs/plot_utils.py", line 11, in
from nibabel import trackvis
ImportError: cannot import name 'trackvis' from 'nibabel' (/home/anaconda3/envs/yh/lib/python3.9/site-packages/nibabel/init.py)

Many thanks!