Jakob Wasserthal

I published a new TractSeg version (v2.6) which should fix the compress_streamlines error. So you do not have to downgrade dipy. Does it work if you simply do `pip install...

Did you install pytorch? This has to be installed before installing TractSeg. When you start a python Terminal and enter `import torch`, do you get any error?

When you do the manual transformation to MNI space as you have described (using flirt) then you do not need to use the `--preprocess` option. `--preprocess` will simply do the...

In version 2.4 I made another bug fix for alignment of the trackings. You could try again with this version.

Which version of TractSeg are you using? And on which operating system are you running it?

Would you be able to share the data so I can try to reproduce the issue?

Thanks for sharing the data. I ran the following commands and everything worked fine for me. ``` TractSeg -i Diffusion.nii.gz --raw_diffusion_input --keep_intermediate_files TractSeg -i tractseg_output/peaks.nii.gz -o tractseg_output --output_type endings_segmentation TractSeg...

File "/home/user/miniconda3/lib/python3.8/site-packages/tractseg/libs/tractometry.py", line 42, in _orient_to_same_start_region if beginnings[int(startpoint[0]), int(startpoint[1]), int(startpoint[2])] == 0: IndexError: index 60 is out of bounds for axis 2 with size 60 This error means that the...

Thanks a lot for this deep dive into the code. That really helps. I was not aware of this problem. Getting all the image and streamline transformations right is a...

Is it working when you add the argument `--tracking_format tck` to `Tracking` and `Tractometry`?