Jakob Wasserthal
Jakob Wasserthal
Interesting. You would have to send me the data again so I can try to reproduce the error.
The `--preprocess` option does not properly work with TOMs unfortunately. Therefore I would recommend the following: Either register your images manually to MNI space and then run TractSeg on those...
Could you specify what your folder structure looks like and what your command to call `plot_tractometry_results` looks like?
Could you try again with the following versions: ``` pip install --upgrade numpy==1.21.5 pip install --upgrade fury==0.8.0 pip install --upgrade dipy==1.5.0 ```
Which version of TractSeg are you using? You might have to upgrade TractSeg to the latest version. ``` pip install --upgrade TractSeg ```
Not sure what the problem is, but I am happy to hear that it finally works.
I am happy to hear that it worked. Yes, you have to run it on a computer with a display.
What are the commands you are using for processing your data?
Can you try again without the `--preprocess` option (because you basically did that yourself with the flirt commands) and without the line `flip_peaks -i tractseg_output/peaks.nii.gz -o tractseg_output/peaks_flipped.nii.gz -a y`. Do...
If you send me the data for one subject where the error occurs I can try to reproduce the issue.