Jakob Wasserthal
Jakob Wasserthal
In general this should work. However, the resulting tractogram will be a lot more sparse. Only starting tracking from one end it is difficult to get a full tracking. To...
If you are a bit familiar with python you could simply run the function `orient_to_same_start_region` on the trackings. Then all of them have the same orientation.
This is quite strange. For TOM it should look for the weights at the same directory as for tract segmentation. Are you sure inside of your `$TRACTSEG_WEIGHTS_DIR` you have downloaded...
Could you post the content of the subjects.txt file or send it to me? Then I can try to reproduce the issue.
Thank you. Could you maybe also print the entire Error message?
Thanks for this hint. This is indeed missing. I added it to `tractseg/resources/utility_scripts/apply_brain_mask.py` and adapted the path in the preprocessing pipeline. Now it should work.
What command are you using to run TractSeg?
Unfortunately I have no idea what the problem might be. Could you share your data so I can try to reproduce the problem?
I think I found the problem. I am working on a fix.
I just pushed a fix to the newest master. Now it should work.