Jakob Wasserthal
Jakob Wasserthal
Would it be possible to send one of the datasets where it is not working so I can try to reproduce the error? I would need peaks.nii.gz, dwi/sub-004_dwi_preproc.nii.gz, dwi/sub-004_dwi_preproc.bvals, dwi/sub-004_dwi_preproc.bvecs...
I did some changes to the code. Could you try again with the newest master branch?
This issue is fixed only in the latest master branch. It is not yet fixed in 2.3. I am planning to do a few more changes and then I will...
Thanks for this detailed analysis. This really helps. I pushed a change to the master branch which checks if the streamline startpoint is within the image dimensions of the beginnings...
Does tractseg for normal input (no bedpostX) work without any memory errors?
You have to install mrtrix to make it work (you need for example the command "dwi2response"). Mrtrix is used to calculate the peaks.
Hi, have you tried to input the Diffusion data and use the option `--raw_diffusion_input` as well as the option `--preprocess`? ``` TractSeg -i Diffusion.nii.gz -o tractseg_output --output_type tract_segmentation --raw_diffusion_input --preprocess...
This is strange. Does it also happen if you do not use the option `--preprocess` ?
You can either manually install an older version of dipy or you install the latest master of TractSeg which solves this issue: ``` pip install https://github.com/MIC-DKFZ/TractSeg/archive/master.zip ```
Unfortunately it is more difficult to test TractSeg on MacOS. It is always tested on Ubuntu. You could try if you can directly install it from github: ``` pip install...