Trouble with TOM

[Hayat921]

Hi Jakob,

I am a PhD student in Psychology at the University of Auckland. I am running a fixel based analysis study and I have completed the pipeline for MSMT-CSD([Fibre density and cross-section - Multi-tissue CSD — MRtrix3 3.0 documentation (https://mrtrix.readthedocs.io/en/dev/fixel_based_analysis/mt_fibre_density_cross-section.html)). Now I would like to use TractSeg to create masks for specific tracts in each subjects template space. I am in the process of writing my script and so far the sh2peaks, tract segmentation and ending segmentations have all gone smoothly however I am having trouble with TOM, I am consistently running into the error "No such file or directory: 'template/tractseg_output//bundle_segmentations/AF_left.nii.gz'" I have attached a screenshot of my script below, any guidance would be greatly appreciated!

[mgreen-neura]

Just check the /tractseg_output/bundle_segmentations folder exists first. It may not have been generated.
Try simply running "TractSeg -i peaks.nii.gz" first and see if it generates the bundle folder.