Dear experts, I am a relatively new user of MRtrix 3 and would be therefore highly thankful for your help and support: I performed automatized preprocessing (dwi2preproc etc.) and wholebrain-tractography (tckgen). Afterwards I segmented the cortico-spinal tract (CST) by using several inclusion and …

Just in case you want to use the MRtrix3 functionality here, the commands you’re after are tcksample and tckresample . These admittedly need to be better documented. The process consists of first re-sampling the streamlines at equivalent locations along the tract of interest, by ‘cutting’ them up ac…

Hi Frederike, I think once you are happy with the created tracts, you should give a try to along-tract statistics software: [image] johncolby/along-tract-stats A MATLAB toolbox for performing along-tract analysis of diffusion tensor imaging (DTI) MRI tractography data. - johncolby/along-…

Hi, Manuel, Your along-tract-stats is good, easy to use and compatible with R. However, your along-tract-stats cannot read the tck file of Mrtrix. We need convert it to trk using the MRTrix2TrackVis function from Nipype, or write matlab code for the conversion. But I think many people may relucta…

Hi Cirong Liu, Sorry for the confusion, I would like to make clear that I’m not the developer, I knew the software and I write here the link because I thought that was appropriate for the topic. I don’t know if is in the plans of the developers or not. Currently, I’m using it with the MRTrix2Track…

Dear MRtrix3 team, I am performing an along-tract-analysis on a segmented tract in .tck format by using MRtrix3’s commands tckresample and tcksample. More specifically, I am following the procedure described in the previous post by means of the following examples: tckresample CST.tck -line 20 1,2…

HI @Frederike great work u have it !! Can you please post the command that you are using for the generation of CST tracks !! Best Regards

MRtrix3 Community

Along tract analysis after tract segmentation

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