Hi,
I am new to tractography. I followed the provided steps of preprocessing, then generated the FOD and streamlines. How do I know if the generated streamlines are correct? I’d appreciate the help.
Thanks.
It’s generally not possible to (reliably) identify mistakes just by examining the final tractogram. Instead, you should thoroughly check the intermediate results at each step of your pipeline to ensure everything is working as intended.
Thank you. I asked because I would like to I filter out a specific ROI for example the corpus callosum from the streamline. I would appreciate it if you could let me know about that step. Should I use tckedit in.tck cropped.tck -mask mask.mif or tckedit in.tck out.tck -include ROI1.mif -include ROI2.mif -minlength 25?
I have figured out filtering out a specific ROI from the streamline! However it looks really choppy. I believe the flow is supposed to be red as the direction is left to right in the corpus callosum. However, it seems as if the water is flowing in all directions. I have attached a screenshot of the file that I obtained after filtering out the corpus callosum streamline.
The preprocessing steps were denoising, unringing and bias correction. And after checking the intermediate results, they looked okay to me. I would appreciate the help.
