Beginner: Connectome pipeline (Updated)

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Do I use maskfilter to dilate the brain mask? Is there a general ACT recommendation for the -npass value?

Yep, that’s the command. No real rule for how many repeats; like I said, you could equally just not pass any mask at all to dwi2fod. The important point is that you don’t want streamlines erroneously terminating in the middle of WM because of an error in the DWI brain masking step.

For now, when I tried to run 5ttgen with FSL, I ran into the following error:

  • I don’t think I’ve ever figured out for certain why standard_space_roi sometimes fails and sometimes works. I tried to have 5ttgen fsl continue even in the presence of such a failure, but I might be creating even more problems for myself, I’m not sure.

  • Looks like after this failure, bet runs, but fast doesn’t find its output image. It could be that bet is failing silently, or it might not be conforming to the expected output format based on the FSLOUTPUTTYPE environment variable. You could run the 5ttgen fsl script with the -nocleanup option and have a look at the temporary directory contents.

  • “Unrecognised option m”: No idea whatsoever. That’s an FSL command, so the internals are out of my control.

Regarding ACT, it is stated that T1 image should be rigidly registered to the DWI series before running 5ttgen and tckgen. I was wrongly under the impression that the registration was being done under the hood of tckgen. How can I do that with MRTrix?

Definitely not any registration going on ‘under the hood’. With MRtrix3 we prefer processing steps to be done explicitly, using small but powerful tools with very specific roles, rather than ‘hiding’ what processing is going on.

You won’t be able to blindly send a DWI series and a T1 image to mrregister. Firstly, it currently only supports a mean-squared image difference metric (which relies on images having equal contrast and intensity range). Secondly, because one is a 3D image and one is 4D - it expects to be registering either a pair of scalar images, or a pair of SH images. I have developments in the pipeline for doing T1->DWI registration with MRtrix3, but they’re not yet ready for public consumption. So for now, stick with whatever you’d perform with another package.