Structural connectivity pipeline

Hi everyone :slight_smile: ,
I have just started to interact with the world of neuroimaging, so I’m opening this topic to ask for explanations from more experienced people in this sector. I am currently working on a project that aims at developing a structural connectivity analysis on different bilingual patients, so as to highlight the differences with monolingual patients. Up to now, using DWI and structural images, I have managed to carry out a preprocessing phase which includes:

  • noise reduction
  • ringing effect removal
  • motion and distortion correction
  • bias field correction

Subsequently I made a registration of the structural data on the diffusion data for each patient, so as to have a correct alignment. Immediately afterwards I managed to generate the fibers, through the use of the HRF of each type of brain tissue (Gray Matter , White Matter and CSF), and to carry out the complete tractography. After various researches, I also managed to record the regions of interest for the study on an atlas, so as to make a group analysis. Now the problem is: how can I register from the MNI standard to the structural space (T1)?

Welcome @neuronoob!

The issue of registration between T1 template and subject-specific T1 images is independent of DWI, and there’s no single accepted solution. FSL’s fsl_anat script includes registration to the MNI template. Personally I’ve used a code snippet from this manuscript for using the ANTs software for this purpose with reasonable success. But I’ve only had very limited experience with this specific task. There’s nothing specifically within MRtrix3 for doing so, and the current limitations of our registration capabilities (having been designed specifically around FOD registration) caused problems the one time I briefly tried it.