Hi! Thanks for the reply.
I checked the coregistered and non-coregistered images, and the coregistered ones were clearly better. I would definitely see the line as beneficial, thank you.
For the mean FA matrix, it is true that inter-hemispheric connections are showing stronger than the intra-hemispheric connections. I’ve seen explanations saying that it could happen (like Weighted mean FA connectomes ?)… but it still seems problematic to me too. I’ve been searching for a good thresholding value, and also been thinking of going for another weighting measure instead of mean FA😂
these are the lines I used for making the connectome, just to add:
dwi2tensor dwi_den_preproc_unbiased.mif tensor.mif
tensor2metric tensor.mif -fa fa.mif
tcksample tracks_10M.tck fa.mif mean_FA_per_streamline.csv -stat_tck meanlabelconvert {SUBJ}_recon/mri/aparc+aseg.mgz FREESURFER_HOME/FreeSurferColorLUT.txt /usr/local/mrtrix3/share/mrtrix3/labelconvert/fs_default.txt {SUBJ}_parcels.mif
mrtransform {SUBJ}_parcels.mif -interp nearest -linear diff2struct_mrtrix.txt -inverse -datatype uint32 {SUBJ}_parcels_coreg.mif
tck2connectome -symmetric -zero_diagonal tracks_10M.tck ${SUBJ}_parcels_coreg.mif mean_FA_connectome.csv -scale_file mean_FA_per_streamline.csv -stat_edge mean
If you see anything I should fix, please do tell.
Thank you again for the reply!