Dear Freesurfer Community,

1) I am just starting out on some diffusion analyses and I'd like to use the dt_recon for this. Is there any information about a general workflow for quality control for the outputs from dt_recon? From the tutorials, I only see information about checking the registration. In particular, I would like to know how dt_recon cope with the occasional flipping/swapping of some components of the diffusion gradient directions?

2) Another aim of mine is to quantify DTI indices in subcortical regions segmented from the ASEG pipeline. How does Freesurfer handle partial volumning via seg-erode in "mri_vol2vol"?

I have pasted my workflow below and I'd like to check if this is correct, thanks!

1) After processing the scans on recon-all and dt_recon , i resample the structural data to diffusion space

mri_vol2vol --mov subjectname/dtrecon/lowb.nii.gz --targ subjectname/mri/aparc+aseg.mgz --inv --interp nearest --o subjectname/mri/aparc+aseg2diff.mgz --reg subjectname/dtrecon/register.dat --no-save-reg

Should I use ASEG instead of APARC+ASEG or WMPARC (which also has labels for the subcortical regions?)

2) Then, I mask the FA/MD maps with

mri_mask subjectname/dtrecon/fa.nii.gz subjectname/mri/aparc+aseg2diff.mgz subjectname/dtrecon/fa-masked_aparcaseg.mgz; done

3) Finally, I collect the FA in the regions with

mri_segstats --seg subjectname/mri/aparc+aseg2diff.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i subjectname/dtrecon/fa-masked_aparcaseg.mgz --seg-erode 1 --sum subjectname/stats/fa_aparc+aseg2diff_segerode_1;done

Thanks a lot for your time and help!

Best Wishes,

Elijah

Elijah Mak

PhD Candidate | Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ