Hi Elijah - You add "set reinit =1" to the config file, (and remember to set the pathlist and subjlist to only what you want to rerun), and then rerun the -prior and -path steps in that order.

Best, a.y

On Thu, 18 Aug 2016, Elijah Mak wrote:

Thanks for the tips on reinitialisation of tracts.

Apologies if I might have missed it in the online tutorial, do you have some general guidelines for reinitialising?

Can I simply add "set reinit =1" to my configuration file, and then re-run trac-all -path. Are there any other parameters I could tweak?

After running through more QC on other subjects, I have also noticed other tracts that were not fully constructed. These tracts appear to be truncated or blob-like, for a lack of better word :) I have attached the screenshot to illustrate what I mean.

In these cases, I do the following QC routine after the general recon-all QC

1. freeview -v dmri/dtifit_FA.nii.gz -v dlabel/diff/aparc+aseg.bbr.nii.gz
2. freeview -v $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz

subjectname/dmri/cvs/dtifit_FA.bbr.nii.gz

Thanks a lot for your help, Anatasia!

Best Wishes, Elijah

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Elijah Mak

PhD Candidate | Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ