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 -- Elijah Mak PhD Candidate | Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
