Dear Bruce,
Thank you for your reply at https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2018-January/055512.ht... regarding the use of grey and white matter masks.
Since you were suggesting that this may be difficult, I have instead tried to introduce external masks at a later stage (ribbons) in the process as follows: running recon-all once (run1), all the way through, then replacing ?h.ribbon.nii and ?h.ribbon.mgz with externally-derived ribbons, before calling recon-all a second time (run2) in FreeSurfer 6.0 as follows:
recon-all -autorecon-pial -parcstats -cortparc2 -parcstats2 -cortparc3 -parcstats3 -subjid s1-freesurfer60-run2-external_ribbon
I have experimented with the following 2 setups for this 2nd run of recon-all: 1. run2-setup1: keeping all the files in the 'mri' directory generated by run 1, except for ?h.ribbon.nii and ?h.ribbon.mgz which I'm replacing by the externally-derived ones 2. run2-setup2: keeping only the files in the 'mri' directory generated by run 1 before ?h.ribbon.nii and ?h.ribbon.mgz. Files generated after those 2 were deleted, and the ribbons were replaced by the externally-derived ones
I have found that in both cases, the ?h.ribbon.mgz are getting modified by the recon-all process, and the stats file is identical to that of run 1, which is not what I was hoping for. Altering the ribbons did not alter the parcellation & corresponding stats.
Could you please advise on the steps that I've missed/done wrongly in order for the ribbon changes to get incorporated? Should I be clearing the 'stats' directory? And is the 2nd run of recon-all correct? Any tips would be greatly appreciated.
Thank you in advance.
Shadia