Hi Shadia,
How did you make the externally-derived ribbons? Can you please send us your recon-all.log and your subject directory so we can take a look? https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange Thanks, Bram ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of MIKHAEL Shadia <s1163...@sms.ed.ac.uk> Sent: Sunday, January 21, 2018 1:58:00 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] external WM and GM masks as input to recon-all? Dear Bruce, Thank you for your reply at https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2018-January/055512.html 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 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -----Original Message----- From: MIKHAEL Shadia Sent: 12 January 2018 18:43 To: freesurfer@nmr.mgh.harvard.edu Subject: external WM and GM masks as input to recon-all? Dear FreeSurfer experts, Could you please advise on whether it would be possible to run recon-all in FreeSurfer 6.0 using externally-derived probabilistic white matter and grey matter masks, both of which include the cerebellum but not the ventricles, and if so, how? Would the flag -autorecon2-pial suffice? Thank you in advance. Shadia _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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