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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of MIKHAEL Shadia <s1163658@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



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-----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


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