Dear FreeSurfer experts, could you please look at the issue mentioned below? I did not receive any answer to my post, probably it got lost unattended.
Antonin Skoch _____ From: Bruce Fischl [mailto:[email protected]] To: Antonin Skoch [mailto:[email protected]] Cc: Nick Schmansky [mailto:[email protected]] Sent: Wed, 15 Apr 2015 14:56:10 +0100 Subject: Re: [Freesurfer] FLAIRpial refinement after manual editing of brainmask Hi Nick could you take a look at this and see if there is a bug in the logic of recon-all as Antonin suggests? thanks Bruce On Wed, 15 Apr 2015, Antonin Skoch wrote: > Dear Freesurfer experts, > > I am reposting this question since I did not get an answer to my post from > last week. > > We are using FLAIR images to refine pial surfaces. It generally performs > well, however in some cases there is still need for manual editing of > brainmask. > After manual editing of brainmask we tried to run: > > recon-all -s subj_id -autorecon-pial -FLAIRpial > > however, we faced the problem that the reconstructed pial surface does not > reflect manual changes in brainmask. We finally found that the files > ?h.woFLAIR.pial are in this case not replaced by new versions of pial files, > i.e. the commands > cp -v ?h.pial ?h.woFLAIR.pial > are not executed and "old" version of files from previous reconstruction > (created when recon-all -all -FLAIRpial is run) is used for FLAIRpial > refienement. > > After manual remove of ?h.woFLAIR.pial files the reconstruction of pial > surface works as expected (i.e. reflecting both brainmask edit and FLAIRpial > refinement). > > Is this bug or expected behavior? Or are we doing something wrong? > > Regards, > > Antonin Skoch > MR Unit > Institute for Clinical and Experimental Medicine > Czech Republic >
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