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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