Re: [Freesurfer] An estimated date for FreeSurfer 7.3 release

External Email - Use Caution Hi Anastasia, Thanks for the quick reply. King-Wai From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Yendiki, Anastasia Sent: Friday, May 6, 2022 3:07 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] An estimated

[Freesurfer] TRACULA in FreeSurfer version 7.3

External Email - Use Caution Hi Anastasia, � Just downloaded FreeSurfer version 7.3 and trying out TRACULA. Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3 However trac-all -prep is looking for ThalamicNuclei.v12.T1.FSvoxelSpace.mgz from segmentThalamicNuclei.s

Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

External Email - Use Caution Hi Douglas, � Thank you for looking into this. It gives the following error. � trac-preproc.sh -c config.file intrareg: Undefined variable. � Thanks, � King-Wai � From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Douglas N. Gr

Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

External Email - Use Caution Hi Douglas, � According to TRACULA tutorial https://secure-web.cisco.com/1YmZsfNNF2-hIwlP4SVMeWmro3S6_ShXDaAbTt2crsEmdQne-MX5QsRlMCMbLBZ4XGjAhQKXN80Ro3gRtSgISkplOshl8Jl9RHNDCdsv_xIhyqjYmDejPNpbxxPXWicOzB32_El09nIHPiVNjsakDv5K-Vm7TuGe1_KRyKDOs4LcQN

Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

External Email - Use Caution I added it to the config file, then it complains interreg: Undefined variable. � When I added interreg = 5, then it complains subj: Undefined variable. � Should I continue fixing it until no more Undefined variable? � From: freesurfer-boun...

Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

External Email - Use Caution Yes, my original config file works with 7.2 � I really appreciate your help. � Thanks. � King-Wai � From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Monday, July 25, 2022 9:23 PM To: freesurfer@nmr.mgh.harva

Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

External Email - Use Caution Hi Anastasia, � The problem is in 7.3, trac-all -prep -c config.file is looking for ThalamicNuclei.v12.T1.FSvoxelSpace.mgz from segmentThalamicNuclei.sh which doesn’t exist. Because in v7.3, segmentThalamicNuclei.sh output a new version v13 (Tha

Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

External Email - Use Caution Hi Anastasia, � I thought he wants me to run trac-preproc.sh he sent to run it directly. I wasn’t told to replace it with the one in the original 7.3. � After replacing the original one with the modified one Doug sent, trac-all -prep -c config.f

Re: [Freesurfer] Tracula - Preproc

External Email - Use Caution Hi Alan, � As Anastasia said, bet is part of FSL. If you don’t have it installed already, you need to install FSL. � Best, � King-Wai � From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Yendiki, Anastasia Sent: Thursday, August 11