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.file runs w/o problem. � Thanks, � King-Wai � From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Yendiki, Anastasia Sent: Monday, August 1, 2022 12:15 AM To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3 � Indeed. Doug sent you a modified version of trac-preproc, which is a script that's called by trac-all. The idea was for you to overwrite $FREESURFER_HOME/bin/trac-preproc with the version that Doug sent, then run trac-all like before. Did you try that? _____ From: freesurfer-boun...@nmr.mgh.harvard.edu <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > on behalf of kingwai....@gmail.com <mailto:kingwai....@gmail.com> <kingwai....@gmail.com <mailto:kingwai....@gmail.com> > Sent: Monday, August 1, 2022 12:10 AM To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > Subject: 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 (ThalamicNuclei.v13.T1.FSvoxelSpace.mgz). � Thanks, � King-Wai � From: freesurfer-boun...@nmr.mgh.harvard.edu <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > On Behalf Of Yendiki, Anastasia Sent: Monday, August 1, 2022 12:03 AM To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3 � Hi King-Wai - You are not supposed to run trac-preproc directly. Run trac-all -c configfile, like before. � Anastasia. � _____ From: freesurfer-boun...@nmr.mgh.harvard.edu <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > on behalf of kingwai....@gmail.com <mailto:kingwai....@gmail.com> <kingwai....@gmail.com <mailto:kingwai....@gmail.com> > Sent: Monday, July 25, 2022 2:11 PM To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > Subject: 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 <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > On Behalf Of Douglas N. Greve Sent: Monday, July 25, 2022 1:55 PM To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3 � Can you copy the attached trac-preproc into $FREESURFER/bin and try again (after removing the link)? On 7/22/2022 8:36 AM, kingwai....@gmail.com <mailto:kingwai....@gmail.com> wrote: � � � � � � � �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.sh which doesn’t exist. Because in v7.3, segmentThalamicNuclei.sh output a new version v13 (ThalamicNuclei.v13.T1.FSvoxelSpace.mgz). I worked around this problem by linking ThalamicNuclei.v12.T1.FSvoxelSpace.mgz � to ThalamicNuclei.v13.T1.FSvoxelSpace.mgz ln -s ThalamicNuclei.v13.T1.FSvoxelSpace.mgz ThalamicNuclei.v12.T1.FSvoxelSpace.mgz � trac-all finished w/o problem. � trac-all -version trac-all 7.3.0 � I seems trac-all in v7.3 forgets to update the fact that segmentThalamicNuclei.sh output v13 of the file. Or it is looking for v12 for a reason? � Is my fix correct? � Thanks, � King-Wai �
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