External Email - Use Caution

There is a change related to that,

Date:   Mon Jul 25 21:24:30 2022 -0400     trac-preproc. #BF. Changed expected thalseg version to 1.3; also added an option to be able to spec the thalseg file. AY should look at it.

- in the latest development builds, which are located under,https://secure-web.cisco.com/16IqsFJkXTetOby5z7oQ2GGW3ceVlc5mNqOcsSHL9k5AAMK... That and some other changes will make it into the 7.3.2 release.

- R. On Aug 1, 2022, at 00:44, kingwai.chu@gmail.com wrote:        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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Yendiki, AnastasiaSent: Monday, August 1, 2022 12:15 AMTo: '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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of kingwai.chu@gmail.com<kingwai.chu@gmail.com>Sent: Monday, August 1, 2022 12:10 AMTo: 'Freesurfer support list' <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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Yendiki, AnastasiaSent: Monday, August 1, 2022 12:03 AMTo: 'Freesurfer support list' <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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of kingwai.chu@gmail.com<kingwai.chu@gmail.com>Sent: Monday, July 25, 2022 2:11 PMTo: 'Freesurfer support list' <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.fileintrareg: Undefined variable. Thanks, King-Wai From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Douglas N.. GreveSent: Monday, July 25, 2022 1:55 PMTo: freesurfer@nmr.mgh.harvard.eduSubject: 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.chu@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 v7.3However 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.mgzln -s ThalamicNuclei.v13.T1.FSvoxelSpace.mgz ThalamicNuclei.v12.T1.FSvoxelSpace.mgz trac-all finished w/o problem. trac-all -versiontrac-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 _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1v-b5JJwuDi1SzLbIsac4ppx7Moeb9XlbmcaO28MpjIUuDq... mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

On Aug 1, 2022, at 00:14, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu> wrote: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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of kingwai.chu@gmail.com <kingwai.chu@gmail.com>Sent: Monday, August 1, 2022 12:10 AMTo: 'Freesurfer support list' <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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Yendiki, AnastasiaSent: Monday, August 1, 2022 12:03 AMTo: 'Freesurfer support list' <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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of kingwai.chu@gmail.com<kingwai.chu@gmail.com>Sent: Monday, July 25, 2022 2:11 PMTo: 'Freesurfer support list' <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.fileintrareg: Undefined variable. Thanks, King-Wai From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Douglas N. GreveSent: Monday, July 25, 2022 1:55 PMTo: freesurfer@nmr.mgh.harvard.eduSubject: 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.chu@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 v7.3However 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.mgzln -s ThalamicNuclei.v13.T1.FSvoxelSpace.mgz ThalamicNuclei.v12.T1.FSvoxelSpace.mgz trac-all finished w/o problem. trac-all -versiontrac-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 _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1v-b5JJwuDi1SzLbIsac4ppx7Moeb9XlbmcaO28MpjIUuDq... mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer