Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
External Email - Use Caution Hi Anastasia, I have posted a solution to the thread "TRACULA -bedp parallel processing" Maybe you can include it in a future release. Thanks, King-Wai On Mon, Aug 1, 2022 at 12:57 AM Yendiki, Anastasia wrote: > Good to hear, thanks for testing it. We'll implement a permanent solution > so you won't have to replace anything in the future. > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of kingwai@gmail.com > > *Sent:* Monday, August 1, 2022 12:44 AM > *To:* 'Freesurfer support list' > *Subject:* 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.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' > *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 < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of kingwai@gmail.com > > *Sent:* Monday, August 1, 2022 12:10 AM > *To:* 'Freesurfer support list' > *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 < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Yendiki, Anastasia > *Sent:* Monday, August 1, 2022 12:03 AM > *To:* 'Freesurfer support list' > *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 < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of kingwai@gmail.com > > *Sent:* Monday, July 25, 2022 2:11 PM > *To:* 'Freesurfer support list' > *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 < > 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 > *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 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 proble
Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
AY did look into it, I just checked in a change on top of that change. Let's go with my change for the release. Thanks! From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of fsbuild Sent: Monday, August 1, 2022 12:57 AM To: freesurfer@nmr.mgh.harvard.edu Cc: kingwai@gmail.com Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3 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, MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/<https://secure-web.cisco.com/16IqsFJkXTetOby5z7oQ2GGW3ceVlc5mNqOcsSHL9k5AAMKLWHm2POf_S0eGJD7LvH-Rx4mlhUvWx6LgQy-q3pHUo6odo2HUzH5uK2pw4hWjukRqykCXncWcvL89U7Ihr1Wy4vWcysi3Yq9UySr4hJBKqO7jh_1gx5bkNy4GVG58Hq8eKCWI8kG1UM8dAm5slogANcs8Hh0lcUCOJcHmo10D2MOEouR8Byjb7CNF0mBxiQcx7v5zXpBfGpqYAp8SlSqB7_L_8uTU7HCxsVAZZlJfNOacSDHlv__n0uWJFLDDcLFPdZHVfrr-BIsETaPpcp5bzQVyMzpRzoFYF35LAXg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2F> That and some other changes will make it into the 7.3.2 release. - R. On Aug 1, 2022, at 00:44, kingwai@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-boun...@nmr.mgh.harvard.edu On Behalf Of Yendiki, Anastasia Sent: Monday, August 1, 2022 12:15 AM To: 'Freesurfer support list' 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> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of kingwai@gmail.com<mailto:kingwai@gmail.com>mailto:kingwai@gmail.com>> Sent: Monday, August 1, 2022 12:10 AM To: 'Freesurfer support list' 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> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Yendiki, Anastasia Sent: Monday, August 1, 2022 12:03 AM To: 'Freesurfer support list' 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> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of kingwai@gmail.com<mailto:kingwai@gmail.com>mailto:kingwai@gmail.com>> Sent: Monday, July 25, 2022 2:11 PM To: 'Freesurfer support list' 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> 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 l
Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
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/16IqsFJkXTetOby5z7oQ2GGW3ceVlc5mNqOcsSHL9k5AAMKLWHm2POf_S0eGJD7LvH-Rx4mlhUvWx6LgQy-q3pHUo6odo2HUzH5uK2pw4hWjukRqykCXncWcvL89U7Ihr1Wy4vWcysi3Yq9UySr4hJBKqO7jh_1gx5bkNy4GVG58Hq8eKCWI8kG1UM8dAm5slogANcs8Hh0lcUCOJcHmo10D2MOEouR8Byjb7CNF0mBxiQcx7v5zXpBfGpqYAp8SlSqB7_L_8uTU7HCxsVAZZlJfNOacSDHlv__n0uWJFLDDcLFPdZHVfrr-BIsETaPpcp5bzQVyMzpRzoFYF35LAXg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2F That and some other changes will make it into the 7.3.2 release. - R. On Aug 1, 2022, at 00:44, kingwai@gmail.com wrote:External Email - Use CautionHi 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-WaiFrom:freesurfer-boun...@nmr.mgh.harvard.edu freesurfer-boun...@nmr.mgh.harvard.eduOn Behalf OfYendiki, AnastasiaSent:Monday, August 1, 2022 12:15 AMTo:'Freesurfer support list' freesurfer@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] TRACULA in FreeSurfer version 7.3Indeed. 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.edufreesurfer-boun...@nmr.mgh.harvard.edu on behalf ofkingwai@gmail.comkingwai@gmail.comSent:Monday, August 1, 2022 12:10 AMTo:'Freesurfer support list' freesurfer@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] TRACULA in FreeSurfer version 7.3External Email - Use CautionHi 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-WaiFrom:freesurfer-boun...@nmr.mgh.harvard.edufreesurfer-boun...@nmr.mgh.harvard.eduOn Behalf OfYendiki, AnastasiaSent:Monday, August 1, 2022 12:03 AMTo:'Freesurfer support list' freesurfer@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] TRACULA in FreeSurfer version 7.3Hi 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.edufreesurfer-boun...@nmr.mgh.harvard.edu on behalf ofkingwai@gmail.comkingwai@gmail.comSent:Monday, July 25, 2022 2:11 PMTo:'Freesurfer support list' freesurfer@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] TRACULA in FreeSurfer version 7.3External Email - Use CautionHi Douglas,Thank you for looking into this.It gives the following error.trac-preproc.sh -c config.fileintrareg: Undefined variable.Thanks,King-WaiFrom:freesurfer-boun...@nmr.mgh.harvard.edufreesurfer-boun...@nmr.mgh.harvard.eduOn Behalf OfDouglas N.. GreveSent:Monday, July 25, 2022 1:55 PMTo:freesur...@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] TRACULA in FreeSurfer version 7.3Can 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.comwrote:External Email - Use CautionHi 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.mgztrac-all finished w/o problem.trac-all -versiontrac-all 7.3.0I 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 listfreesur...@nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be
Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
Good to hear, thanks for testing it. We'll implement a permanent solution so
you won't have to replace anything in the future.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of kingwai@gmail.com
Sent: Monday, August 1, 2022 12:44 AM
To: 'Freesurfer support list'
Subject: 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.file runs w/o problem.
Thanks,
King-Wai
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Yendiki, Anastasia
Sent: Monday, August 1, 2022 12:15 AM
To: 'Freesurfer support list'
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>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of kingwai@gmail.com<mailto:kingwai@gmail.com>
mailto:kingwai@gmail.com>>
Sent: Monday, August 1, 2022 12:10 AM
To: 'Freesurfer support list'
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>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Yendiki, Anastasia
Sent: Monday, August 1, 2022 12:03 AM
To: 'Freesurfer support list'
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>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of kingwai@gmail.com<mailto:kingwai@gmail.com>
mailto:kingwai@gmail.com>>
Sent: Monday, July 25, 2022 2:11 PM
To: 'Freesurfer support list'
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>
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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Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
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claiming to be
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfe
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.file runs w/o problem. � Thanks, � King-Wai � From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Yendiki, Anastasia Sent: Monday, August 1, 2022 12:15 AM To: 'Freesurfer support list' 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> mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > on behalf of kingwai@gmail.com <mailto:kingwai@gmail.com> mailto:kingwai@gmail.com> > Sent: Monday, August 1, 2022 12:10 AM To: 'Freesurfer support list' 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> mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > On Behalf Of Yendiki, Anastasia Sent: Monday, August 1, 2022 12:03 AM To: 'Freesurfer support list' 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> mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > on behalf of kingwai@gmail.com <mailto:kingwai@gmail.com> mailto:kingwai@gmail.com> > Sent: Monday, July 25, 2022 2:11 PM To: 'Freesurfer support list' 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> 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 � ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to contin
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 on behalf of kingwai@gmail.com Sent: Monday, August 1, 2022 12:10 AM To: 'Freesurfer support list' 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 On Behalf Of Yendiki, Anastasia Sent: Monday, August 1, 2022 12:03 AM To: 'Freesurfer support list' 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> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of kingwai@gmail.com<mailto:kingwai@gmail.com> mailto:kingwai@gmail.com>> Sent: Monday, July 25, 2022 2:11 PM To: 'Freesurfer support list' 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> 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://secure-web.cisco.com/1mfowdBcxH4LnEHqsQ4eF-CAYl64n3ckGL8BGt4nPbtL4OeGumkxM8MllrxFKmlByW-LDM0iMEYy94ixKM1KG3D-kKHOVUO8yLsvCtRWCmCwq0XtztyJyTf4VVuC9j4oGmFvWyMZHOnLCIisJpgKeApdTCX-4yI8tH5YJehBsANpbd_YTkwiTtKJMmy3b2t9gJoR0e19abaQXY_1HDz5kr8IlMEUasxk6j9EZY4il5LllVP2dIL6ENMUR3_yH1DE_Jx0srZwfJk-1YClbUR44-7qjZtjJNof8WulEr0kzdYcSPacrNREGNjxFBBnDIBqlC0sAF6ORBWT3SuDX5McR9w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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 On Behalf Of Yendiki, Anastasia Sent: Monday, August 1, 2022 12:03 AM To: 'Freesurfer support list' 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> mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > on behalf of kingwai@gmail.com <mailto:kingwai@gmail.com> mailto:kingwai@gmail.com> > Sent: Monday, July 25, 2022 2:11 PM To: 'Freesurfer support list' 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> 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 � ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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 on behalf of kingwai@gmail.com Sent: Monday, July 25, 2022 2:11 PM To: 'Freesurfer support list' 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 On Behalf Of Douglas N. Greve Sent: Monday, July 25, 2022 1:55 PM To: 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://secure-web.cisco.com/1mfowdBcxH4LnEHqsQ4eF-CAYl64n3ckGL8BGt4nPbtL4OeGumkxM8MllrxFKmlByW-LDM0iMEYy94ixKM1KG3D-kKHOVUO8yLsvCtRWCmCwq0XtztyJyTf4VVuC9j4oGmFvWyMZHOnLCIisJpgKeApdTCX-4yI8tH5YJehBsANpbd_YTkwiTtKJMmy3b2t9gJoR0e19abaQXY_1HDz5kr8IlMEUasxk6j9EZY4il5LllVP2dIL6ENMUR3_yH1DE_Jx0srZwfJk-1YClbUR44-7qjZtjJNof8WulEr0kzdYcSPacrNREGNjxFBBnDIBqlC0sAF6ORBWT3SuDX5McR9w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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.harvard.edu Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3 � I don't know; Anastasia is the author. She's busy today and tomorrow, I was just trying to push it forward. Does it work with the given config file in 7.2? On 7/25/2022 5:46 PM, kingwai@gmail.com <mailto:kingwai@gmail.com> wrote: � � � � � � � �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...@nmr.mgh.harvard.edu <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Douglas N. Greve Sent: Monday, July 25, 2022 5:42 PM To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3 � I think the wiki is wrong. Try setting it to 3 in the config On 7/25/2022 5:30 PM, kingwai@gmail.com <mailto:kingwai@gmail.com> wrote: � � � � � � � �External Email - Use Caution � � � � � � � � Hi Douglas, � According to TRACULA tutorial <https://secure-web.cisco.com/1YmZsfNNF2-hIwlP4SVMeWmro3S6_ShXDaAbTt2crsEmdQne-MX5QsRlMCMbLBZ4XGjAhQKXN80Ro3gRtSgISkplOshl8Jl9RHNDCdsv_xIhyqjYmDejPNpbxxPXWicOzB32_El09nIHPiVNjsakDv5K-Vm7TuGe1_KRyKDOs4LcQNgZjekQ12oNoOGOGjRrrHXUePaAnan4hRAYvDCG4qnZ6i98TicZFC2XhfswWCkw90-ynses9onW4e5LLnSwJZrKtsXXmWTMKtxDuhBP1yIOC2hDf8LlSWmmSubzclnlh9I4h_VVVRQToywBLfcGR1QIAdleURvGUR8e9UqoMzQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTracula> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1zSA_b4ezKCEwgchIiEjJkTpIEBtecsFaamd9vKJ9u9cVmSkAQgnUAuAvI4uXSMMmrEh26h_MAYnwauVVNGcw_oVyzeG7nY4f4TYvyUJszcbvL5b-cNT2d4mQCl-LlqWW-RDYZFsXRUkKcKMPqtGKZp3Dqr-WlgKEC85pfBEmYQv0KLDuoSU6SnwmafZ-Og9_oDVRrW47SZYBDmLTpOZ9f5US6U7H7cfq5fcq90pyh6d6f9Afsp7QX1KObzxlMYnaAXoq4fcvax2sgQF3nWNcyL1jU3-TmppzASKqM6L-nhXvFTBDq2BGxf1pLOVNxwG2l2s-Nv6Maq6oR8gHg8tDCw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTracula � A very simple configuration file, where only the absolutely necessary inputs are specified, intrareg is not there. and it works on v7.2.0. w/o it explicitly specified. � From the same site above, Step 12: Specify the intra-subject registration method “The options are 1 (FLIRT with a correlation ratio cost), 2 (FLIRT with a mutual information cost), and 3 (bbregister, which uses a boundary-based cost). The default is option 3 (bbregister).” � If I don’t specify it in the config file, it should automatically use the default setting which is intrareg = 3. � I will add it to the config file and try again. � Thanks, � King-Wai � � � � � From: freesurfer-boun...@nmr.mgh.harvard.edu <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Douglas N. Greve Sent: Monday, July 25, 2022 5:02 PM To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3 � are you sure the config file is right? it should be defining the intrareg variable On 7/25/2022 2:11 PM, kingwai@gmail.com <mailto:kingwai@gmail.com> wrote: � � � � � � � �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> <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 v
Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
I don't know; Anastasia is the author. She's busy today and tomorrow, I
was just trying to push it forward. Does it work with the given config
file in 7.2?
On 7/25/2022 5:46 PM, kingwai@gmail.com wrote:
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...@nmr.mgh.harvard.edu
*On Behalf Of *Douglas N. Greve
*Sent:* Monday, July 25, 2022 5:42 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
I think the wiki is wrong. Try setting it to 3 in the config
On 7/25/2022 5:30 PM, kingwai@gmail.com wrote:
*External Email - Use Caution *
Hi Douglas,
According to
TRACULA tutorial
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https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
<https://secure-web.cisco.com/1YmZsfNNF2-hIwlP4SVMeWmro3S6_ShXDaAbTt2crsEmdQne-MX5QsRlMCMbLBZ4XGjAhQKXN80Ro3gRtSgISkplOshl8Jl9RHNDCdsv_xIhyqjYmDejPNpbxxPXWicOzB32_El09nIHPiVNjsakDv5K-Vm7TuGe1_KRyKDOs4LcQNgZjekQ12oNoOGOGjRrrHXUePaAnan4hRAYvDCG4qnZ6i98TicZFC2XhfswWCkw90-ynses9onW4e5LLnSwJZrKtsXXmWTMKtxDuhBP1yIOC2hDf8LlSWmmSubzclnlh9I4h_VVVRQToywBLfcGR1QIAdleURvGUR8e9UqoMzQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTracula>
A very simple configuration file, where only the absolutely
necessary inputs are specified, intrareg is not there.
and it works on v7.2.0. w/o it explicitly specified.
From the same site above,
Step 12: Specify the intra-subject registration method
“The options are 1 (FLIRT with a correlation ratio cost), 2 (FLIRT
with a mutual information cost), and 3 (bbregister, which uses a
boundary-based cost). The default is option 3 (bbregister).”
If I don’t specify it in the config file, it should automatically
use the default setting which is intrareg = 3.
I will add it to the config file and try again.
Thanks,
King-Wai
*From:*freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of
*Douglas N. Greve
*Sent:* Monday, July 25, 2022 5:02 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
are you sure the config file is right? it should be defining the
intrareg variable
On 7/25/2022 2:11 PM, kingwai@gmail.com wrote:
*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> *On Behalf Of
*Douglas N. Greve
*Sent:* Monday, July 25, 2022 1:55 PM
*To:* 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 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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<https://s
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...@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Monday, July 25, 2022 5:42 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3 � I think the wiki is wrong. Try setting it to 3 in the config On 7/25/2022 5:30 PM, kingwai@gmail.com <mailto:kingwai@gmail.com> wrote: � � � � � � � �External Email - Use Caution � � � � � � � � Hi Douglas, � According to TRACULA tutorial <https://secure-web.cisco.com/1YmZsfNNF2-hIwlP4SVMeWmro3S6_ShXDaAbTt2crsEmdQne-MX5QsRlMCMbLBZ4XGjAhQKXN80Ro3gRtSgISkplOshl8Jl9RHNDCdsv_xIhyqjYmDejPNpbxxPXWicOzB32_El09nIHPiVNjsakDv5K-Vm7TuGe1_KRyKDOs4LcQNgZjekQ12oNoOGOGjRrrHXUePaAnan4hRAYvDCG4qnZ6i98TicZFC2XhfswWCkw90-ynses9onW4e5LLnSwJZrKtsXXmWTMKtxDuhBP1yIOC2hDf8LlSWmmSubzclnlh9I4h_VVVRQToywBLfcGR1QIAdleURvGUR8e9UqoMzQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTracula> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Wawa7n82Ac-dxyJdbIRzWGaYawZoqFkIMlb_ww0U2WwkYe4a7CvsMhBeHTBltzM_nC85mYlouQphexPPQ6ihjTl3vAqjloh2FMNkxTysJSZwu3sjMnTnXiRz9FAXBklwR10UIEfypeaB7qT5j3j15xwPxBnAypiFfFknqFShA7d3AN66P4sjI9z0dcIw11RCFvlKF2fgf_4-t3u3MMdhzkm5YnySFWjQ3CkSFs7ATIcnue9LG-E6O4q9J70fV3oVNWPG_9frl8LlGflnqGToNZSiCbAKkZO_rwnGGZJW7lOMfg1SV9q3vCGwGa8cPvK7ei4mhf3nO-MBh5BzD4Oj0Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTracula � A very simple configuration file, where only the absolutely necessary inputs are specified, intrareg is not there. and it works on v7.2.0. w/o it explicitly specified. � From the same site above, Step 12: Specify the intra-subject registration method “The options are 1 (FLIRT with a correlation ratio cost), 2 (FLIRT with a mutual information cost), and 3 (bbregister, which uses a boundary-based cost). The default is option 3 (bbregister).” � If I don’t specify it in the config file, it should automatically use the default setting which is intrareg = 3. � I will add it to the config file and try again. � Thanks, � King-Wai � � � � � From: freesurfer-boun...@nmr.mgh.harvard.edu <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Douglas N. Greve Sent: Monday, July 25, 2022 5:02 PM To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3 � are you sure the config file is right? it should be defining the intrareg variable On 7/25/2022 2:11 PM, kingwai@gmail.com <mailto:kingwai@gmail.com> wrote: � � � � � � � �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> <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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addresse
Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
I think the wiki is wrong. Try setting it to 3 in the config
On 7/25/2022 5:30 PM, kingwai@gmail.com wrote:
External Email - Use Caution
Hi Douglas,
According to
TRACULA tutorial
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
<https://secure-web.cisco.com/1YmZsfNNF2-hIwlP4SVMeWmro3S6_ShXDaAbTt2crsEmdQne-MX5QsRlMCMbLBZ4XGjAhQKXN80Ro3gRtSgISkplOshl8Jl9RHNDCdsv_xIhyqjYmDejPNpbxxPXWicOzB32_El09nIHPiVNjsakDv5K-Vm7TuGe1_KRyKDOs4LcQNgZjekQ12oNoOGOGjRrrHXUePaAnan4hRAYvDCG4qnZ6i98TicZFC2XhfswWCkw90-ynses9onW4e5LLnSwJZrKtsXXmWTMKtxDuhBP1yIOC2hDf8LlSWmmSubzclnlh9I4h_VVVRQToywBLfcGR1QIAdleURvGUR8e9UqoMzQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTracula>
A very simple configuration file, where only the absolutely necessary
inputs are specified, intrareg is not there.
and it works on v7.2.0. w/o it explicitly specified.
From the same site above,
Step 12: Specify the intra-subject registration method
“The options are 1 (FLIRT with a correlation ratio cost), 2 (FLIRT
with a mutual information cost), and 3 (bbregister, which uses a
boundary-based cost). The default is option 3 (bbregister).”
If I don’t specify it in the config file, it should automatically use
the default setting which is intrareg = 3.
I will add it to the config file and try again.
Thanks,
King-Wai
*From:*freesurfer-boun...@nmr.mgh.harvard.edu
*On Behalf Of *Douglas N. Greve
*Sent:* Monday, July 25, 2022 5:02 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
are you sure the config file is right? it should be defining the
intrareg variable
On 7/25/2022 2:11 PM, kingwai@gmail.com wrote:
*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> *On Behalf Of
*Douglas N. Greve
*Sent:* Monday, July 25, 2022 1:55 PM
*To:* 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 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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
*MailScanner has detected a possible fraud attempt from
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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_KRyKDOs4LcQNgZjekQ12oNoOGOGjRrrHXUePaAnan4hRAYvDCG4qnZ6i98TicZFC2XhfswWCkw90-ynses9onW4e5LLnSwJZrKtsXXmWTMKtxDuhBP1yIOC2hDf8LlSWmmSubzclnlh9I4h_VVVRQToywBLfcGR1QIAdleURvGUR8e9UqoMzQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTracula � A very simple configuration file, where only the absolutely necessary inputs are specified, intrareg is not there. and it works on v7.2.0. w/o it explicitly specified. � From the same site above, Step 12: Specify the intra-subject registration method “The options are 1 (FLIRT with a correlation ratio cost), 2 (FLIRT with a mutual information cost), and 3 (bbregister, which uses a boundary-based cost). The default is option 3 (bbregister).” � If I don’t specify it in the config file, it should automatically use the default setting which is intrareg = 3. � I will add it to the config file and try again. � Thanks, � King-Wai � � � � � From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Monday, July 25, 2022 5:02 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3 � are you sure the config file is right? it should be defining the intrareg variable On 7/25/2022 2:11 PM, kingwai@gmail.com <mailto:kingwai@gmail.com> wrote: � � � � � � � �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> <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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
are you sure the config file is right? it should be defining the intrareg variable On 7/25/2022 2:11 PM, kingwai@gmail.com wrote: 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. Greve *Sent:* Monday, July 25, 2022 1:55 PM *To:* 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 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1mfowdBcxH4LnEHqsQ4eF-CAYl64n3ckGL8BGt4nPbtL4OeGumkxM8MllrxFKmlByW-LDM0iMEYy94ixKM1KG3D-kKHOVUO8yLsvCtRWCmCwq0XtztyJyTf4VVuC9j4oGmFvWyMZHOnLCIisJpgKeApdTCX-4yI8tH5YJehBsANpbd_YTkwiTtKJMmy3b2t9gJoR0e19abaQXY_1HDz5kr8IlMEUasxk6j9EZY4il5LllVP2dIL6ENMUR3_yH1DE_Jx0srZwfJk-1YClbUR44-7qjZtjJNof8WulEr0kzdYcSPacrNREGNjxFBBnDIBqlC0sAF6ORBWT3SuDX5McR9w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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. Greve Sent: Monday, July 25, 2022 1:55 PM To: 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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 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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
#! /bin/tcsh -f
#
# trac-preproc
#
# Tractography pre-processing for a single subject
#
# Original Author: Anastasia Yendiki
#
# Copyright © 2011 The General Hospital Corporation (Boston, MA) "MGH"
#
# Terms and conditions for use, reproduction, distribution and contribution
# are found in the 'FreeSurfer Software License Agreement' contained
# in the file 'LICENSE' found in the FreeSurfer distribution, and here:
#
# https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense
#
# Reporting: freesurfer@nmr.mgh.harvard.edu
#
#
umask 002
set VERSION = 'trac-preproc @FS_VERSION@';
set ProgName = `basename $0`
set inputargs = ($argv)
set thalseg = ThalamicNuclei.v13.T1.FSvoxelSpace
# Set default options -#
set PrintHelp = 0 # Print help and exit
set debug = 0 # Generate more output
set DoTime = 0 # Time main commands
set fs_time = ()
set rcfile = () # Name of input run command file
set LF = () # Name of log file
set CF = () # Name of command file
set DoIsRunning = 1 # Create a lock file while processing continues
set RunIt = 1 # If 0, do everything but run commands (for debugging)
# Parse input arguments ---#
if ($#argv == 0) goto usage_exit
set n = `echo $argv | egrep -e -help | wc -l`
if ($n != 0) then
set PrintHelp = 1
goto usage_exit
endif
set n = `echo $argv | egrep -e -version | wc -l`
if ($n != 0) then
echo $VERSION
exit 0
endif
source $FREESURFER_HOME/sources.csh
goto parse_args
parse_args_return:
goto check_params
check_params_return:
# Read configuration file -#
source $rcfile
if ($intrareg == 1 || $intrareg == 2) then
set reg = flt
else if ($intrareg == 3) then
set reg = bbr
endif
if ($interreg == 1 || $interreg == 2) then
set xspace = mni
else if ($interreg == 3) then
set xspace = rob
else if ($interreg == 4) then
set xspace = cvs
set cvstempdir = `dirname $intertrg` # Assuming ../mri/norm.mgz
set cvstempdir = `dirname $cvstempdir`
set cvstemp= `basename $cvstempdir`
set cvstempdir = `dirname $cvstempdir`
set cvswarp = final_CVSmorph_to$cvstemp
else if ($interreg == 5) then
set xspace = syn
setenv MY_MORPHS_DO_NOT_CONFORM_DEAL_WITH_IT
else if ($interreg == 6) then
set xspace = fnt
endif
if ($DoTime) then
fs_time ls >& /dev/null
if (! $status) set fs_time = fs_time
endif
printf '\n\n' >> $LF
echo "New invocation of $ProgName" >> $LF
printf '\n\n' >> $LF
whoami >> $LF
hostname >> $LF
uname -a >> $LF
limit >> $LF
if (-e /usr/bin/free) then
echo "" >> $LF
/usr/bin/free >> $LF
echo "" >> $LF
endif
if ("`uname -s`" == "Darwin") then
echo "" >> $LF
/usr/bin/top -l 1 | grep PhysMem >> $LF
echo "" >> $LF
endif
#-- Is this a longitudinal base template? ---#
set dobase = 0
if ($?tplist) then
if ($#tplist > 0) set dobase = 1
endif
#-- Create output directories ---#
set dtdir = $dtroot/$subj
set fsdir = $SUBJECTS_DIR/$subj
set dwidir = $dtdir/dmri
set xfmdir = $dwidir/xfms
set labdir = $dtdir/dlabel
set touchdir = $dtdir/touch
mkdir -p $dwidir $xfmdir $labdir
#-- Handle run status files -#
# Delete the error file. This is created when error_exit is run.
set ErrorFile = $dtdir/scripts/trac-all.error
rm -f $ErrorFile
# Delete the done file. This is created when the program exits normally.
set DoneFile = $dtdir/scripts/$ProgName
[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.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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
