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

2022-05-06 Thread kingwai.chu 
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 date for FreeSurfer 7.3 release

  

Hi King-Wai - I maintain that list of TRACULA features that are in the dev 
version now and therefore will definitely be included in 7.3, but that doesn't 
necessarily mean that 7.3 is imminent. I'd use the 7.2 version for now, or the 
dev version if you're specifically interested in what's on that list.

  

Anastasia. 

  _  

From: freesurfer-boun...@nmr.mgh.harvard.edu 
  
mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > on behalf of King-Wai Chu 
mailto:kingwai@gmail.com> >
Sent: Friday, May 6, 2022 2:53 PM
To: freesurfer@nmr.mgh.harvard.edu   
mailto:freesurfer@nmr.mgh.harvard.edu> >
Subject: [Freesurfer] An estimated date for FreeSurfer 7.3 release 

  

External Email - Use Caution

Hello,

  

I saw in  

 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://secure-web.cisco.com/1A0KXeegfFsr-cg6Q7L02PhS1IdxpetLYuoKZcnb0LMpbVhckaCWSJzAn2ya7h7EZPRTcraTlXNz1X0UtrkXO6NocNMx-HR19o0Mu550aHoQB221jRB6whhLs-JZBjnpSqS9w-AvTf2ViRZrnTx-HVZheeUxTroNx1Ceq0l37UWmrKMiAH4m4k4o1NlQzOt36qOX-rZl8QRBej9WEpK_JDHsna7VHWp4vhcHov9scTBzgaiXuYeRwCR0iDi2JdJ20-csAvybqRTqfczmYFAMyd-VIuoSl1HYcFn33tPDBlsj5-vTrqR8mZnvCxpjQPBSdQb2TBuP25r14Q7_wJ7tV6A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FTracula
 that TRACULA in FreeSurfer 7.3 is upcoming.

Do you have an estimated date of when that will happen?

  

We want to update our version 7.1.1 to the latest release.

If 7.3 is coming out in a couple of months, we can wait for it.

Or should we install 7.2 instead?

  

Thanks,

  

King-Wai

  

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[Freesurfer] TRACULA in FreeSurfer version 7.3

2022-07-22 Thread kingwai.chu 
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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Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

2022-07-25 Thread kingwai.chu 
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





___
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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 
 .
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 
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receiving this message means you understand and accept this risk and wish to 
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Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

2022-07-25 Thread kingwai.chu 
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   
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
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 
 .
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

2022-07-25 Thread kingwai.chu 
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

 

 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 
   
 
 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 
   
 
 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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The information in this e-mail is intended only for the person to whom it is 
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cont

Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

2022-07-25 Thread kingwai.chu 
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   
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

 

 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 
   
 
 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 
   
 
 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 ThalamicNu

Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

2022-07-31 Thread kingwai.chu 
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> > on behalf of 
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> > 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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Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

2022-07-31 Thread kingwai.chu 
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> > on behalf of 
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> > 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> > on behalf of 
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> > 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
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 
 .
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 s

Re: [Freesurfer] Tracula - Preproc

2022-08-11 Thread kingwai.chu 
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, 2022 3:42 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula - Preproc

 �

Yes that's from FSL. It's needs to be in $FSLDIR.

  _  

From: freesurfer-boun...@nmr.mgh.harvard.edu 
  
mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > on behalf of Alan Francis 
mailto:alandarkene...@gmail.com> >
Sent: Thursday, August 11, 2022 3:30 PM
To: Freesurfer mailto:freesurfer@nmr.mgh.harvard.edu> >
Subject: [Freesurfer] Tracula - Preproc 

 �

 � � � � � � � �External Email - Use Caution � � � � � � � �

Hi Anastasia, King Wei:

 �

I did as you suggested with the config file and the preprocessing ran for a bit 
but then an error occurred. I have attached the run script. It says BET not 
found. Is this the Brain Extraction tool?

 �

Could you please shed some light on this?

 �

thanks so much,

 �

Alan


-- 

|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|


Alan N. Francis PhD
Assistant Professor of Neuroscience
Institute of Neuroscience

University of Texas, School of Medicine

Rio Grande Valley

Texas.



 

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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 
 .
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.