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
Can you copy the attached trac-preproc into $FREESURFER/bin and try again (after removing the link)?
On 7/22/2022 8:36 AM, kingwai.chu@gmail.com wrote:
External Email - Use Caution
Hi Anastasia,
Just downloaded FreeSurfer version 7.3 and trying out TRACULA.
Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3
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
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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.chu@gmail.com mailto:kingwai.chu@gmail.com wrote:
� � � � � � � �External Email - Use Caution � � � � � � � �
Hi Anastasia,
�
Just downloaded FreeSurfer version 7.3 and trying out TRACULA.
Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3
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
are you sure the config file is right? it should be defining the intrareg variable
On 7/25/2022 2:11 PM, kingwai.chu@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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.chu@gmail.com wrote:
* External Email - Use Caution * Hi Anastasia, Just downloaded FreeSurfer version 7.3 and trying out TRACULA. Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3 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
External Email - Use Caution
Hi Douglas,
�
According to
TRACULA tutorial
https://secure-web.cisco.com/1YmZsfNNF2-hIwlP4SVMeWmro3S6_ShXDaAbTt2crsEmdQn...
�
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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.chu@gmail.com mailto:kingwai.chu@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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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.chu@gmail.com mailto:kingwai.chu@gmail.com wrote:
� � � � � � � �External Email - Use Caution � � � � � � � �
Hi Anastasia,
�
Just downloaded FreeSurfer version 7.3 and trying out TRACULA.
Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3
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
I think the wiki is wrong. Try setting it to 3 in the config
On 7/25/2022 5:30 PM, kingwai.chu@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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.chu@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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@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.chu@gmail.com wrote: * External Email - Use Caution * Hi Anastasia, Just downloaded FreeSurfer version 7.3 and trying out TRACULA. Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3 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 *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/1e10JLv4mIf0c2B9W8-Vttq_K21QjjPLlLNR5Iqx3W-aDRJTXVGx15cFnCowePO8QXamOuYggKxY56E7h2aX_l9oxqDG-xTbOhubHkZJLmtQL9xBBHDphyOZT6lrZhGHJQiAOaxCl7SecB4TsthMwMg-4GnFcK_OfbZdiVGoGWYmyxSf_fMAq-TW15QnMnUnWMbjcuBx-NhNvwYW-g_7wjRKigoYVI6S22CEurLYcssGvF99aQhDyUp2XFCfy3eeUHj-x1sa5l-aFQnt9cZci8fUWkh5Lum-hXePyDjMj9sBYLb_fSOOGNNDvZRfdUHni4C_JsiaREhPgebQ0V8St9A/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
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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.chu@gmail.com mailto:kingwai.chu@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_ww0U2WwkYe...
�
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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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.chu@gmail.com mailto:kingwai.chu@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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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.chu@gmail.com mailto:kingwai.chu@gmail.com wrote:
� � � � � � � �External Email - Use Caution � � � � � � � �
Hi Anastasia,
�
Just downloaded FreeSurfer version 7.3 and trying out TRACULA.
Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3
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
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.chu@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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.chu@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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@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.chu@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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@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.chu@gmail.com wrote: * External Email - Use Caution * Hi Anastasia, Just downloaded FreeSurfer version 7.3 and trying out TRACULA. Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3 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 *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/1e10JLv4mIf0c2B9W8-Vttq_K21QjjPLlLNR5Iqx3W-aDRJTXVGx15cFnCowePO8QXamOuYggKxY56E7h2aX_l9oxqDG-xTbOhubHkZJLmtQL9xBBHDphyOZT6lrZhGHJQiAOaxCl7SecB4TsthMwMg-4GnFcK_OfbZdiVGoGWYmyxSf_fMAq-TW15QnMnUnWMbjcuBx-NhNvwYW-g_7wjRKigoYVI6S22CEurLYcssGvF99aQhDyUp2XFCfy3eeUHj-x1sa5l-aFQnt9cZci8fUWkh5Lum-hXePyDjMj9sBYLb_fSOOGNNDvZRfdUHni4C_JsiaREhPgebQ0V8St9A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> _______________________________________________ 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/1takmwuiGWIJ8aqAZFhWLZ_LMEhpEPdSqzP_VyDyh8RisG9LHDC6MZgbPJfGRVsJbTPHpb73jccWMFJGdw7fN3esmKaiFCIUdnJH9sxBd9KrKbgIBMZ_yK_yPfVGoIQDiADYKUUETAvjR0mp-BMJgcW6rUXxJvVRyNirfrAoy4R4v4QMgX5opFuRfqx1p3KVPEi-7ljhm_yahD5fw0AE0RbqBncZzRInIARdmdVUpFSBytaRBJO7R8ZgQ0NgvwjMEHy9C1as51tp3byQdLZ1QrHCP2sZxdyS2eqHDh6cX5bKlDam2LSV5FUjUweaXmzEk5Tx6Bx0oK9T_ADSU_WHCng/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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Yes, my original config file works with 7.2
�
I really appreciate your help.
�
Thanks.
�
King-Wai
�
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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.chu@gmail.com mailto:kingwai.chu@gmail.com wrote:
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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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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.chu@gmail.com mailto:kingwai.chu@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_b4ezKCEwgchIiEjJkTpIEBtecsFaamd9vKJ9u9cVmS...
�
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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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.chu@gmail.com mailto:kingwai.chu@gmail.com wrote:
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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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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.chu@gmail.com mailto:kingwai.chu@gmail.com wrote:
� � � � � � � �External Email - Use Caution � � � � � � � �
Hi Anastasia,
�
Just downloaded FreeSurfer version 7.3 and trying out TRACULA.
Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3
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
https://secure-web.cisco.com/1AQOqrVn211CtYM48OjffKrqb_crYJt6lw0JJYnqHW3zvTL...
Hi King-Wai - You are not supposed to run trac-preproc directly. Run trac-all -c configfile, like before.
Anastasia.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of kingwai.chu@gmail.com kingwai.chu@gmail.com Sent: Monday, July 25, 2022 2:11 PM To: 'Freesurfer support list' freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
External Email - Use Caution
Hi Douglas,
Thank you for looking into this.
It gives the following error.
trac-preproc.sh -c config.file
intrareg: Undefined variable.
Thanks,
King-Wai
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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.chu@gmail.commailto:kingwai.chu@gmail.com wrote:
External Email - Use Caution
Hi Anastasia,
Just downloaded FreeSurfer version 7.3 and trying out TRACULA.
Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3
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.edumailto: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/freesurferhttps://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
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Hi Anastasia,
�
The problem is in 7.3, trac-all -prep -c config.file is looking for ThalamicNuclei.v12.T1.FSvoxelSpace.mgz from segmentThalamicNuclei.sh which doesn’t exist.
Because in v7.3, segmentThalamicNuclei.sh output a new version v13 (ThalamicNuclei.v13.T1.FSvoxelSpace.mgz).
�
Thanks,
�
King-Wai
�
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Yendiki, Anastasia Sent: Monday, August 1, 2022 12:03 AM To: 'Freesurfer support list' freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
�
Hi King-Wai - You are not supposed to run trac-preproc directly. Run trac-all -c configfile, like before.
�
Anastasia.
�
_____
From: freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu > on behalf of kingwai.chu@gmail.com mailto:kingwai.chu@gmail.com <kingwai.chu@gmail.com mailto:kingwai.chu@gmail.com > Sent: Monday, July 25, 2022 2:11 PM To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
�
� � � � � � � �External Email - Use Caution � � � � � � � �
Hi Douglas,
�
Thank you for looking into this.
It gives the following error.
�
trac-preproc.sh -c config.file
intrareg: Undefined variable.
�
Thanks,
�
King-Wai
�
From: freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@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.chu@gmail.com mailto:kingwai.chu@gmail.com wrote:
� � � � � � � �External Email - Use Caution � � � � � � � �
Hi Anastasia,
�
Just downloaded FreeSurfer version 7.3 and trying out TRACULA.
Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3
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
�
Indeed. Doug sent you a modified version of trac-preproc, which is a script that's called by trac-all. The idea was for you to overwrite $FREESURFER_HOME/bin/trac-preproc with the version that Doug sent, then run trac-all like before. Did you try that? ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of kingwai.chu@gmail.com kingwai.chu@gmail.com Sent: Monday, August 1, 2022 12:10 AM To: 'Freesurfer support list' freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
External Email - Use Caution
Hi Anastasia,
The problem is in 7.3, trac-all -prep -c config.file is looking for ThalamicNuclei.v12.T1.FSvoxelSpace.mgz from segmentThalamicNuclei.sh which doesn’t exist.
Because in v7.3, segmentThalamicNuclei.sh output a new version v13 (ThalamicNuclei.v13.T1.FSvoxelSpace.mgz).
Thanks,
King-Wai
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Yendiki, Anastasia Sent: Monday, August 1, 2022 12:03 AM To: 'Freesurfer support list' freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
Hi King-Wai - You are not supposed to run trac-preproc directly. Run trac-all -c configfile, like before.
Anastasia.
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of kingwai.chu@gmail.commailto:kingwai.chu@gmail.com <kingwai.chu@gmail.commailto:kingwai.chu@gmail.com> Sent: Monday, July 25, 2022 2:11 PM To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Douglas N. Greve Sent: Monday, July 25, 2022 1:55 PM To: freesurfer@nmr.mgh.harvard.edumailto: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.chu@gmail.commailto:kingwai.chu@gmail.com wrote:
External Email - Use Caution
Hi Anastasia,
Just downloaded FreeSurfer version 7.3 and trying out TRACULA.
Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3
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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External Email - Use Caution
Hi Anastasia,
�
I thought he wants me to run trac-preproc.sh he sent to run it directly.
I wasn’t told to replace it with the one in the original 7.3.
�
After replacing the original one with the modified one Doug sent, trac-all -prep -c config.file runs w/o problem.
�
Thanks,
�
King-Wai
�
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Yendiki, Anastasia Sent: Monday, August 1, 2022 12:15 AM To: 'Freesurfer support list' freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
�
Indeed. Doug sent you a modified version of trac-preproc, which is a script that's called by trac-all. The idea was for you to overwrite $FREESURFER_HOME/bin/trac-preproc with the version that Doug sent, then run trac-all like before. Did you try that?
_____
From: freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu > on behalf of kingwai.chu@gmail.com mailto:kingwai.chu@gmail.com <kingwai.chu@gmail.com mailto:kingwai.chu@gmail.com > Sent: Monday, August 1, 2022 12:10 AM To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
�
� � � � � � � �External Email - Use Caution � � � � � � � �
Hi Anastasia,
�
The problem is in 7.3, trac-all -prep -c config.file is looking for ThalamicNuclei.v12.T1.FSvoxelSpace.mgz � from segmentThalamicNuclei.sh which doesn’t exist.
Because in v7.3, segmentThalamicNuclei.sh output a new version v13 (ThalamicNuclei.v13.T1.FSvoxelSpace.mgz).
�
Thanks,
�
King-Wai
�
From: freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu > On Behalf Of Yendiki, Anastasia Sent: Monday, August 1, 2022 12:03 AM To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
�
Hi King-Wai - You are not supposed to run trac-preproc directly. Run trac-all -c configfile, like before.
�
Anastasia.
�
_____
From: freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu > on behalf of kingwai.chu@gmail.com mailto:kingwai.chu@gmail.com <kingwai.chu@gmail.com mailto:kingwai.chu@gmail.com > Sent: Monday, July 25, 2022 2:11 PM To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
�
� � � � � � � �External Email - Use Caution � � � � � � � �
Hi Douglas,
�
Thank you for looking into this.
It gives the following error.
�
trac-preproc.sh -c config.file
intrareg: Undefined variable.
�
Thanks,
�
King-Wai
�
From: freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@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.chu@gmail.com mailto:kingwai.chu@gmail.com wrote:
� � � � � � � �External Email - Use Caution � � � � � � � �
Hi Anastasia,
�
Just downloaded FreeSurfer version 7.3 and trying out TRACULA.
Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3
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
�
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of kingwai.chu@gmail.com kingwai.chu@gmail.com Sent: Monday, August 1, 2022 12:44 AM To: 'Freesurfer support list' freesurfer@nmr.mgh.harvard.edu 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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Yendiki, Anastasia Sent: Monday, August 1, 2022 12:15 AM To: 'Freesurfer support list' freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
Indeed. Doug sent you a modified version of trac-preproc, which is a script that's called by trac-all. The idea was for you to overwrite $FREESURFER_HOME/bin/trac-preproc with the version that Doug sent, then run trac-all like before. Did you try that?
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of kingwai.chu@gmail.commailto:kingwai.chu@gmail.com <kingwai.chu@gmail.commailto:kingwai.chu@gmail.com> Sent: Monday, August 1, 2022 12:10 AM To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
External Email - Use Caution
Hi Anastasia,
The problem is in 7.3, trac-all -prep -c config.file is looking for ThalamicNuclei.v12.T1.FSvoxelSpace.mgz from segmentThalamicNuclei.sh which doesn’t exist.
Because in v7.3, segmentThalamicNuclei.sh output a new version v13 (ThalamicNuclei.v13.T1.FSvoxelSpace.mgz).
Thanks,
King-Wai
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Yendiki, Anastasia Sent: Monday, August 1, 2022 12:03 AM To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
Hi King-Wai - You are not supposed to run trac-preproc directly. Run trac-all -c configfile, like before.
Anastasia.
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of kingwai.chu@gmail.commailto:kingwai.chu@gmail.com <kingwai.chu@gmail.commailto:kingwai.chu@gmail.com> Sent: Monday, July 25, 2022 2:11 PM To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Douglas N. Greve Sent: Monday, July 25, 2022 1:55 PM To: freesurfer@nmr.mgh.harvard.edumailto: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.chu@gmail.commailto:kingwai.chu@gmail.com wrote:
External Email - Use Caution
Hi Anastasia,
Just downloaded FreeSurfer version 7.3 and trying out TRACULA.
Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3
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.edumailto: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/freesurferhttps://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
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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 AYENDIKI@mgh.harvard.edu 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-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of kingwai.chu@gmail.com kingwai.chu@gmail.com *Sent:* Monday, August 1, 2022 12:44 AM *To:* 'Freesurfer support list' freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
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-Wai
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Yendiki, Anastasia *Sent:* Monday, August 1, 2022 12:15 AM *To:* 'Freesurfer support list' freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
Indeed. Doug sent you a modified version of trac-preproc, which is a script that's called by trac-all. The idea was for you to overwrite $FREESURFER_HOME/bin/trac-preproc with the version that Doug sent, then run trac-all like before. Did you try that?
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of kingwai.chu@gmail.com kingwai.chu@gmail.com *Sent:* Monday, August 1, 2022 12:10 AM *To:* 'Freesurfer support list' freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
External Email - Use Caution *Hi Anastasia,
The problem is in 7.3, trac-all -prep -c config.file is looking for ThalamicNuclei.v12.T1.FSvoxelSpace.mgz from segmentThalamicNuclei.sh which doesn’t exist.
Because in v7.3, segmentThalamicNuclei.sh output a new version v13 (ThalamicNuclei.v13.T1.FSvoxelSpace.mgz).
Thanks,
King-Wai
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Yendiki, Anastasia *Sent:* Monday, August 1, 2022 12:03 AM *To:* 'Freesurfer support list' freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
Hi King-Wai - You are not supposed to run trac-preproc directly. Run trac-all -c configfile, like before.
Anastasia.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of kingwai.chu@gmail.com kingwai.chu@gmail.com *Sent:* Monday, July 25, 2022 2:11 PM *To:* 'Freesurfer support list' freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
External Email - Use Caution *Hi Douglas,
Thank you for looking into this.
It gives the following error.
trac-preproc.sh -c config.file
intrareg: Undefined variable.
Thanks,
King-Wai
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@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.chu@gmail.com wrote:
External Email - Use Caution *Hi Anastasia,
Just downloaded FreeSurfer version 7.3 and trying out TRACULA.
Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3
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
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freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
King-Wai Chu -
kingwai.chu＠gmail.com
-
Yendiki, Anastasia