Re: [Freesurfer] unknown option in new brainstem segmentation

2016-03-14 Thread Claudia Testa 
Hi Douglas,
I downloaded the current version of Freesurfer 6.0
and now recon-all  with brainstem option works!

Thanks a lot

Claudia 

Da: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] per conto di Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Inviato: venerdì 11 marzo 2016 21.04
A: freesurfer@nmr.mgh.harvard.edu
Oggetto: Re: [Freesurfer] unknown option in new brainstem segmentation

I think that must have been a bug introduced into recon-all just before
you downloaded the development version. It is not there in the current
dev. Part of the danger when using the dev version.

On 03/11/2016 07:00 AM, Claudia Testa wrote:
> Hi Douglas
>
> sure. Let me know if you need any other info
>
> Claudia
> 
> Da: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] per conto di Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Inviato: giovedì 10 marzo 2016 18.22
> A: freesurfer@nmr.mgh.harvard.edu
> Oggetto: Re: [Freesurfer] unknown option in new brainstem segmentation
>
> Can you send the log file?
>
> On 03/10/2016 07:02 AM, Claudia Testa wrote:
>> Hi Eugenio,
>>
>> yes the error seems in the option of mri_apar2aseg.
>> I run as line in the shell:
>> " mri_aparc2aseg --s 11960 --volmask -aseg aseg.presurf.hypos --annot 
>> aparc.DKTatlas40"
>> and it succeded.
>>
>> the recon-all -all command did not complete successfully, it stopped giving 
>> me the ERROR in the atlas option
>> of mri_apar2aseg
>>
>> Claudia
>> 
>> Da: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] per conto di Eugenio Iglesias 
>> [e.igles...@bcbl.eu]
>> Inviato: giovedì 10 marzo 2016 12.37
>> A: Freesurfer support list
>> Oggetto: Re: [Freesurfer] unknown option in new  brainstem segmentation
>>
>> Hi Claudia.
>> Does the recon-all command complete successfully? The error seems to be in 
>> mri_aparc2aseg, right?
>>
>> Juan Eugenio Iglesias
>> Postdoctoral researcher BCBL
>> www.jeiglesias.com
>> www.bcbl.eu
>>
>> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>>
>> - Original Message -
>> From: "Marmaduke" <marmaduke.wood...@univ-amu.fr>
>> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
>> Sent: Thursday, March 10, 2016 10:46:19 AM
>> Subject: Re: [Freesurfer] unknown option in new  brainstem segmentation
>>
>> On March 10, 2016 10:41:12 AM GMT+01:00, Claudia Testa 
>> <claudia.te...@unibo.it> wrote:
>>> Dear Freesurfers,
>>> I've installed Freesurfer 6.0 beta in a virtual machine,
>>> and run the -brainstem-structures option to recon-all.
>>>
>>> The process stopped with an error:  "ERROR: Option --DKTatlas40
>>> unknown"
>>>
>>> In the following, all the information:
>>> _
>>> FREESURFER_HOME: /usr/local/freesurfer
>>>
>>> Build stamp: freesurfer_Linux_centos6_x86_64-dev-20160229
>>>
>>> RedHat release: CentOS release 6.7 (Final)
>>>
>>> Kernel info: Linux 2.6.32-573.el6.x86_64 x86_64
>>>
>>> __
>>>
>>> 1) subject name is 11960
>>> 2) the command line is:
>>> recon-all -all -i /usr/local/freesurfer/input/11960_3D_lf.nii.gz  -s
>>> 11960 -brainstem-structures
>>> 3) mri_aparc2aseg --s 11960 --volmask --aseg aseg.presurf.hypos
>>> --DKTatlas40
>>>
>>> ERROR: Option --DKTatlas40 unknown
>>> Linux freesurfer-fabio 2.6.32-573.el6.x86_64 #1 SMP Thu Jul 23 15:44:03
>>> UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
>>>
>>> recon-all -s 11960 exited with ERRORS at Wed Mar  9 23:53:10 CET 2016
>>>
>>> 4) in attach the recon-all.log file
>>>
>>>
>>> Thank you for your help
>>>
>>> Claudia
>>>
>>>
>>>
>>> 
>>>
>>> ___
>>> 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 believ

Re: [Freesurfer] unknown option in new brainstem segmentation

2016-03-11 Thread Douglas N Greve 
I think that must have been a bug introduced into recon-all just before 
you downloaded the development version. It is not there in the current 
dev. Part of the danger when using the dev version.

On 03/11/2016 07:00 AM, Claudia Testa wrote:
> Hi Douglas
>
> sure. Let me know if you need any other info
>
> Claudia
> 
> Da: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] per conto di Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Inviato: giovedì 10 marzo 2016 18.22
> A: freesurfer@nmr.mgh.harvard.edu
> Oggetto: Re: [Freesurfer] unknown option in new brainstem segmentation
>
> Can you send the log file?
>
> On 03/10/2016 07:02 AM, Claudia Testa wrote:
>> Hi Eugenio,
>>
>> yes the error seems in the option of mri_apar2aseg.
>> I run as line in the shell:
>> " mri_aparc2aseg --s 11960 --volmask -aseg aseg.presurf.hypos --annot 
>> aparc.DKTatlas40"
>> and it succeded.
>>
>> the recon-all -all command did not complete successfully, it stopped giving 
>> me the ERROR in the atlas option
>> of mri_apar2aseg
>>
>> Claudia
>> 
>> Da: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] per conto di Eugenio Iglesias 
>> [e.igles...@bcbl.eu]
>> Inviato: giovedì 10 marzo 2016 12.37
>> A: Freesurfer support list
>> Oggetto: Re: [Freesurfer] unknown option in new  brainstem segmentation
>>
>> Hi Claudia.
>> Does the recon-all command complete successfully? The error seems to be in 
>> mri_aparc2aseg, right?
>>
>> Juan Eugenio Iglesias
>> Postdoctoral researcher BCBL
>> www.jeiglesias.com
>> www.bcbl.eu
>>
>> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>>
>> - Original Message -
>> From: "Marmaduke" <marmaduke.wood...@univ-amu.fr>
>> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
>> Sent: Thursday, March 10, 2016 10:46:19 AM
>> Subject: Re: [Freesurfer] unknown option in new  brainstem segmentation
>>
>> On March 10, 2016 10:41:12 AM GMT+01:00, Claudia Testa 
>> <claudia.te...@unibo.it> wrote:
>>> Dear Freesurfers,
>>> I've installed Freesurfer 6.0 beta in a virtual machine,
>>> and run the -brainstem-structures option to recon-all.
>>>
>>> The process stopped with an error:  "ERROR: Option --DKTatlas40
>>> unknown"
>>>
>>> In the following, all the information:
>>> _
>>> FREESURFER_HOME: /usr/local/freesurfer
>>>
>>> Build stamp: freesurfer_Linux_centos6_x86_64-dev-20160229
>>>
>>> RedHat release: CentOS release 6.7 (Final)
>>>
>>> Kernel info: Linux 2.6.32-573.el6.x86_64 x86_64
>>>
>>> __
>>>
>>> 1) subject name is 11960
>>> 2) the command line is:
>>> recon-all -all -i /usr/local/freesurfer/input/11960_3D_lf.nii.gz  -s
>>> 11960 -brainstem-structures
>>> 3) mri_aparc2aseg --s 11960 --volmask --aseg aseg.presurf.hypos
>>> --DKTatlas40
>>>
>>> ERROR: Option --DKTatlas40 unknown
>>> Linux freesurfer-fabio 2.6.32-573.el6.x86_64 #1 SMP Thu Jul 23 15:44:03
>>> UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
>>>
>>> recon-all -s 11960 exited with ERRORS at Wed Mar  9 23:53:10 CET 2016
>>>
>>> 4) in attach the recon-all.log file
>>>
>>>
>>> Thank you for your help
>>>
>>> Claudia
>>>
>>>
>>>
>>> 
>>>
>>> ___
>>> 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 Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>> in error
>>> but does not contain patient information, please contact the sender and
>>> properly
>>> dispose of the e-mail.
>> hi
>>
>> I had this as well, you have to rerun th

Re: [Freesurfer] unknown option in new brainstem segmentation

2016-03-10 Thread Douglas N Greve 
Can you send the log file?

On 03/10/2016 07:02 AM, Claudia Testa wrote:
> Hi Eugenio,
>
> yes the error seems in the option of mri_apar2aseg.
> I run as line in the shell:
> " mri_aparc2aseg --s 11960 --volmask -aseg aseg.presurf.hypos --annot 
> aparc.DKTatlas40"
> and it succeded.
>
> the recon-all -all command did not complete successfully, it stopped giving 
> me the ERROR in the atlas option
> of mri_apar2aseg
>
> Claudia
> 
> Da: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] per conto di Eugenio Iglesias 
> [e.igles...@bcbl.eu]
> Inviato: giovedì 10 marzo 2016 12.37
> A: Freesurfer support list
> Oggetto: Re: [Freesurfer] unknown option in new  brainstem segmentation
>
> Hi Claudia.
> Does the recon-all command complete successfully? The error seems to be in 
> mri_aparc2aseg, right?
>
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
>
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>
> - Original Message -
> From: "Marmaduke" <marmaduke.wood...@univ-amu.fr>
> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> Sent: Thursday, March 10, 2016 10:46:19 AM
> Subject: Re: [Freesurfer] unknown option in new  brainstem segmentation
>
> On March 10, 2016 10:41:12 AM GMT+01:00, Claudia Testa 
> <claudia.te...@unibo.it> wrote:
>> Dear Freesurfers,
>> I've installed Freesurfer 6.0 beta in a virtual machine,
>> and run the -brainstem-structures option to recon-all.
>>
>> The process stopped with an error:  "ERROR: Option --DKTatlas40
>> unknown"
>>
>> In the following, all the information:
>> _
>> FREESURFER_HOME: /usr/local/freesurfer
>>
>> Build stamp: freesurfer_Linux_centos6_x86_64-dev-20160229
>>
>> RedHat release: CentOS release 6.7 (Final)
>>
>> Kernel info: Linux 2.6.32-573.el6.x86_64 x86_64
>>
>> __
>>
>> 1) subject name is 11960
>> 2) the command line is:
>> recon-all -all -i /usr/local/freesurfer/input/11960_3D_lf.nii.gz  -s
>> 11960 -brainstem-structures
>> 3) mri_aparc2aseg --s 11960 --volmask --aseg aseg.presurf.hypos
>> --DKTatlas40
>>
>> ERROR: Option --DKTatlas40 unknown
>> Linux freesurfer-fabio 2.6.32-573.el6.x86_64 #1 SMP Thu Jul 23 15:44:03
>> UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
>>
>> recon-all -s 11960 exited with ERRORS at Wed Mar  9 23:53:10 CET 2016
>>
>> 4) in attach the recon-all.log file
>>
>>
>> Thank you for your help
>>
>> Claudia
>>
>>
>>
>> 
>>
>> ___
>> 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 Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
> hi
>
> I had this as well, you have to rerun the last step manually with the correct 
> atlas flag.
>
>
> ___
> 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
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] unknown option in new brainstem segmentation

2016-03-10 Thread Eugenio Iglesias 
Hi again,
the brainstem module is at the end of the recon-all stream, and because 
recon-all stopped because of the error, the brainstem code never ran.

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

- Original Message -
From: "Claudia Testa" <claudia.te...@unibo.it>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Sent: Thursday, March 10, 2016 1:02:26 PM
Subject: Re: [Freesurfer] unknown option in new  brainstem segmentation

Hi Eugenio,

yes the error seems in the option of mri_apar2aseg.
I run as line in the shell:
" mri_aparc2aseg --s 11960 --volmask -aseg aseg.presurf.hypos --annot 
aparc.DKTatlas40  "
and it succeded.

the recon-all -all command did not complete successfully, it stopped giving me 
the ERROR in the atlas option
of mri_apar2aseg

Claudia 

Da: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] per conto di Eugenio Iglesias 
[e.igles...@bcbl.eu]
Inviato: giovedì 10 marzo 2016 12.37
A: Freesurfer support list
Oggetto: Re: [Freesurfer] unknown option in new  brainstem segmentation

Hi Claudia.
Does the recon-all command complete successfully? The error seems to be in 
mri_aparc2aseg, right?

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

- Original Message -
From: "Marmaduke" <marmaduke.wood...@univ-amu.fr>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Sent: Thursday, March 10, 2016 10:46:19 AM
Subject: Re: [Freesurfer] unknown option in new  brainstem segmentation

On March 10, 2016 10:41:12 AM GMT+01:00, Claudia Testa <claudia.te...@unibo.it> 
wrote:
>
>Dear Freesurfers,
>I've installed Freesurfer 6.0 beta in a virtual machine,
>and run the -brainstem-structures option to recon-all.
>
>The process stopped with an error:  "ERROR: Option --DKTatlas40
>unknown"
>
>In the following, all the information:
>_
>FREESURFER_HOME: /usr/local/freesurfer
>
>Build stamp: freesurfer_Linux_centos6_x86_64-dev-20160229
>
>RedHat release: CentOS release 6.7 (Final)
>
>Kernel info: Linux 2.6.32-573.el6.x86_64 x86_64
>
>__
>
>1) subject name is 11960
>2) the command line is:
>recon-all -all -i /usr/local/freesurfer/input/11960_3D_lf.nii.gz  -s
>11960 -brainstem-structures
>3) mri_aparc2aseg --s 11960 --volmask --aseg aseg.presurf.hypos
>--DKTatlas40
>
>ERROR: Option --DKTatlas40 unknown
>Linux freesurfer-fabio 2.6.32-573.el6.x86_64 #1 SMP Thu Jul 23 15:44:03
>UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
>
>recon-all -s 11960 exited with ERRORS at Wed Mar  9 23:53:10 CET 2016
>
>4) in attach the recon-all.log file
>
>
>Thank you for your help
>
>Claudia
>
>
>
>
>
>___
>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 Partners Compliance
>HelpLine at
>http://www.partners.org/complianceline . If the e-mail was sent to you
>in error
>but does not contain patient information, please contact the sender and
>properly
>dispose of the e-mail.

hi

I had this as well, you have to rerun the last step manually with the correct 
atlas flag.


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Re: [Freesurfer] unknown option in new brainstem segmentation

2016-03-10 Thread Claudia Testa 
Hi Eugenio,

yes the error seems in the option of mri_apar2aseg.
I run as line in the shell:
" mri_aparc2aseg --s 11960 --volmask -aseg aseg.presurf.hypos --annot 
aparc.DKTatlas40  "
and it succeded.

the recon-all -all command did not complete successfully, it stopped giving me 
the ERROR in the atlas option
of mri_apar2aseg

Claudia 

Da: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] per conto di Eugenio Iglesias 
[e.igles...@bcbl.eu]
Inviato: giovedì 10 marzo 2016 12.37
A: Freesurfer support list
Oggetto: Re: [Freesurfer] unknown option in new  brainstem segmentation

Hi Claudia.
Does the recon-all command complete successfully? The error seems to be in 
mri_aparc2aseg, right?

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

- Original Message -
From: "Marmaduke" <marmaduke.wood...@univ-amu.fr>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Sent: Thursday, March 10, 2016 10:46:19 AM
Subject: Re: [Freesurfer] unknown option in new  brainstem segmentation

On March 10, 2016 10:41:12 AM GMT+01:00, Claudia Testa <claudia.te...@unibo.it> 
wrote:
>
>Dear Freesurfers,
>I've installed Freesurfer 6.0 beta in a virtual machine,
>and run the -brainstem-structures option to recon-all.
>
>The process stopped with an error:  "ERROR: Option --DKTatlas40
>unknown"
>
>In the following, all the information:
>_
>FREESURFER_HOME: /usr/local/freesurfer
>
>Build stamp: freesurfer_Linux_centos6_x86_64-dev-20160229
>
>RedHat release: CentOS release 6.7 (Final)
>
>Kernel info: Linux 2.6.32-573.el6.x86_64 x86_64
>
>__
>
>1) subject name is 11960
>2) the command line is:
>recon-all -all -i /usr/local/freesurfer/input/11960_3D_lf.nii.gz  -s
>11960 -brainstem-structures
>3) mri_aparc2aseg --s 11960 --volmask --aseg aseg.presurf.hypos
>--DKTatlas40
>
>ERROR: Option --DKTatlas40 unknown
>Linux freesurfer-fabio 2.6.32-573.el6.x86_64 #1 SMP Thu Jul 23 15:44:03
>UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
>
>recon-all -s 11960 exited with ERRORS at Wed Mar  9 23:53:10 CET 2016
>
>4) in attach the recon-all.log file
>
>
>Thank you for your help
>
>Claudia
>
>
>
>
>
>___
>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 Partners Compliance
>HelpLine at
>http://www.partners.org/complianceline . If the e-mail was sent to you
>in error
>but does not contain patient information, please contact the sender and
>properly
>dispose of the e-mail.

hi

I had this as well, you have to rerun the last step manually with the correct 
atlas flag.


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Re: [Freesurfer] unknown option in new brainstem segmentation

2016-03-10 Thread Eugenio Iglesias 
Hi Claudia.
Does the recon-all command complete successfully? The error seems to be in 
mri_aparc2aseg, right?

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

- Original Message -
From: "Marmaduke" <marmaduke.wood...@univ-amu.fr>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Sent: Thursday, March 10, 2016 10:46:19 AM
Subject: Re: [Freesurfer] unknown option in new  brainstem segmentation

On March 10, 2016 10:41:12 AM GMT+01:00, Claudia Testa <claudia.te...@unibo.it> 
wrote:
>
>Dear Freesurfers,
>I've installed Freesurfer 6.0 beta in a virtual machine,
>and run the -brainstem-structures option to recon-all.
>
>The process stopped with an error:  "ERROR: Option --DKTatlas40
>unknown"
>
>In the following, all the information:
>_
>FREESURFER_HOME: /usr/local/freesurfer
>
>Build stamp: freesurfer_Linux_centos6_x86_64-dev-20160229
>
>RedHat release: CentOS release 6.7 (Final)
>
>Kernel info: Linux 2.6.32-573.el6.x86_64 x86_64
>
>__
>
>1) subject name is 11960
>2) the command line is:
>recon-all -all -i /usr/local/freesurfer/input/11960_3D_lf.nii.gz  -s
>11960 -brainstem-structures
>3) mri_aparc2aseg --s 11960 --volmask --aseg aseg.presurf.hypos
>--DKTatlas40
>
>ERROR: Option --DKTatlas40 unknown
>Linux freesurfer-fabio 2.6.32-573.el6.x86_64 #1 SMP Thu Jul 23 15:44:03
>UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
>
>recon-all -s 11960 exited with ERRORS at Wed Mar  9 23:53:10 CET 2016
>
>4) in attach the recon-all.log file
>
>
>Thank you for your help
>
>Claudia
>
>
>
>
>
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>
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>contains patient information, please contact the Partners Compliance
>HelpLine at
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>properly
>dispose of the e-mail.

hi

I had this as well, you have to rerun the last step manually with the correct 
atlas flag.


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Re: [Freesurfer] unknown option in new brainstem segmentation

2016-03-10 Thread Marmaduke 
On March 10, 2016 10:41:12 AM GMT+01:00, Claudia Testa  
wrote:
>
>Dear Freesurfers,
>I've installed Freesurfer 6.0 beta in a virtual machine,
>and run the -brainstem-structures option to recon-all.
>
>The process stopped with an error:  "ERROR: Option --DKTatlas40
>unknown"
>
>In the following, all the information:
>_
>FREESURFER_HOME: /usr/local/freesurfer
>
>Build stamp: freesurfer_Linux_centos6_x86_64-dev-20160229
>
>RedHat release: CentOS release 6.7 (Final)
>
>Kernel info: Linux 2.6.32-573.el6.x86_64 x86_64
>
>__
>
>1) subject name is 11960
>2) the command line is:
>recon-all -all -i /usr/local/freesurfer/input/11960_3D_lf.nii.gz  -s
>11960 -brainstem-structures
>3) mri_aparc2aseg --s 11960 --volmask --aseg aseg.presurf.hypos
>--DKTatlas40
>
>ERROR: Option --DKTatlas40 unknown
>Linux freesurfer-fabio 2.6.32-573.el6.x86_64 #1 SMP Thu Jul 23 15:44:03
>UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
>
>recon-all -s 11960 exited with ERRORS at Wed Mar  9 23:53:10 CET 2016
>
>4) in attach the recon-all.log file
>
>
>Thank you for your help
>
>Claudia
>
>
>
>
>
>___
>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 Partners Compliance
>HelpLine at
>http://www.partners.org/complianceline . If the e-mail was sent to you
>in error
>but does not contain patient information, please contact the sender and
>properly
>dispose of the e-mail.

hi

I had this as well, you have to rerun the last step manually with the correct 
atlas flag.


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