unknown option in new brainstem segmentation

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Claudia Testa

10 Mar 2016 10 Mar '16

4:41 a.m.

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

Attachments:

recon-all.log (application/octet-stream — 337.2 KB)

Show replies by date

Marmaduke

10 Mar 10 Mar

4:46 a.m.

On March 10, 2016 10:41:12 AM GMT+01:00, Claudia Testa claudia.testa@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

subject name is 11960

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

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.

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

Eugenio Iglesias

6:37 a.m.

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.woodman@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.testa@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

subject name is 11960

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

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.

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

Claudia Testa

7:02 a.m.

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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] per conto di Eugenio Iglesias [e.iglesias@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

On March 10, 2016 10:41:12 AM GMT+01:00, Claudia Testa claudia.testa@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

subject name is 11960

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

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.

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

Eugenio Iglesias

7:07 a.m.

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.testa@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

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

On March 10, 2016 10:41:12 AM GMT+01:00, Claudia Testa claudia.testa@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

subject name is 11960

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

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.

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

Douglas N Greve

12:22 p.m.

New subject: 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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] per conto di Eugenio Iglesias [e.iglesias@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.woodman@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.testa@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

subject name is 11960

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

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 greve@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/

Claudia Testa

11 Mar 11 Mar

7 a.m.

New subject: unknown option in new brainstem segmentation

Hi Douglas

sure. Let me know if you need any other info

Claudia ________________________________________ Da: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] per conto di Douglas N Greve [greve@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] per conto di Eugenio Iglesias [e.iglesias@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.woodman@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.testa@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

subject name is 11960

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

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 greve@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/

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Douglas N Greve

3:04 p.m.

New subject: 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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] per conto di Douglas N Greve [greve@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] per conto di Eugenio Iglesias [e.iglesias@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.woodman@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.testa@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

subject name is 11960

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

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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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Claudia Testa

14 Mar 14 Mar

10:51 a.m.

New subject: unknown option in new brainstem segmentation

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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] per conto di Douglas N Greve [greve@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] per conto di Douglas N Greve [greve@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] per conto di Eugenio Iglesias [e.iglesias@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.woodman@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.testa@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

subject name is 11960

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

in attach the recon-all.log file

Thank you for your help

Claudia

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hi

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

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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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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Claudia Testa
Douglas N Greve
Eugenio Iglesias
Marmaduke