Re: [Freesurfer] 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-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
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
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/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] unknown option in new brainstem segmentation
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. ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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. ___ 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
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
Re: [Freesurfer] unknown option in new brainstem segmentation
On March 10, 2016 10:41:12 AM GMT+01:00, Claudia Testawrote: > >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