Hi Douglas, I downloaded the current version of Freesurfer 6.0 and now recon-all with brainstem option works!
Thanks a lot Claudia ________________________________________ Da: [email protected] [[email protected]] per conto di Douglas N Greve [[email protected]] Inviato: venerdì 11 marzo 2016 21.04 A: [email protected] 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: [email protected] > [[email protected]] per conto di Douglas N Greve > [[email protected]] > Inviato: giovedì 10 marzo 2016 18.22 > A: [email protected] > 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: [email protected] >> [[email protected]] per conto di Eugenio Iglesias >> [[email protected]] >> 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" <[email protected]> >> To: "Freesurfer support list" <[email protected]> >> 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 >> <[email protected]> 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 >>> [email protected] >>> 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 >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [email protected] > 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 > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] 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 [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
