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
