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