Hello Renata, Their was a brief period of time in the Dev version of freesurfer when certain labels didnt exist in the fsaverage subject. You just happen to download and install that version. I believe if you download the latest version from this page (see "Development Version") that error will go away:
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall#Download -Zeke On 07/20/2016 03:35 AM, Vaz pandolfo, Renata wrote: > Dear FreeSurfer developers, > > I am running recon-all on a healthy subject and I am also trying to get > the hippocampal subfields segmentation. > On the mri directory there is no hippocampus output, and the recon-all > exited with errors. > > Command: > > recon-all -all \ > -i > ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/co_T1_20110815.nii.gz > -s no_T2_20110815 \ > -sd ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/ \ > -hippocampal-subfields-T1 > > Error: > > SUBJECTS_DIR > /home/lub_jungs/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815 > FREESURFER_HOME /usr/local/freesurfer > Loading source label. > Invalid argument > ERROR reading > /home/lub_jungs/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/fsaverage/label/lh.BA1_exvivo.label > Linux lundb2 4.4.0-28-generic #47-Ubuntu SMP Fri Jun 24 10:09:13 UTC > 2016 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s no_T2_20110815 exited with ERRORS at Do 7. Jul 22:26:35 > CEST 2016 > > Extra info: > > Freesurfer version: freesurfer-Linux-centos6_x86_64-dev-20160616-8264611 > uname -a: Linux lundb2 4.4.0-24-generic #43-Ubuntu SMP Wed Jun 8 > 19:27:37 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux > logs: recon-all and hippocampal-subfields-T1T2 attached > > > Thank you! > > > > > _______________________________________________ > 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 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.
