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!
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