Dear FreeSurfer Users,
I was trying to segment hippocampal subfields using FreeSurfer 6 with data that have already undergone the FreeSurfer 5 pipeline recon-all -all. According to the usage described on the webpage of HippocampalSubfields (http://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields), I ran the command: recon-all -s ${Mysubject} -hippocampal-subfields-T1 Then the following errors occurred. It seems that the program 'segmentSubjectT1_autoEstimateAlveusML (line 113)' was trying to make a directory in a Read-only place. But the error message did not indicate where this place was. I have tried to look codes in 'run_ segmentSubjectT1_autoEstimateAlveusML.sh" . But it does not have this information either. As segmentSubjectT1_autoEstimateAlveusML is a binary file, I could not dig out any more info. Does anyone know how to solve this error? Or know where the program was trying to mkdir?
Thank you.
Here begins the error message:
hippocampus:/<2>hippocampus/HMN/data/FG_Temp: #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) left Wed Nov 18 21:57:45 EST 2015 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/cell_root/software/freesurfer/dev/sys/MCRv80/runtime/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/bin/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/os/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/cell_root/software/gsl/current/sys/lib:/cell_root/software/fastx/current/lib/fastx_server/lib Warning: application is running on a locale different from the original platform locale. Error using mkdir Read-only file system
Error in segmentSubjectT1_autoEstimateAlveusML (line 113)
MATLAB:MKDIR:OSError #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) right Wed Nov 18 21:57:50 EST 2015 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/cell_root/software/freesurfer/dev/sys/MCRv80/runtime/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/bin/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/os/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/cell_root/software/gsl/current/sys/lib:/cell_root/software/fastx/current/lib/fastx_server/lib Warning: application is running on a locale different from the original platform locale. Error using mkdir Read-only file system
Error in segmentSubjectT1_autoEstimateAlveusML (line 113)
MATLAB:MKDIR:OSError
End of error message.
Best Regards!
Fengji
--- Fengji