thanks Fengji
sounds like something we should fix.
cheers Bruce On Thu, 3 Dec 2015, Fengji Geng wrote:
Dear all, I am currently using freesurfer 6.0 (development version) to run hippocampal subfields segmentation and encountered a 'mkdir' error, which is attached below. Our troubleshooting found that some scripts in the ...freesurfer/dev/sys/bin directory with things like:
if(-e /scratch) set tmpdir = /scratch/tmpdir.bbmask.$$ if(! -e /scratch) set tmpdir = $outdir/tmpdir.bbmask.$$ However, /scratch is a directory that is not writable in our server. So, we made changes to all of the scripts that testing the existence of /scratch. However, there are several places where they incorrectly test for the /scratch directory using -e instead of -dw, the /scratch is hard coded in there so it can't be changed.
Looking forward to hearing suggestions and comments.
Fengji
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/so ftware/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/cell_root/soft ware/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/cell_root/software/frees urfer/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/s oftware/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/so ftware/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/cell_root/soft ware/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/cell_root/software/frees urfer/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/s oftware/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.