Dear FreeSurfer Users,
I sent an email to this maillist a couple of weeks ago asking help for the
error that I encountered after running 'recon-all -s ${Mysubject}
-hippocampal-subfields-T1' with freesurfer 6. The content of this email is
attached below. Since then, my colleague and I have been working on figuring
out where the error is from, but we got two more questions here:
First, is it possible that we can set the tmpdir to /tmp or something else
globally? How can I do this?
Second, is it possible to fix test for '-e/scratch' to test for '-dw/scratch',
which is a directory writable by current user?
Any comments and suggestions are appreciated. Thanks in advance!
Fengji
Previous email:
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?
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)
--------------------------------------------------------------------------------------------------------
-----
Fengji
_______________________________________________
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.
