Hello Bruce,

Happy New Year!

After we reported the error related to '/scratch' several weeks ago (see the email attached below), we tested the newest version of freesurfer 6.0 recently, it looks likes that a lot of "if (-e /scratch)" have been changed to "if (-dw /scratch)". However, there are still a lot of binaries in the bin directory that match the string "scratch", which cause the same error that I encountered before. I am wondering if it is possible for you to fix '/scratch' in the bin directory.

Thank you!

-----

Fengji

From: Fengji Geng
Sent: Thursday, December 03, 2015 8:30 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: problem with hard coded directory (/scratch)

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/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