Hi Bruce, 

I reported the error related to '/scratch' a couple of weeks ago. We just tested the newest version of freesurfer 6.0. 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". Could you also fix them?

Thank you! 

-----
Fengji

From: Fengji Geng
Sent: Sunday, December 06, 2015 9:01 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: FW: problem with hard coded directory (/scratch)

Hi Bruce, 

Thank you for your response on my question. 

I am also wondering how long it would take to fix the bug. As we are looking forwarding to use freesurfer 6.0 to run our data as soon as possible, we may choose to modify our server if it takes time to fix the bug. Thanks again!

Best,

-----
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

------------------------------------------

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.