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.
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.
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.
Hi Fengji
we are looking into it and will hopefully have an answer in the next day or so
cheers Bruce On Mon, 7 Dec 2015, Fengji Geng wrote:
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/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.
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.
what do you mean "match the string scratch"? Can you point us to a problematic binary?
On 12/22/15 11:28 AM, Fengji Geng wrote:
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello experts,
I reported the error related to '/scratch' a couple of weeks ago. We 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.
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 ------------------------------------------ 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.
Can you give us specific examples of problem programs?
On 01/04/2016 09:54 AM, Fengji Geng wrote:
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
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.
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Fengji Geng