[Freesurfer] unit for hippocampus segmentation results
Hi freesurfer experts, We used the development version of freesurfer 6.0 to segment hippocampus. We are wondering what the unit is for the segmentation results. Thanks, -- Fengji Geng ___ 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.
[Freesurfer] freesurfer 6.0 release date
Hi fs developers, I am wondering if you have any estimation when fs 6.0 will come out. The reason that I ask this is because we are running some analysis using fs 5.1 and planning to switch to a more recent version of fs. If fs 6.0 will come out soon, we will probably hold and wait for it. If not, we will just switch to fs 5.3. Thanks! -- Fengji Geng ___ 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.
[Freesurfer] Error using mkdir for the segmentation of hippocampal subfields using FreeSurfer 6
Dear FreeSurfer Users,
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?
Thank you.
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.
Best Regards!
Fengji
---
Fengji
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[Freesurfer] 'mkdir' error during the segmentation of hippocampal subfields using FreeSurfer 6 [2nd request for help]
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
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
[Freesurfer] 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 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.
[Freesurfer] 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 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.
[Freesurfer] segmentation fault (core dumped)
Hi Bruce, I have uploaded all the data to the server. The command that I run is 'recon-all -all -s $s -hippocampal-subfields-T1T2 $s/T2/*.mgz T1T2'. It would be great if you could keep us updated on how the fixing is going. Thanks! --- Message: 1 Date: Mon, 21 Dec 2015 10:38:08 -0500 (EST) From: Bruce Fischl Subject: Re: [Freesurfer] FW: segmentation fault (core dumped) To: Freesurfer support list Message-ID: Content-Type: text/plain; charset="iso-8859-1" Hi Fengji hmmm, I don't remember ever seeing a core dump in mri-segstats before. If you upload the entire subject dir (tarred and gzipped) to our ftp site we will fix it. cheers Bruce - 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.
[Freesurfer] FW: problem with hard coded directory (/scratch)
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 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.
[Freesurfer] FW: problem with hard coded directory (/scratch)
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. ___ 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.
[Freesurfer] FW: problem with hard coded directory (/scratch)
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. ___ 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.
Re: [Freesurfer] FW: problem with hard coded directory (/scratch)
Hi Douglas, You asked us to give you an example of the problem program. I will try to do it here, but if it is not what you want, please let me know. we ran recon-all -all -s -hippocampal-subfields-T1T2 . We saw the program tried to create /scratch/$subject_hippoSF_T1_v10_right directory and failing with (Read-only file system) because the user does not have permission to write to /scratch. I can also send you the strace output if needed. Thank you! - Message: 4 Date: Mon, 4 Jan 2016 13:37:48 -0500 From: Douglas N Greve Subject: Re: [Freesurfer] FW: problem with hard coded directory (/scratch) To: freesurfer@nmr.mgh.harvard.edu Message-ID: <568abbfc.5000...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed 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 ___ 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.
[Freesurfer] FW: FW: problem with hard coded directory (/scratch)
Hi FS's experts, I sent out a couple of emails to seek for help on an error from running recon-all using freesurfer 6.0 beta. Could anyone help with the question? Thank you! - Fengji From: Fengji Geng Sent: Thursday, January 07, 2016 8:15 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: problem with hard coded directory (/scratch) Hi Douglas, You asked us to give you an example of the problem program. I will try to do it here, but if it is not what you want, please let me know. we ran recon-all -all -s -hippocampal-subfields-T1T2 . We saw the program tried to create /scratch/$subject_hippoSF_T1_v10_right directory and failing with (Read-only file system) because the user does not have permission to write to /scratch. I can also send you the strace output if needed. Thank you! - Message: 4 Date: Mon, 4 Jan 2016 13:37:48 -0500 From: Douglas N Greve Subject: Re: [Freesurfer] FW: problem with hard coded directory (/scratch) To: freesurfer@nmr.mgh.harvard.edu Message-ID: <568abbfc.5000...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed 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 ___ 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.
[Freesurfer] FW: problem with hard coded directory (/scratch)
Hi Doug,
After reading your most recent reply, I just found that many of previous
freesurfer emails had gone to my junk box automatically, so I missed some of
your replies. Sorry!
Looking at the strace output I generated last time, here are the lines where
the program tries to stat and mkdir something in /scratch. And, the prev
execve() system call.
So, I'm guessing that bin/segmentSubjectT1_autoEstimateAlveusML or something
it in turn runs is leading to "/scratch" directory problem.
=
13174
execve("/cell_root/software/freesurfer/dev/sys/bin/segmentSubjectT1_autoEstimateAlveusML",
["/cell_root/software/freesurfer/d"..., "HMN042",
"/export/extra/pkd-fstest/FG_Temp", "0.33"...,
"/cell_root/software/freesurfer/d"..., "/cell_root/software/freesurfer/d"...,
"/cell_root/software/freesurfer/d"..., "0.05", "left", "ConjGrad", "v10",
"/cell_root/software/freesurfer/d"..., "0"], [/* 86 vars */]) = 0
13182 stat("/scratch/", {st_mode=S_IFDIR|0555, st_size=512, ...}) = 0
13182 stat("/scratch/HMN042_hippoSF_T1_v10_left/", 0x7f4e226015b0) = -1 ENOENT
(No such file or directory)
13182 stat("/scratch/HMN042_hippoSF_T1_v10_left/", 0x7f4e226015e0) = -1 ENOENT
(No such file or directory)
13182 lstat("/scratch", {st_mode=S_IFDIR|0555, st_size=512, ...}) = 0
13182 lstat("/scratch/HMN042_hippoSF_T1_v10_left", 0x7f4e226004b0) = -1 ENOENT
(No such file or directory)
13182 stat("/scratch", {st_mode=S_IFDIR|0555, st_size=512, ...}) = 0
13182 mkdir("/scratch/HMN042_hippoSF_T1_v10_left", 0775) = -1 EROFS (Read-only
file system)
=
I do see, however, MCRv80 references to before the
mkdir("/scratch/HMN042_hippoSF_T1_v10_left" call. So, it could be something in
the MCRv80 addition that's causing this issue.
And, things like this:
=
13182
open("/mathworks/BLR/devel/bat/A3p1/build/3p/install/319992/glnxa64/ITK/share/gdcm/gdcm.dic",
O_RDONLY) = -1 ENOENT (No such file or directory)
13182
open("/mathworks/BLR/devel/bat/A3p1/build/3p/install/319992/glnxa64/ITK/share/gdcm/dicomVR.dic",
O_RDONLY) = -1 ENOENT (No such file or directory)
13182
open("/mathworks/BLR/devel/bat/A3p1/build/3p/install/319992/glnxa64/ITK/share/gdcm/dicomTS.dic",
O_RDONLY) = -1 ENOENT (No such file or directory)
13182
open("/mathworks/BLR/devel/bat/A3p1/build/3p/install/319992/glnxa64/ITK/share/gdcm/DictGroupName.dic",
O_RDONLY) = -1 ENOENT (No such file or directory)
13182
open("/mathworks/BLR/devel/bat/A3p1/build/3p/install/319992/glnxa64/ITK/share/gdcm/DicomDir.dic",
O_RDONLY) = -1 ENOENT (No such file or directory)
=
are probably more MCRv80 (matlab runtime) package related and referencing a
/mathworks/BLR directory on the machine that it was built, but not on our
systems.
Please let me know if you need more information. I will keep my eyes wide open
this time.
Thanks!!
---
Hi Fengji, you have sent several emails. I keep asking you to give us a
specific binary that has the problem, but you seem to ignore my request,
wait a couple of weeks, then post the question back to the list. I'm
happy to take look, but please send me something more specific!
thanks
doug
-
Fengji
From: Fengji Geng
Sent: Thursday, January 14, 2016 1:46 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: FW: [Freesurfer] FW: problem with hard coded directory (/scratch)
Hi FS's experts,
I sent out a couple of emails to seek for help on an error from running
recon-all using freesurfer 6.0 beta. Could anyone help with the question?
Thank you!
-
Fengji
From: Fengji Geng
Sent: Thursday, January 07, 2016 8:15 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FW: problem with hard coded directory (/scratch)
Hi Douglas,
You asked us to give you an example of the problem program. I will try to do it
here, but if it is not what you want, please let me know.
we ran recon-all -all -s -hippocampal-subfields-T1T2 . We saw the program tried to create
/scratch/$subject_hippoSF_T1_v10_right directory and failing with (Read-only
file system) because the user does not have permission to write to /scratch.
I can also send you the strace output if needed.
Thank you!
-
Message: 4
Date: Mon, 4 Jan 2016 13:37:48 -0500
From: Douglas N Greve
Subject: Re: [Freesurfer] FW: problem with hard coded directory
(/scratch)
To: freesurfer@nmr.mgh.ha
Re: [Freesurfer] recon-all: core dumped error (Bruce Fischl)
Hi Bruce, Did you mean an updated version of mri_parcellate? If so, it would be great. Thanks! Hi Fengji this is a known bug in mris_parcellate. We can give you an updated version if you want, but you should probably rerun all your subjects using it. The good news is that it's fast - just a couple of min/hemi cheers Bruce On Tue, 26 Jan 2016, Fengji Geng wrote: > Hello fs experts, > > We ran a command like ?recon-all -all -s HMN002 -hippocampal-subfields-T1T2 > HMN002/T2/*.mgz T1T2?. Then, there was an error as ?Abort (core dumped)? > (which is also attached below). The error log file is also attached here.? > > Error msg: > --- > -- > setting seed for random number generator to 1234 > using ../mri/aseg.presurf.mgz aseg volume to correct midline > $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ > ? $Id: mrisurf.c,v 1.775 2015/12/10 21:16:09 fischl Exp $ > reading atlas > from/cell_root/software/freesurfer/dev/sys/average/lh.curvature.buckner40.fille > d.desikan_killiany.2010-03-25.gcs... > reading color table from GCSA file > average std = 1.0?? using min determinant for regularization = 0.011 > 0 singular and 384 ill-conditioned covariance matrices regularized > input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature > labeling surface... > 1592 labels changed using aseg > relabeling using gibbs priors... > 000:?? 2975 changed, 134786 examined... > 001:??? 698 changed, 12707 examined... > 002:??? 152 changed, 3873 examined... > 003: 50 changed, 880 examined... > 004: 29 changed, 284 examined... > 005: 16 changed, 164 examined... > 006:? 7 changed, 87 examined... > 007:? 1 changed, 42 examined... > 008:? 0 changed, 4 examined... > 206 labels changed using aseg > 000: 105 total segments, 64 labels (264 vertices) changed > 001: 43 total segments, 4 labels (14 vertices) changed > 002: 39 total segments, 0 labels (0 vertices) changed > 1 filter iterations complete (10 requested, 0 changed) > Abort (core dumped) > Linux hippocampus.umd.edu 2.6.32-573.12.1.el6.x86_64 #1 SMP Mon Nov 23 > 12:55:32 EST 2015 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s HMN002 exited with ERRORS at Tue Jan 26 00:23:40 EST 2016 > > Our freesurfer information: > freesurfer-Linux-centos6_x86_64-dev-20151215 > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME?? /cell_root/software/freesurfer/dev/sys > FSFAST_HOME?? /cell_root/software/freesurfer/dev/sys/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR? /export/data/hippocampus/HMN/data > MNI_DIR?? /cell_root/software/freesurfer/dev/sys/mni > FSL_DIR?? /cell_root/software/fsl/new/sys > > Looking forward to hearing how we can resolve this error. Also, thanks in > advance. > > Best, > > - Fengji > > > --- 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.
Re: [Freesurfer] recon-all: core dumped error
Hi Bruce, Below is our hardware/software information. Also curious, will install the newest development version of fs 6.0 solve our problem either? Thanks a lot! Linux 2.6.32-573.12.1.el6.x86_64 LSB Version: :base-4.0-amd64:base-4.0-ia32:base-4.0-noarch:core-4.0-amd64:core-4.0-ia32:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-ia32:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-ia32:printing-4.0-noarch Distributor ID:RedHatEnterpriseServer Description:Red Hat Enterprise Linux Server release 6.7 (Santiago) Release: 6.7 Codename:Santiago freesurfer-Linux-centos6_x86_64-dev-20151215 Hi Fengji, it's called mris_ca_label, and yes, that is what I mean. If you tell us your hardware/software environment Zeke can get you a binary On Thu, 28 Jan 2016, Fengji Geng wrote: > > Hi Bruce, > > Did you mean an updated version of mri_parcellate? If so, it would be great. > > Thanks! > > ? > > > > ? > > ? > > Hi Fengji > > ? > > this is a known bug in mris_parcellate. We can give you an updated > version > > if you want, but you should probably rerun all your subjects using it. > The > > good news is that it's fast - just a couple of min/hemi > > ? > > cheers > > Bruce > > ? On Tue, 26 Jan > > 2016, Fengji Geng wrote: > > ? > > > Hello fs experts, > > > > > > We ran a command like ?recon-all -all -s HMN002 > -hippocampal-subfields-T1T2 > > > HMN002/T2/*.mgz T1T2?. Then, there was an error as ?Abort (core dumped)? > > > (which is also attached below). The error log file is also attached here.? > > > > > > Error msg: > > >- > >-- > > > -- > > > setting seed for random number generator to 1234 > > > using ../mri/aseg.presurf.mgz aseg volume to correct midline > > > $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ > > > ? $Id: mrisurf.c,v 1.775 2015/12/10 21:16:09 fischl Exp $ > > > reading > > atlasfrom/cell_root/software/freesurfer/dev/sys/average/lh.curvature > > .buckner40.f > ille > > > d.desikan_killiany.2010-03-25.gcs... > > > reading color table from GCSA file > > > average std = 1.0?? using min determinant for regularization = 0.011 > > > 0 singular and 384 ill-conditioned covariance matrices regularized > > > input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature > > > labeling surface... > > > 1592 labels changed using aseg > > > relabeling using gibbs priors... > > > 000:?? 2975 changed, 134786 examined... > > > 001:??? 698 changed, 12707 examined... > > > 002:??? 152 changed, 3873 examined... > > > 003: 50 changed, 880 examined... > > > 004: 29 changed, 284 examined... > > > 005: 16 changed, 164 examined... > > > 006:? 7 changed, 87 examined... > > > 007:? 1 changed, 42 examined... > > > 008:? 0 changed, 4 examined... > > > 206 labels changed using aseg > > > 000: 105 total segments, 64 labels (264 vertices) changed > > > 001: 43 total segments, 4 labels (14 vertices) changed > > > 002: 39 total segments, 0 labels (0 vertices) changed > > > 1 filter iterations complete (10 requested, 0 changed) > > > Abort (core dumped) > > > Linux hippocampus.umd.edu 2.6.32-573.12.1.el6.x86_64 #1 SMP Mon Nov > > 23 > > > 12:55:32 EST 2015 x86_64 x86_64 x86_64 GNU/Linux > > > > > > recon-all -s HMN002 exited with ERRORS at Tue Jan 26 00:23:40 EST > > 2016 > > > > > > Our freesurfer information: > > > freesurfer-Linux-centos6_x86_64-dev-20151215 > > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > > FREESURFER_HOME?? /cell_root/software/freesurfer/dev/sys > > > FSFAST_HOME?? /cell_root/software/freesurfer/dev/sys/fsfast > > > FSF_OUTPUT_FORMAT nii.gz > > > SUBJECTS_DIR? /export/data/hippocampus/HMN/data > > > MNI_DIR?? /cell_root/software/freesurfer/dev/sys/mni > > > FSL_DIR?? /cell_root/software/fsl/new/sys > > > > > > Looking forward to hearing how we can resolve this error
[Freesurfer] running two versions of fs in the same dataset
Dear fs developers, we are attempting to use the stable version of fs 5.1 for processing while also using the most current version for hippocampal segmentation on the same set of subjects (freesurfer 6.0 dev version on 28-Jan-2016). However, when the develop version of fs 6 was installed, we began having an issue with the fsaverage folder linking to the newest version, when we need it to link to version 5.1 during processing. The label files that we need for processing in version 5.1 are not accessible in the new version’s fsaverage folder. However, before we updated to fs 6.0 dev version on 28-Jan-2016, we never had this issue. So, we are wondering if the newest develop version of fs 6.0 does not allow two versions of fs to be used in the same data. Looking forward to hearing from you and thanks in advance. Best, - 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.
Re: [Freesurfer] running two versions of fs in the same
Hi Bruce, The command that we ran is recon-all. Below is the error msg: mri_label2label --srcsubject fsaverage --srclabel /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA2.label --trgsubject HMN122 --trglabel ./lh.BA2.label --hemi lh --regmethod surface No such file or directory mri_label2label: could not open label file /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA2.label srclabel = /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA2.label srcsubject = fsaverage trgsubject = HMN122 trglabel = ./lh.BA2.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR/export/data/hippocampus/HMN/data FREESURFER_HOME /cell_root/software/freesurfer/current/sys Loading source label. Invalid argument ERROR reading /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA2.label Linux hippocampus.umd.edu 2.6.32-573.12.1.el6.x86_64 #1 SMP Mon Nov 23 12:55:32 EST 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s HMN122 exited with ERRORS at Tue Feb 23 16:40:01 EST 2016 -- Hi Fengji you need to give us more details about the problems before we can help you. What commands failed? What was the screen output? Note that there is still no such thing as FS 6.0. We are hoping to have it in the relatively near term, but it doesn't exist yet. cheers Bruce On Tue, 1 Mar 2016, Fengji Geng wrote: > Dear fs developers,? > > we are attempting to use the stable version of fs 5.1 for processing while > also using the most current version for hippocampal segmentation on the same > set of subjects (freesurfer 6.0 dev version on 28-Jan-2016). However, when > the develop version of fs 6 was installed, we began having an issue with the > fsaverage folder linking to the newest version, when we need it to link to > version 5.1 during processing. The label files that we need for processing > in version 5.1 are not accessible in the new version?s fsaverage > folder.?However, before we updated to fs 6.0 dev version on 28-Jan-2016, we > never had this issue. So, we are wondering if the newest develop version of > fs 6.0 does not allow?two versions of fs to be used in the same data.? > > Looking forward to hearing from you and thanks in advance. > > Best, > > - Fengji --- 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.
