Dear all,
I am currently running cortical thickness analysis using Freesurfer v5.2 on a high performance computing cluster however, when I run the 'recon_all' command I get the following error
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 INFO: SUBJECTS_DIR is /home/users/kellys37/CT_TEST/CON3140 Actual FREESURFER_HOME /home/support/tcin/apps/freesurfer/5.2.0 Linux tcin-n02.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03 EST 2012 x86_64 x86_64 x86_64 GNU/Linux nu_correct: Command not found. #-------------------------------------------- #@# MotionCor Thu Mar 7 11:44:10 GMT 2013 Found 1 runs /home/users/kellys37/CT_TEST/CON3140/001/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue.
cp /home/users/kellys37/CT_TEST/CON3140/001/mri/orig/001.mgz /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz
/home/users/kellys37/CT_TEST/CON3140/001
mri_convert /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz --conform
mri_convert /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.9997, 0.0244327, -0.00148148) j_ras = (0.0239203, 0.987991, 0.152651) k_ras = (-0.00519336, -0.15257, 0.988279) Original Data has (0.898438, 0.898438, 0.9) mm size and (256, 256, 180) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz...
mri_add_xform_to_header -c /home/users/kellys37/CT_TEST/CON3140/001/mri/transforms/talairach.xfm /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz
INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Mar 7 11:44:32 GMT 2013 /home/users/kellys37/CT_TEST/CON3140/001/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
Linux tcin-n02.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03 EST 2012 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 001 exited with ERRORS at Thu Mar 7 11:44:38 GMT 2013
For more details, see the log file /home/users/kellys37/CT_TEST/CON3140/001/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
I had did not encounter this error when using an older version of Freesurfer on our clusters. Do you know if there is any way to resolve this problem? Any advice would be appreciated.
Kind regards,
Sinead
Sinead,
Is 'nu_correct' in your freesurfer/mni/bin directory? Are you being careful to run the setup script for just freeview 5.2 and not other packages or versions which might mess-up the perl paths?
Nick
On Fri, 2013-03-08 at 09:50 +0000, Sinead Kelly wrote:
Dear all,
I am currently running cortical thickness analysis using Freesurfer v5.2 on a high performance computing cluster however, when I run the 'recon_all' command I get the following error
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 INFO: SUBJECTS_DIR is /home/users/kellys37/CT_TEST/CON3140 Actual FREESURFER_HOME /home/support/tcin/apps/freesurfer/5.2.0 Linux tcin-n02.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03 EST 2012 x86_64 x86_64 x86_64 GNU/Linux nu_correct: Command not found. #-------------------------------------------- #@# MotionCor Thu Mar 7 11:44:10 GMT 2013 Found 1 runs /home/users/kellys37/CT_TEST/CON3140/001/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue.
cp /home/users/kellys37/CT_TEST/CON3140/001/mri/orig/001.mgz /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz
/home/users/kellys37/CT_TEST/CON3140/001
mri_convert /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz --conform
mri_convert /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.9997, 0.0244327, -0.00148148) j_ras = (0.0239203, 0.987991, 0.152651) k_ras = (-0.00519336, -0.15257, 0.988279) Original Data has (0.898438, 0.898438, 0.9) mm size and (256, 256, 180) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz...
mri_add_xform_to_header -c /home/users/kellys37/CT_TEST/CON3140/001/mri/transforms/talairach.xfm /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz
INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Mar 7 11:44:32 GMT 2013 /home/users/kellys37/CT_TEST/CON3140/001/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
Linux tcin-n02.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03 EST 2012 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 001 exited with ERRORS at Thu Mar 7 11:44:38 GMT 2013
For more details, see the log file /home/users/kellys37/CT_TEST/CON3140/001/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
I had did not encounter this error when using an older version of Freesurfer on our clusters. Do you know if there is any way to resolve this problem? Any advice would be appreciated.
Kind regards,
Sinead
-- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Nick,
I had a look in the bin directory and there is a command called 'mri_nu_correct.mni'. Is this the command the script is trying to call? This is the only nu_correct command I could find. I specify v5.2 in the script as there are other versions installed on the clusters.
Thanks again for your help!
Sinead
On 9 March 2013 23:23, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Sinead,
Is 'nu_correct' in your freesurfer/mni/bin directory? Are you being careful to run the setup script for just freeview 5.2 and not other packages or versions which might mess-up the perl paths?
Nick
On Fri, 2013-03-08 at 09:50 +0000, Sinead Kelly wrote:
Dear all,
I am currently running cortical thickness analysis using Freesurfer v5.2 on a high performance computing cluster however, when I run the 'recon_all' command I get the following error
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 INFO: SUBJECTS_DIR is /home/users/kellys37/CT_TEST/CON3140 Actual FREESURFER_HOME /home/support/tcin/apps/freesurfer/5.2.0 Linux tcin-n02.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03 EST 2012 x86_64 x86_64 x86_64 GNU/Linux nu_correct: Command not found. #-------------------------------------------- #@# MotionCor Thu Mar 7 11:44:10 GMT 2013 Found 1 runs /home/users/kellys37/CT_TEST/CON3140/001/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue.
cp /home/users/kellys37/CT_TEST/CON3140/001/mri/orig/001.mgz
/home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz
/home/users/kellys37/CT_TEST/CON3140/001
mri_convert /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz
/home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz --conform
mri_convert /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz
/home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz --conform
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.9997, 0.0244327, -0.00148148) j_ras = (0.0239203, 0.987991, 0.152651) k_ras = (-0.00519336, -0.15257, 0.988279) Original Data has (0.898438, 0.898438, 0.9) mm size and (256, 256, 180) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz...
mri_add_xform_to_header -c /home/users/kellys37/CT_TEST/CON3140/001/mri/transforms/talairach.xfm
/home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz
INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Mar 7 11:44:32 GMT 2013 /home/users/kellys37/CT_TEST/CON3140/001/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
Linux tcin-n02.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03 EST 2012 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 001 exited with ERRORS at Thu Mar 7 11:44:38 GMT 2013
For more details, see the log file /home/users/kellys37/CT_TEST/CON3140/001/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
I had did not encounter this error when using an older version of Freesurfer on our clusters. Do you know if there is any way to resolve this problem? Any advice would be appreciated.
Kind regards,
Sinead
-- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8 _______________________________________________ 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.
Sinead,
In your freesurfer directory, is there an 'mni' directory? under that directory is a 'bin' directory where nu_correct should be.
Nick
Hi Nick,
I had a look in the bin directory and there is a command called 'mri_nu_correct.mni'. Is this the command the script is trying to call? This is the only nu_correct command I could find. I specify v5.2 in the script as there are other versions installed on the clusters.
Thanks again for your help!
Sinead
On 9 March 2013 23:23, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Sinead,
Is 'nu_correct' in your freesurfer/mni/bin directory? Are you being careful to run the setup script for just freeview 5.2 and not other packages or versions which might mess-up the perl paths?
Nick
On Fri, 2013-03-08 at 09:50 +0000, Sinead Kelly wrote:
Dear all,
I am currently running cortical thickness analysis using Freesurfer v5.2 on a high performance computing cluster however, when I run the 'recon_all' command I get the following error
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 INFO: SUBJECTS_DIR is /home/users/kellys37/CT_TEST/CON3140 Actual FREESURFER_HOME /home/support/tcin/apps/freesurfer/5.2.0 Linux tcin-n02.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03 EST 2012 x86_64 x86_64 x86_64 GNU/Linux nu_correct: Command not found. #-------------------------------------------- #@# MotionCor Thu Mar 7 11:44:10 GMT 2013 Found 1 runs /home/users/kellys37/CT_TEST/CON3140/001/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue.
cp /home/users/kellys37/CT_TEST/CON3140/001/mri/orig/001.mgz
/home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz
/home/users/kellys37/CT_TEST/CON3140/001
mri_convert /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz
/home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz --conform
mri_convert /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz
/home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz --conform
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.9997, 0.0244327, -0.00148148) j_ras = (0.0239203, 0.987991, 0.152651) k_ras = (-0.00519336, -0.15257, 0.988279) Original Data has (0.898438, 0.898438, 0.9) mm size and (256, 256, 180) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz...
mri_add_xform_to_header -c
/home/users/kellys37/CT_TEST/CON3140/001/mri/transforms/talairach.xfm /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz
INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Mar 7 11:44:32 GMT 2013 /home/users/kellys37/CT_TEST/CON3140/001/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
Linux tcin-n02.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03 EST 2012 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 001 exited with ERRORS at Thu Mar 7 11:44:38 GMT 2013
For more details, see the log file /home/users/kellys37/CT_TEST/CON3140/001/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
I had did not encounter this error when using an older version of Freesurfer on our clusters. Do you know if there is any way to resolve this problem? Any advice would be appreciated.
Kind regards,
Sinead
-- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8 _______________________________________________ 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.
-- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8
I have encountered this error in the past, and I think it was because I was not sourcing SetUpFreeSurfer.sh correctly. That is the the script that sets up the MNI_DIR I think.
echo $MNI_DIR or whatever it is called and it should show you if it is being setup properly. It may be pointing to the system default as you say or more likely the variable is not defined at all.
On Mon, Mar 11, 2013 at 7:58 AM, Nick Schmansky nicks@nmr.mgh.harvard.eduwrote:
Sinead,
In your freesurfer directory, is there an 'mni' directory? under that directory is a 'bin' directory where nu_correct should be.
Nick
Hi Nick,
I had a look in the bin directory and there is a command called 'mri_nu_correct.mni'. Is this the command the script is trying to call? This is the only nu_correct command I could find. I specify v5.2 in the script as there are other versions installed on the clusters.
Thanks again for your help!
Sinead
On 9 March 2013 23:23, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Sinead,
Is 'nu_correct' in your freesurfer/mni/bin directory? Are you being careful to run the setup script for just freeview 5.2 and not other packages or versions which might mess-up the perl paths?
Nick
On Fri, 2013-03-08 at 09:50 +0000, Sinead Kelly wrote:
Dear all,
I am currently running cortical thickness analysis using Freesurfer v5.2 on a high performance computing cluster however, when I run the 'recon_all' command I get the following error
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 INFO: SUBJECTS_DIR is /home/users/kellys37/CT_TEST/CON3140 Actual FREESURFER_HOME /home/support/tcin/apps/freesurfer/5.2.0 Linux tcin-n02.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03 EST 2012 x86_64 x86_64 x86_64 GNU/Linux nu_correct: Command not found. #-------------------------------------------- #@# MotionCor Thu Mar 7 11:44:10 GMT 2013 Found 1 runs /home/users/kellys37/CT_TEST/CON3140/001/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue.
cp /home/users/kellys37/CT_TEST/CON3140/001/mri/orig/001.mgz
/home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz
/home/users/kellys37/CT_TEST/CON3140/001
mri_convert /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz
/home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz --conform
mri_convert /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz
/home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz --conform
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.9997, 0.0244327, -0.00148148) j_ras = (0.0239203, 0.987991, 0.152651) k_ras = (-0.00519336, -0.15257, 0.988279) Original Data has (0.898438, 0.898438, 0.9) mm size and (256, 256, 180) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz...
mri_add_xform_to_header -c
/home/users/kellys37/CT_TEST/CON3140/001/mri/transforms/talairach.xfm /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz
INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Mar 7 11:44:32 GMT 2013 /home/users/kellys37/CT_TEST/CON3140/001/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
Linux tcin-n02.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03 EST 2012 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 001 exited with ERRORS at Thu Mar 7 11:44:38 GMT 2013
For more details, see the log file /home/users/kellys37/CT_TEST/CON3140/001/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
I had did not encounter this error when using an older version of Freesurfer on our clusters. Do you know if there is any way to resolve this problem? Any advice would be appreciated.
Kind regards,
Sinead
-- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8 _______________________________________________ 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.
-- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Christopher Bell -
Nick Schmansky -
Sinead Kelly