[Freesurfer] ERROR: nu_correct
External Email - Use Caution Hi, I've been processing some 3T MRI scans through Freesurfer and recently implemented the use of the -3T flag for nu-correction. I have processed about 200 scans and the majority of them have gone through with out an issue. However there are a handful that I received and error: nu_correct message in the recon-all log. I've visually inspected these images and there appears to be nothing wrong with them. I've attached the error code below. Does anyone know what might be causing this? Furthermore, one of these images had actually been processed without a 3T flag prior without issues so it appears to be intrinsic to flag. Assertion failed: (pxp->bf_refcount <= 0), function ncio_px_sync, file ./posixio.c, line 798. nu_evaluate: crashed while running minc_modify_header (termination status=6) nu_correct: crashed while running nu_evaluate (termination status=65280) ERROR: nu_correct ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ERROR: nu_correct
External Email - Use Caution Hm, that's not the error I thought you were getting. nu_correct is on your PATH and your setup looks good. I've never seen such an error, sorry. Best, Tim > On April 4, 2019 at 9:40 AM Sevan Harootonian > wrote: > > > External Email - Use Caution > > Hi Tim, > > I'm running freesurfer on linux. And the exact error is: > > > ncvarput: ncid 5: Protocol error > > miicv_put: MINC package entry point > > nu_estimate_np_and_em: crashed while running mincmath (termination > > status=768) > > nu_correct: crashed while running nu_estimate_np_and_em (termination > > status=768) > > ERROR: nu_correct > > Linux neurodebian 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt9-3~deb8u1 > > (2015-04-24) x86_64 GNU/Linux > > > > here are the outputs for the directories. > 1) /home/brain/freesurfer > 2)-rwxr-xr-x 1 brain brain 20569 Jun 19 2015 > /home/brain/freesurfer/mni/bin/nu_correct > > Any idea? I've tried it on several datasets and still the problem, though > the example data sample-001.nii.gz doesn't throw this error. > > best, > sev > > > On Mon, Apr 1, 2019 at 1:43 AM Tim Schäfer wrote: > > > External Email - Use Caution > > > > Dear Sevan, > > > > Which version of FreeSurfer are you running on which system (Mac, Linux?), > > and what is the exact command line and error message? > > > > In case it is about nu_correct not being found: it should be in > > $FREESURFER_HOME/mni/bin/nu_correct, and if you get that error, most likely > > your environment variable $FREESURFER_HOME is not setup correctly for your > > shell. > > > > Please also report the output of these 2 commands so we can know more: > > > > 1) echo $FREESURFER_HOME > > 2) ls -l $FREESURFER_HOME/mni/bin/nu_correct > > > > Best, > > > > Tim > > > > > On April 1, 2019 at 2:22 AM Sevan Harootonian > > wrote: > > > > > > > > > External Email - Use Caution > > > > > > Hello Freesurfers, > > > > > > I'm running recond-all and getting ERROR: nu_correct. I see a lot of > > people > > > online have had this problem but I've failed to found a solution. Any > > > suggestions? > > > > > > I'm running freesurfer on a virtual machine and I've attached > > > my recon-all.log > > > > > > thanks, > > > sev > > > > > > -- > > > > > > Sevan Harootonian > > > research specialist > > > > > > Ekstrom's Lab > > > University of Arizona Psychology Department > > > ___ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > -- > > Dr. Tim Schäfer > > Postdoc Computational Neuroimaging > > Department of Child and Adolescent Psychiatry, Psychosomatics and > > Psychotherapy > > University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Sevan Harootonian > research specialist > > Ekstrom's Lab > University of Arizona Psychology Department > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Best, Tim -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ERROR: nu_correct
External Email - Use Caution Hi Tim, I'm running freesurfer on linux. And the exact error is: > ncvarput: ncid 5: Protocol error > miicv_put: MINC package entry point > nu_estimate_np_and_em: crashed while running mincmath (termination > status=768) > nu_correct: crashed while running nu_estimate_np_and_em (termination > status=768) > ERROR: nu_correct > Linux neurodebian 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt9-3~deb8u1 > (2015-04-24) x86_64 GNU/Linux here are the outputs for the directories. 1) /home/brain/freesurfer 2)-rwxr-xr-x 1 brain brain 20569 Jun 19 2015 /home/brain/freesurfer/mni/bin/nu_correct Any idea? I've tried it on several datasets and still the problem, though the example data sample-001.nii.gz doesn't throw this error. best, sev On Mon, Apr 1, 2019 at 1:43 AM Tim Schäfer wrote: > External Email - Use Caution > > Dear Sevan, > > Which version of FreeSurfer are you running on which system (Mac, Linux?), > and what is the exact command line and error message? > > In case it is about nu_correct not being found: it should be in > $FREESURFER_HOME/mni/bin/nu_correct, and if you get that error, most likely > your environment variable $FREESURFER_HOME is not setup correctly for your > shell. > > Please also report the output of these 2 commands so we can know more: > > 1) echo $FREESURFER_HOME > 2) ls -l $FREESURFER_HOME/mni/bin/nu_correct > > Best, > > Tim > > > On April 1, 2019 at 2:22 AM Sevan Harootonian > wrote: > > > > > > External Email - Use Caution > > > > Hello Freesurfers, > > > > I'm running recond-all and getting ERROR: nu_correct. I see a lot of > people > > online have had this problem but I've failed to found a solution. Any > > suggestions? > > > > I'm running freesurfer on a virtual machine and I've attached > > my recon-all.log > > > > thanks, > > sev > > > > -- > > > > Sevan Harootonian > > research specialist > > > > Ekstrom's Lab > > University of Arizona Psychology Department > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > Dr. Tim Schäfer > Postdoc Computational Neuroimaging > Department of Child and Adolescent Psychiatry, Psychosomatics and > Psychotherapy > University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Sevan Harootonian research specialist Ekstrom's Lab University of Arizona Psychology Department ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ERROR: nu_correct
External Email - Use Caution Dear Sevan, Which version of FreeSurfer are you running on which system (Mac, Linux?), and what is the exact command line and error message? In case it is about nu_correct not being found: it should be in $FREESURFER_HOME/mni/bin/nu_correct, and if you get that error, most likely your environment variable $FREESURFER_HOME is not setup correctly for your shell. Please also report the output of these 2 commands so we can know more: 1) echo $FREESURFER_HOME 2) ls -l $FREESURFER_HOME/mni/bin/nu_correct Best, Tim > On April 1, 2019 at 2:22 AM Sevan Harootonian > wrote: > > > External Email - Use Caution > > Hello Freesurfers, > > I'm running recond-all and getting ERROR: nu_correct. I see a lot of people > online have had this problem but I've failed to found a solution. Any > suggestions? > > I'm running freesurfer on a virtual machine and I've attached > my recon-all.log > > thanks, > sev > > -- > > Sevan Harootonian > research specialist > > Ekstrom's Lab > University of Arizona Psychology Department > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ERROR: nu_correct
External Email - Use Caution Hello Freesurfers, I'm running recond-all and getting ERROR: nu_correct. I see a lot of people online have had this problem but I've failed to found a solution. Any suggestions? I'm running freesurfer on a virtual machine and I've attached my recon-all.log thanks, sev -- Sevan Harootonian research specialist Ekstrom's Lab University of Arizona Psychology Department recon-all.log Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ERROR: nu_correct
External Email - Use Caution Dear Freesurfer Experts, I am having trouble with recon-all (Freesurfer 6.0). After running a shell script on my subjects I get the following error: Iteration 1 Fri Apr 20 13:22:37 CEST 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.14731/nu0.mnc ./tmp.mri_nu_correct.mni.14731/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.14731/0/ -iterations 1000 -distance 50 Cannot read input file: ./tmp.mri_nu_correct.mni.14731/nu0.mnc [XXX.XXX@XXX-pc26://projects//main/user//subject_c0_200/mri/] [2018-04-20 13:22:37] running: /ropt/freesurfer_6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.14731/0/ ./tmp.mri_nu_correct.mni.14731/nu0.mnc ./tmp.mri_nu_correct.mni.14731/nu1.imp nu_correct: crashed while running nu_estimate_np_and_em (termination status=512) ERROR: nu_correct Linux xxx-pc26 4.9.0-4-amd64 #1 SMP Debian 4.9.65-3 (2017-12-03) x86_64 GNU/Linux recon-all -s subject_c0_200 exited with ERRORS at Fri Apr 20 13:22:37 CEST 2018 Any suggestions what I can do are welcome! Best regards Dusan ___ 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] ERROR: nu_correct
I had the same problem with one server. The freesurfer version is freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c. The system is openSUSE13.2 for both servers. But one works well (A), while another one showed this problem (B). I found the kernel is somehow different, though I am not sure whether this is the point. kernel for A is 3.16.7-35-desktop, while kernel for B is 3.16.6-2-desktop. They have the same verion of perl, v5.20.1. Hope this case would be helpful for fixing the issue. Best, Xiangzhen On Tue, Apr 11, 2017 at 8:12 PM, Z K wrote: > What version of freesurfer are you using? My guess is 5.3 or earlier? > > With pre v6.0 versions of freesurfer, the Talairach transform step will > fail at the mri_nu_correct.mni command on newer Linux distributions that > come with perl version 5.22 (and higher) due to an incompatibility with > the mni tools shipped with FreeSurfer and newer versions of perl. The > issue has been fixed in version 6.0. > > On 04/05/2017 05:12 PM, Das S. wrote: > > Dear Freesurfer Developers, > > I was trying to use the recon-all -autorecon1 -subjid bert and got an > error. When I checked I found the error was coming while executing the > below command: > > nu_correct -clobber ./tmp.mri_nu_correct.mni.7555/nu0.mnc > ./tmp.mri_nu_correct.mni.7555/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.7555/0/ -iterations 1000 -distance 50 > > > > When I executed the command separately I got below error message: > > > > Can't use 'defined(@array)' (Maybe you should just omit the defined()?) > at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165. > > nu_correct: crashed while running nu_estimate_np_and_em (termination > status=65280) > > ERROR: nu_correct > > > > > > Can you please suggest why the error is coming and how to remove it. > > Many thanks > > Sarbani > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > ___ > 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. > > -- - Kong Xiangzhen State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China, 100875. ___ 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] ERROR: nu_correct
What version of freesurfer are you using? My guess is 5.3 or earlier? With pre v6.0 versions of freesurfer, the Talairach transform step will fail at the mri_nu_correct.mni command on newer Linux distributions that come with perl version 5.22 (and higher) due to an incompatibility with the mni tools shipped with FreeSurfer and newer versions of perl. The issue has been fixed in version 6.0. On 04/05/2017 05:12 PM, Das S. wrote: > Dear Freesurfer Developers, > I was trying to use the recon-all -autorecon1 -subjid bert and got an error. > When I checked I found the error was coming while executing the below command: > nu_correct -clobber ./tmp.mri_nu_correct.mni.7555/nu0.mnc > ./tmp.mri_nu_correct.mni.7555/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.7555/0/ -iterations 1000 -distance 50 > > When I executed the command separately I got below error message: > > Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165. > nu_correct: crashed while running nu_estimate_np_and_em (termination > status=65280) > ERROR: nu_correct > > > Can you please suggest why the error is coming and how to remove it. > Many thanks > Sarbani > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ 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: nu_correct
Dear Freesurfer Developers, I was trying to use the recon-all -autorecon1 -subjid bert and got an error. When I checked I found the error was coming while executing the below command: nu_correct -clobber ./tmp.mri_nu_correct.mni.7555/nu0.mnc ./tmp.mri_nu_correct.mni.7555/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.7555/0/ -iterations 1000 -distance 50 When I executed the command separately I got below error message: Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165. nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) ERROR: nu_correct Can you please suggest why the error is coming and how to remove it. Many thanks Sarbani ___ 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] ERROR: nu_correct
Sounds like it ran out of memory. Is that possible? Bruce On Jan 20, 2013, at 4:14 AM, Andrea Tateo wrote: > Hi freesurfer experts, > > my jobs are finished with this output > > Processing:.Done > Killed > ERROR: nu_correct > > > Can you help me? > > endless thanks > > Andrea > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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: nu_correct
Hi freesurfer experts, my jobs are finished with this output Processing:.DoneKilledERROR: nu_correct Can you help me? endless thanks Andrea ___ 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] error nu_correct
Stefan, Centos4 on VMWare on WindowsXP? Sounds interesting, and hope it can be made to work. What if you type: nu_correct Does it return something like this? nu_correct, version 1.10 Usage: nu_correct [-help] [options] in.mnc out.mnc If not, then please send me the error message. nu_correct is a script which assumes that perl is installed in /usr/bin/perl. If it is not instaled there (and it is by default on centos), then the script fixup_mni_paths will correct the mni scripts to point to your perl path. Also confirm that the environment variables MNI_DATAPATH and MNI_PERL5LIB point into the $FREESURFER_HOME/mni path. You should try running the MNI tools, like nu_correct, and others (see $FREESURFER_HOME/mni/bin) to confirm they work, since there may be some funny interaction with VMWare (but I obviously don't know this just yet). Nick > Hi freesurfers, > > the script crashed when running "recon-all -s bert -all" to test a newly > installed CentOS 4 version (v3.0.3) on a Windows XP system with VMware and > Fedora Core 4. The path for both nu_correct (and nu_estimate_np_and_em: > see second error message) seem to be correct > (/mnt/d/Freesurfer/freesurfer/mni/bin/nu_correct). > > Any suggestions greatly appriciated > > Thanks, > > Stefan > > > The error is as follows: > > [EMAIL PROTECTED] Nu Intensity Correction Thu Jul 20 07:47:00 BST 2006 > > mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 > > /mnt/d/Freesurfer/freesurfer/subjects/bert/mri > /mnt/d/Freesurfer/freesurfer/bin/mri_nu_correct.mni > --i orig.mgz --o nu.mgz --n 2 > nIters 2 > $Id: mri_nu_correct.mni,v 1.3 2005/12/08 01:27:21 greve Exp $ > Linux localhost.localdomain 2.6.15-1.1830_FC4 #1 Thu Feb 2 17:23:41 EST > 2006 i686 athlon i386 GNU/Linux > Thu Jul 20 07:47:00 BST 2006 > Setuid/gid script is writable by world. > tmpdir is ./tmp.mri_nu_correct.mni.10059 > /mnt/d/Freesurfer/freesurfer/subjects/bert/mri > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10059/nu0.mnc > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10059/nu0.mnc > reading from orig.mgz... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 0, -1) > k_ras = (0, 1, 0) > writing to ./tmp.mri_nu_correct.mni.10059/nu0.mnc... > > > Iteration 1 Thu Jul 20 07:47:09 BST 2006 > nu_correct -clobber ./tmp.mri_nu_correct.mni.10059/nu0.mnc > /tmp.mri_nu_correct.mni.10059/nu1.mnc > Setuid/gid script is writable by world. > ERROR: nu_correct > Linux localhost.localdomain 2.6.15-1.1830_FC4 #1 Thu Feb 2 17:23:41 EST > 2006 i686 athlon i386 GNU/Linux > > recon-all exited with ERRORS at Thu Jul 20 07:47:09 BST 2006 > > > ***the error is slightly different with one of myt own subjctes: > # > [EMAIL PROTECTED] Nu Intensity Correction Thu Jul 20 07:32:48 BST 2006 > > mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 > > /mnt/d/Freesurfer/freesurfer/subjects/sMS04134/mri > /mnt/d/Freesurfer/freesurfer/bin/mri_nu_correct.mni > --i orig.mgz --o nu.mgz --n 2 > nIters 2 > $Id: mri_nu_correct.mni,v 1.3 2005/12/08 01:27:21 greve Exp $ > Linux localhost.localdomain 2.6.15-1.1830_FC4 #1 Thu Feb 2 17:23:41 EST > 2006 i686 athlon i386 GNU/Linux > Thu Jul 20 07:32:48 BST 2006 > Program nu_correct, built from: > Package MNI N3, version 1.10, compiled by [EMAIL PROTECTED] > (i686-pc-linux-gnu) > on 2005-11-15 at 21:02:27 > tmpdir is ./tmp.mri_nu_correct.mni.9466 > /mnt/d/Freesurfer/freesurfer/subjects/sMS04134/mri > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9466/nu0.mnc > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9466/nu0.mnc > Can't find the talairach xform > '/mnt/d/Freesurfer/freesurfer/subjects/sMS04134/mri/transforms/talairach.xfm' > Transform is not loaded into mri > reading from orig.mgz... > Talairach transform > /mnt/d/Freesurfer/freesurfer/subjects/sMS04134/mri/transforms/talairach.xfm > does not exist ... > Cannot load tal xfm file > /mnt/d/Freesurfer/freesurfer/subjects/sMS04134/mri/transforms/talairach.xfm > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 0, -1) > k_ras = (0, 1, 0) > writing to ./tmp.mri_nu_correct.mni.9466/nu0.mnc... > > > Iteration 1 Thu Jul 20 07:32:57 BST 2006 > nu_correct -clobber ./tmp.mri_nu_correct.mni.9466/nu0.mnc > /tmp.mri_nu_correct.mni.9466/nu1.mnc > Setuid/gid script is writable by world. > nu_correct: crashed while running nu_estimate_np_and_em (termination > status=6400) > ERROR: nu_correct > Linux localhost.localdomain 2.6.15-1.1830_FC4 #1 Thu Feb 2 17:23:41 EST > 2006 i686 athlon i386 > GNU/Linux > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/
[Freesurfer] error nu_correct
Hi freesurfers, the script crashed when running "recon-all -s bert -all" to test a newly installed CentOS 4 version (v3.0.3) on a Windows XP system with VMware and Fedora Core 4. The path for both nu_correct (and nu_estimate_np_and_em: see second error message) seem to be correct (/mnt/d/Freesurfer/freesurfer/mni/bin/nu_correct). Any suggestions greatly appriciated Thanks, Stefan The error is as follows: [EMAIL PROTECTED] Nu Intensity Correction Thu Jul 20 07:47:00 BST 2006 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 /mnt/d/Freesurfer/freesurfer/subjects/bert/mri /mnt/d/Freesurfer/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.3 2005/12/08 01:27:21 greve Exp $ Linux localhost.localdomain 2.6.15-1.1830_FC4 #1 Thu Feb 2 17:23:41 EST 2006 i686 athlon i386 GNU/Linux Thu Jul 20 07:47:00 BST 2006 Setuid/gid script is writable by world. tmpdir is ./tmp.mri_nu_correct.mni.10059 /mnt/d/Freesurfer/freesurfer/subjects/bert/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10059/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10059/nu0.mnc reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to ./tmp.mri_nu_correct.mni.10059/nu0.mnc... Iteration 1 Thu Jul 20 07:47:09 BST 2006 nu_correct -clobber ./tmp.mri_nu_correct.mni.10059/nu0.mnc /tmp.mri_nu_correct.mni.10059/nu1.mnc Setuid/gid script is writable by world. ERROR: nu_correct Linux localhost.localdomain 2.6.15-1.1830_FC4 #1 Thu Feb 2 17:23:41 EST 2006 i686 athlon i386 GNU/Linux recon-all exited with ERRORS at Thu Jul 20 07:47:09 BST 2006 ***the error is slightly different with one of myt own subjctes: # [EMAIL PROTECTED] Nu Intensity Correction Thu Jul 20 07:32:48 BST 2006 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 /mnt/d/Freesurfer/freesurfer/subjects/sMS04134/mri /mnt/d/Freesurfer/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.3 2005/12/08 01:27:21 greve Exp $ Linux localhost.localdomain 2.6.15-1.1830_FC4 #1 Thu Feb 2 17:23:41 EST 2006 i686 athlon i386 GNU/Linux Thu Jul 20 07:32:48 BST 2006 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by [EMAIL PROTECTED] (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 tmpdir is ./tmp.mri_nu_correct.mni.9466 /mnt/d/Freesurfer/freesurfer/subjects/sMS04134/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9466/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9466/nu0.mnc Can't find the talairach xform '/mnt/d/Freesurfer/freesurfer/subjects/sMS04134/mri/transforms/talairach.xfm' Transform is not loaded into mri reading from orig.mgz... Talairach transform /mnt/d/Freesurfer/freesurfer/subjects/sMS04134/mri/transforms/talairach.xfm does not exist ... Cannot load tal xfm file /mnt/d/Freesurfer/freesurfer/subjects/sMS04134/mri/transforms/talairach.xfm TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to ./tmp.mri_nu_correct.mni.9466/nu0.mnc... Iteration 1 Thu Jul 20 07:32:57 BST 2006 nu_correct -clobber ./tmp.mri_nu_correct.mni.9466/nu0.mnc /tmp.mri_nu_correct.mni.9466/nu1.mnc Setuid/gid script is writable by world. nu_correct: crashed while running nu_estimate_np_and_em (termination status=6400) ERROR: nu_correct Linux localhost.localdomain 2.6.15-1.1830_FC4 #1 Thu Feb 2 17:23:41 EST 2006 i686 athlon i386 GNU/Linux ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ERROR: nu_correct
Ok. Sorry about the hassle. On Wed, 2005-08-24 at 12:34 -0400, Keyma Prince wrote: > Ok it look good now > > thanks > > Keyma Prince > Massachusetts Institute of Technology > Department of Brain and Cognitive Sciences > NE20-392 > Cambridge, MA 02139 > > On Wed, 24 Aug 2005, Nick Schmansky wrote: > > > Ok, how about now? > > > > > > On Wed, 2005-08-24 at 12:10 -0400, Keyma Prince wrote: > > > I get the same error. > > > > > > Here is output you asked for: > > > > > > [miracle:STRUCS] (nmr-std-env) cat /etc/redhat-release > > > CentOS release 4.1 (Final) > > > [miracle:STRUCS] (nmr-std-env) uname -a > > > Linux miracle 2.6.9-11.ELsmp #1 SMP Wed Jun 8 17:54:20 CDT 2005 i686 > > > athlon i386 GNU/Linux > > > [miracle:STRUCS] (nmr-std-env) > > > > > > > > > Keyma Prince > > > Massachusetts Institute of Technology > > > Department of Brain and Cognitive Sciences > > > NE20-392 > > > Cambridge, MA 02139 > > > > > > On Wed, 24 Aug 2005, Nick Schmansky wrote: > > > > > > > Kayma, > > > > > > > > Can you give it a try now? > > > > > > > > Also, can you type the following for me? > > > > > > > > cat /etc/redhat-release > > > > uname -a > > > > > > > > This will tell me the machine OS and type. Unfortunately, I can't login > > > > to miracle. > > > > > > > > Nick > > > > > > > > > > > > On Wed, 2005-08-24 at 11:40 -0400, Keyma Prince wrote: > > > > > this is on miracle. I opened a new terminal window and here is the > > > > > output > > > > > from nu_correct > > > > > > > > > > [miracle:STRUCS] (nmr-std-env) nu_correct > > > > > Can't locate MNI/Startup.pm in @INC (@INC contains: > > > > > /usr/lib/perl5/5.8.5/i386-li nux-thread-multi /usr/lib/perl5/5.8.5 > > > > > /usr/lib/perl5/site_perl/5.8.5/i386-linux- thread-multi > > > > > /usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi /usr/lib/per > > > > > l5/site_perl/5.8.3/i386-linux-thread-multi > > > > > /usr/lib/perl5/site_perl/5.8.2/i386-l inux-thread-multi > > > > > /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi /usr/li > > > > > b/perl5/site_perl/5.8.0/i386-linux-thread-multi > > > > > /usr/lib/perl5/site_perl/5.8.5 / usr/lib/perl5/site_perl/5.8.4 > > > > > /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site _perl/5.8.2 > > > > > /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 /usr/l > > > > > ib/perl5/site_perl > > > > > /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi /usr > > > > > /lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi > > > > > /usr/lib/perl5/vendor_perl/ 5.8.3/i386-linux-thread-multi > > > > > /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread -multi > > > > > /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi > > > > > /usr/lib/perl5/v > > > > > endor_perl/5.8.0/i386-linux-thread-multi > > > > > /usr/lib/perl5/vendor_perl/5.8.5 > > > > > /usr/l ib/perl5/vendor_perl/5.8.4 /usr/lib/perl5/vendor_perl/5.8.3 > > > > > /usr/lib/perl5/vendo r_perl/5.8.2 /usr/lib/perl5/vendor_perl/5.8.1 > > > > > /usr/lib/perl5/vendor_perl/5.8.0 / usr/lib/perl5/vendor_perl .) at > > > > > /usr/pubsw/packages/mni/current/bin/nu_correct l ine 37. > > > > > BEGIN failed--compilation aborted at > > > > > /usr/pubsw/packages/mni/current/bin/nu_corr ect line 37. > > > > > > > > > > > > > > > Keyma Prince > > > > > Massachusetts Institute of Technology > > > > > Department of Brain and Cognitive Sciences > > > > > NE20-392 > > > > > Cambridge, MA 02139 > > > > > > > > > > On Wed, 24 Aug 2005, Nick Schmansky wrote: > > > > > > > > > > > Keyma, > > > > > > > > > > > > Hi, on which machine does this occur? If you start a new shell, and > > > > > > type: > > > > > > > > > > > > nu_correct > > > > > > > > > > > > What does it display? > > > > > > > > > > > > Nick > > > > > > > > > > > > > > > > > > On Wed, 2005-08-24 at 11:34 -0400, Keyma Prince wrote: > > > > > > > I just tried to run the following command and I got an error > > > > > > > which has > > > > > > > appeared before on the freesurfer list after the MINC toolkit was > > > > > > > rebuilt. > > > > > > > Can you let me know if this has happened again and what I can do > > > > > > > about it? > > > > > > > > > > > > > > thanks, > > > > > > > > > > > > > > -Keyma > > > > > > > > > > > > > > > > > > > > > Command: recon-all -stage1 -subjid Y24_031905a_STRUC > > > > > > > > > > > > > > Error output: > > > > > > > > > > > > > > i_ras = (-1, 0, 0) > > > > > > > j_ras = (0, -0, -1) > > > > > > > k_ras = (-0, 1, 0) > > > > > > > Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. > > > > > > > Data is conformed to 1 mm size and 256 voxels for all directions > > > > > > > writing to > > > > > > > Started at: Wed Aug 24 11:21:42 EDT 2005 > > > > > > > Ended at: Wed Aug 24 11:23:46 EDT 2005 > > > > > > > mri_motion_correct2: done > > > > > > > - > > > > > > > Nu Intensity Correction Wed Aug 24 11:23:46 EDT 2005 > > > > > > > mri_convert orig nu0.mnc > > > > > > > mri_convert orig nu0.mnc > > > > > > > reading f
Re: [Freesurfer] ERROR: nu_correct
I get the same error. Here is output you asked for: [miracle:STRUCS] (nmr-std-env) cat /etc/redhat-release CentOS release 4.1 (Final) [miracle:STRUCS] (nmr-std-env) uname -a Linux miracle 2.6.9-11.ELsmp #1 SMP Wed Jun 8 17:54:20 CDT 2005 i686 athlon i386 GNU/Linux [miracle:STRUCS] (nmr-std-env) Keyma Prince Massachusetts Institute of Technology Department of Brain and Cognitive Sciences NE20-392 Cambridge, MA 02139 On Wed, 24 Aug 2005, Nick Schmansky wrote: > Kayma, > > Can you give it a try now? > > Also, can you type the following for me? > > cat /etc/redhat-release > uname -a > > This will tell me the machine OS and type. Unfortunately, I can't login > to miracle. > > Nick > > > On Wed, 2005-08-24 at 11:40 -0400, Keyma Prince wrote: > > this is on miracle. I opened a new terminal window and here is the output > > from nu_correct > > > > [miracle:STRUCS] (nmr-std-env) nu_correct > > Can't locate MNI/Startup.pm in @INC (@INC contains: > > /usr/lib/perl5/5.8.5/i386-li nux-thread-multi /usr/lib/perl5/5.8.5 > > /usr/lib/perl5/site_perl/5.8.5/i386-linux- thread-multi > > /usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi /usr/lib/per > > l5/site_perl/5.8.3/i386-linux-thread-multi > > /usr/lib/perl5/site_perl/5.8.2/i386-l inux-thread-multi > > /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi /usr/li > > b/perl5/site_perl/5.8.0/i386-linux-thread-multi > > /usr/lib/perl5/site_perl/5.8.5 / usr/lib/perl5/site_perl/5.8.4 > > /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site _perl/5.8.2 > > /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 /usr/l > > ib/perl5/site_perl > > /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi /usr > > /lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi > > /usr/lib/perl5/vendor_perl/ 5.8.3/i386-linux-thread-multi > > /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread -multi > > /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/v > > endor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.5 > > /usr/l ib/perl5/vendor_perl/5.8.4 /usr/lib/perl5/vendor_perl/5.8.3 > > /usr/lib/perl5/vendo r_perl/5.8.2 /usr/lib/perl5/vendor_perl/5.8.1 > > /usr/lib/perl5/vendor_perl/5.8.0 / usr/lib/perl5/vendor_perl .) at > > /usr/pubsw/packages/mni/current/bin/nu_correct l ine 37. > > BEGIN failed--compilation aborted at > > /usr/pubsw/packages/mni/current/bin/nu_corr ect line 37. > > > > > > Keyma Prince > > Massachusetts Institute of Technology > > Department of Brain and Cognitive Sciences > > NE20-392 > > Cambridge, MA 02139 > > > > On Wed, 24 Aug 2005, Nick Schmansky wrote: > > > > > Keyma, > > > > > > Hi, on which machine does this occur? If you start a new shell, and > > > type: > > > > > > nu_correct > > > > > > What does it display? > > > > > > Nick > > > > > > > > > On Wed, 2005-08-24 at 11:34 -0400, Keyma Prince wrote: > > > > I just tried to run the following command and I got an error which has > > > > appeared before on the freesurfer list after the MINC toolkit was > > > > rebuilt. > > > > Can you let me know if this has happened again and what I can do about > > > > it? > > > > > > > > thanks, > > > > > > > > -Keyma > > > > > > > > > > > > Command: recon-all -stage1 -subjid Y24_031905a_STRUC > > > > > > > > Error output: > > > > > > > > i_ras = (-1, 0, 0) > > > > j_ras = (0, -0, -1) > > > > k_ras = (-0, 1, 0) > > > > Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. > > > > Data is conformed to 1 mm size and 256 voxels for all directions > > > > writing to > > > > Started at: Wed Aug 24 11:21:42 EDT 2005 > > > > Ended at: Wed Aug 24 11:23:46 EDT 2005 > > > > mri_motion_correct2: done > > > > - > > > > Nu Intensity Correction Wed Aug 24 11:23:46 EDT 2005 > > > > mri_convert orig nu0.mnc > > > > mri_convert orig nu0.mnc > > > > reading from orig... > > > > TR=2530.00, TE=3.30, TI=1100.00, flip angle=7.00 > > > > i_ras = (-1, 0, 0) > > > > j_ras = (0, -0, -1) > > > > k_ras = (-0, 1, 0) > > > > writing to nu0.mnc... > > > > nu_correct -clobber nu0.mnc nu1.mnc > > > > Can't locate MNI/Startup.pm in @INC (@INC contains: > > > > /usr/lib/perl5/5.8.5/i386-linux-thread-multi /usr/lib/perl5/5.8.5 > > > > /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi > > > > /usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi > > > > /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi > > > > /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi > > > > /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi > > > > /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi > > > > /usr/lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl/5.8.4 > > > > /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2 > > > > /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 > > > > /usr/lib/perl5/site_perl > > > > /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi > > > > /usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi > > > > /usr/lib/perl5/
Re: [Freesurfer] ERROR: nu_correct
Kayma, Can you give it a try now? Also, can you type the following for me? cat /etc/redhat-release uname -a This will tell me the machine OS and type. Unfortunately, I can't login to miracle. Nick On Wed, 2005-08-24 at 11:40 -0400, Keyma Prince wrote: > this is on miracle. I opened a new terminal window and here is the output > from nu_correct > > [miracle:STRUCS] (nmr-std-env) nu_correct > Can't locate MNI/Startup.pm in @INC (@INC contains: > /usr/lib/perl5/5.8.5/i386-li nux-thread-multi /usr/lib/perl5/5.8.5 > /usr/lib/perl5/site_perl/5.8.5/i386-linux- thread-multi > /usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi /usr/lib/per > l5/site_perl/5.8.3/i386-linux-thread-multi > /usr/lib/perl5/site_perl/5.8.2/i386-l inux-thread-multi > /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi /usr/li > b/perl5/site_perl/5.8.0/i386-linux-thread-multi > /usr/lib/perl5/site_perl/5.8.5 / usr/lib/perl5/site_perl/5.8.4 > /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site _perl/5.8.2 > /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 /usr/l > ib/perl5/site_perl > /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi /usr > /lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi > /usr/lib/perl5/vendor_perl/ 5.8.3/i386-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread -multi > /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/v > endor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.5 > /usr/l ib/perl5/vendor_perl/5.8.4 /usr/lib/perl5/vendor_perl/5.8.3 > /usr/lib/perl5/vendo r_perl/5.8.2 /usr/lib/perl5/vendor_perl/5.8.1 > /usr/lib/perl5/vendor_perl/5.8.0 / usr/lib/perl5/vendor_perl .) at > /usr/pubsw/packages/mni/current/bin/nu_correct l ine 37. > BEGIN failed--compilation aborted at > /usr/pubsw/packages/mni/current/bin/nu_corr ect line 37. > > > Keyma Prince > Massachusetts Institute of Technology > Department of Brain and Cognitive Sciences > NE20-392 > Cambridge, MA 02139 > > On Wed, 24 Aug 2005, Nick Schmansky wrote: > > > Keyma, > > > > Hi, on which machine does this occur? If you start a new shell, and > > type: > > > > nu_correct > > > > What does it display? > > > > Nick > > > > > > On Wed, 2005-08-24 at 11:34 -0400, Keyma Prince wrote: > > > I just tried to run the following command and I got an error which has > > > appeared before on the freesurfer list after the MINC toolkit was rebuilt. > > > Can you let me know if this has happened again and what I can do about it? > > > > > > thanks, > > > > > > -Keyma > > > > > > > > > Command: recon-all -stage1 -subjid Y24_031905a_STRUC > > > > > > Error output: > > > > > > i_ras = (-1, 0, 0) > > > j_ras = (0, -0, -1) > > > k_ras = (-0, 1, 0) > > > Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. > > > Data is conformed to 1 mm size and 256 voxels for all directions > > > writing to > > > Started at: Wed Aug 24 11:21:42 EDT 2005 > > > Ended at: Wed Aug 24 11:23:46 EDT 2005 > > > mri_motion_correct2: done > > > - > > > Nu Intensity Correction Wed Aug 24 11:23:46 EDT 2005 > > > mri_convert orig nu0.mnc > > > mri_convert orig nu0.mnc > > > reading from orig... > > > TR=2530.00, TE=3.30, TI=1100.00, flip angle=7.00 > > > i_ras = (-1, 0, 0) > > > j_ras = (0, -0, -1) > > > k_ras = (-0, 1, 0) > > > writing to nu0.mnc... > > > nu_correct -clobber nu0.mnc nu1.mnc > > > Can't locate MNI/Startup.pm in @INC (@INC contains: > > > /usr/lib/perl5/5.8.5/i386-linux-thread-multi /usr/lib/perl5/5.8.5 > > > /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi > > > /usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi > > > /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi > > > /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi > > > /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi > > > /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi > > > /usr/lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl/5.8.4 > > > /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2 > > > /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 > > > /usr/lib/perl5/site_perl > > > /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi > > > /usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi > > > /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi > > > /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi > > > /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi > > > /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi > > > /usr/lib/perl5/vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl/5.8.4 > > > /usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2 > > > /usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0 > > > /usr/lib/perl5/vendor_perl .) at > > > /usr/pubsw/packages/mni/current/bin/nu_correct line 37. > > > BEGIN failed--compilation aborted at > > > /usr/pubsw/packages/mni/current/bin/nu_correct line 37. > > > ERROR: nu_correct > > > -
Re: [Freesurfer] ERROR: nu_correct
this is on miracle. I opened a new terminal window and here is the output from nu_correct [miracle:STRUCS] (nmr-std-env) nu_correct Can't locate MNI/Startup.pm in @INC (@INC contains: /usr/lib/perl5/5.8.5/i386-li nux-thread-multi /usr/lib/perl5/5.8.5 /usr/lib/perl5/site_perl/5.8.5/i386-linux- thread-multi /usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi /usr/lib/per l5/site_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.2/i386-l inux-thread-multi /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi /usr/li b/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.5 / usr/lib/perl5/site_perl/5.8.4 /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site _perl/5.8.2 /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 /usr/l ib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi /usr /lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/ 5.8.3/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread -multi /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/v endor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.5 /usr/l ib/perl5/vendor_perl/5.8.4 /usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendo r_perl/5.8.2 /usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0 / usr/lib/perl5/vendor_perl .) at /usr/pubsw/packages/mni/current/bin/nu_correct l ine 37. BEGIN failed--compilation aborted at /usr/pubsw/packages/mni/current/bin/nu_corr ect line 37. Keyma Prince Massachusetts Institute of Technology Department of Brain and Cognitive Sciences NE20-392 Cambridge, MA 02139 On Wed, 24 Aug 2005, Nick Schmansky wrote: > Keyma, > > Hi, on which machine does this occur? If you start a new shell, and > type: > > nu_correct > > What does it display? > > Nick > > > On Wed, 2005-08-24 at 11:34 -0400, Keyma Prince wrote: > > I just tried to run the following command and I got an error which has > > appeared before on the freesurfer list after the MINC toolkit was rebuilt. > > Can you let me know if this has happened again and what I can do about it? > > > > thanks, > > > > -Keyma > > > > > > Command: recon-all -stage1 -subjid Y24_031905a_STRUC > > > > Error output: > > > > i_ras = (-1, 0, 0) > > j_ras = (0, -0, -1) > > k_ras = (-0, 1, 0) > > Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. > > Data is conformed to 1 mm size and 256 voxels for all directions > > writing to > > Started at: Wed Aug 24 11:21:42 EDT 2005 > > Ended at: Wed Aug 24 11:23:46 EDT 2005 > > mri_motion_correct2: done > > - > > Nu Intensity Correction Wed Aug 24 11:23:46 EDT 2005 > > mri_convert orig nu0.mnc > > mri_convert orig nu0.mnc > > reading from orig... > > TR=2530.00, TE=3.30, TI=1100.00, flip angle=7.00 > > i_ras = (-1, 0, 0) > > j_ras = (0, -0, -1) > > k_ras = (-0, 1, 0) > > writing to nu0.mnc... > > nu_correct -clobber nu0.mnc nu1.mnc > > Can't locate MNI/Startup.pm in @INC (@INC contains: > > /usr/lib/perl5/5.8.5/i386-linux-thread-multi /usr/lib/perl5/5.8.5 > > /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi > > /usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi > > /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi > > /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi > > /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi > > /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi > > /usr/lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl/5.8.4 > > /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2 > > /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 > > /usr/lib/perl5/site_perl > > /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi > > /usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi > > /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi > > /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi > > /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi > > /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi > > /usr/lib/perl5/vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl/5.8.4 > > /usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2 > > /usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0 > > /usr/lib/perl5/vendor_perl .) at > > /usr/pubsw/packages/mni/current/bin/nu_correct line 37. > > BEGIN failed--compilation aborted at > > /usr/pubsw/packages/mni/current/bin/nu_correct line 37. > > ERROR: nu_correct > > -- > > Filesystem 1K-blocks Used Available Use% Mounted on > > engram:/local_mount/space/engram/11 > > 68682136 44104560 24577576 65% > > /autofs/space/engram_011 > > -- > > recon-all exited with errors at Wed Aug 24 11:24:01 EDT 2005 > > > > > > Keyma Prince > > Massachusetts Institute of Technology > > Department of Brain and Cognitive Sciences > > NE20-392 > > Cambridge, MA 02139 >
Re: [Freesurfer] ERROR: nu_correct
Keyma, Hi, on which machine does this occur? If you start a new shell, and type: nu_correct What does it display? Nick On Wed, 2005-08-24 at 11:34 -0400, Keyma Prince wrote: > I just tried to run the following command and I got an error which has > appeared before on the freesurfer list after the MINC toolkit was rebuilt. > Can you let me know if this has happened again and what I can do about it? > > thanks, > > -Keyma > > > Command: recon-all -stage1 -subjid Y24_031905a_STRUC > > Error output: > > i_ras = (-1, 0, 0) > j_ras = (0, -0, -1) > k_ras = (-0, 1, 0) > Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. > Data is conformed to 1 mm size and 256 voxels for all directions > writing to > Started at: Wed Aug 24 11:21:42 EDT 2005 > Ended at: Wed Aug 24 11:23:46 EDT 2005 > mri_motion_correct2: done > - > Nu Intensity Correction Wed Aug 24 11:23:46 EDT 2005 > mri_convert orig nu0.mnc > mri_convert orig nu0.mnc > reading from orig... > TR=2530.00, TE=3.30, TI=1100.00, flip angle=7.00 > i_ras = (-1, 0, 0) > j_ras = (0, -0, -1) > k_ras = (-0, 1, 0) > writing to nu0.mnc... > nu_correct -clobber nu0.mnc nu1.mnc > Can't locate MNI/Startup.pm in @INC (@INC contains: > /usr/lib/perl5/5.8.5/i386-linux-thread-multi /usr/lib/perl5/5.8.5 > /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi > /usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi > /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi > /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi > /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi > /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi > /usr/lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl/5.8.4 > /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2 > /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 > /usr/lib/perl5/site_perl > /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl/5.8.4 > /usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2 > /usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0 > /usr/lib/perl5/vendor_perl .) at > /usr/pubsw/packages/mni/current/bin/nu_correct line 37. > BEGIN failed--compilation aborted at > /usr/pubsw/packages/mni/current/bin/nu_correct line 37. > ERROR: nu_correct > -- > Filesystem 1K-blocks Used Available Use% Mounted on > engram:/local_mount/space/engram/11 > 68682136 44104560 24577576 65% > /autofs/space/engram_011 > -- > recon-all exited with errors at Wed Aug 24 11:24:01 EDT 2005 > > > Keyma Prince > Massachusetts Institute of Technology > Department of Brain and Cognitive Sciences > NE20-392 > Cambridge, MA 02139 > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ERROR: nu_correct
I just tried to run the following command and I got an error which has appeared before on the freesurfer list after the MINC toolkit was rebuilt. Can you let me know if this has happened again and what I can do about it? thanks, -Keyma Command: recon-all -stage1 -subjid Y24_031905a_STRUC Error output: i_ras = (-1, 0, 0) j_ras = (0, -0, -1) k_ras = (-0, 1, 0) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions writing to Started at: Wed Aug 24 11:21:42 EDT 2005 Ended at: Wed Aug 24 11:23:46 EDT 2005 mri_motion_correct2: done - Nu Intensity Correction Wed Aug 24 11:23:46 EDT 2005 mri_convert orig nu0.mnc mri_convert orig nu0.mnc reading from orig... TR=2530.00, TE=3.30, TI=1100.00, flip angle=7.00 i_ras = (-1, 0, 0) j_ras = (0, -0, -1) k_ras = (-0, 1, 0) writing to nu0.mnc... nu_correct -clobber nu0.mnc nu1.mnc Can't locate MNI/Startup.pm in @INC (@INC contains: /usr/lib/perl5/5.8.5/i386-linux-thread-multi /usr/lib/perl5/5.8.5 /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl/5.8.4 /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2 /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl/5.8.4 /usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2 /usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at /usr/pubsw/packages/mni/current/bin/nu_correct line 37. BEGIN failed--compilation aborted at /usr/pubsw/packages/mni/current/bin/nu_correct line 37. ERROR: nu_correct -- Filesystem 1K-blocks Used Available Use% Mounted on engram:/local_mount/space/engram/11 68682136 44104560 24577576 65% /autofs/space/engram_011 -- recon-all exited with errors at Wed Aug 24 11:24:01 EDT 2005 Keyma Prince Massachusetts Institute of Technology Department of Brain and Cognitive Sciences NE20-392 Cambridge, MA 02139 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ERROR: nu_correct
ok, it is working now. thanks! margaret On Fri, 17 Jun 2005, Nick Schmansky wrote: Try it now. I have recently rebuilt the MINC toolkit, but it seems I overlooked its dependencies, and just now reverted the path back to where it was (and will leave it that way). Sorry for the hassle. On Fri, 2005-06-17 at 16:32 -0400, Margaret Duff wrote: Hi, I have just recently gotten an error when running recon-all-nmr. I am on the computer troy and my command line is recon-all-nmr -stage1 -subjid SM2S2 and my SUBJECTS_DIR is /space/troy/1/users/FREESURFER. I tried resetting my LANG to C and en_US and neither made a difference. It seems like it can't find a start up file, which I found in /usr/lib/perl5/5.8.5/MNI, but this doesn't seem to be one of the paths its looking in. Is there anything I can do to prevent this error? I have attached the error file from the terminal window below. Thanks, Margaret (nmr-std-env) recon-all-nmr -stage1 -subjid SM2S2 program versions used $Id: recon-all-nmr,v 1.53 2004/12/08 20:45:06 greve Exp $ $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ mri_convert --version stable2 minctracc.c $Id: talairach2,v 1.7 2004/08/31 18:07:37 tosa Exp $ mri_convert --version stable2 # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ # $Id: nu_estimate.in,v 1.1 2003/04/16 14:29:34 bert Exp $ stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 ### INFO: SUBJECTS_DIR is /autofs/space/troy_001/users/FREESURFER WARNING: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer/beta Previous: /usr/local/freesurfer/dev - MotionCor Fri Jun 17 16:16:50 EDT 2005 /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig mri_motion_correct2 -o . -i 001 -i 002 tmpdir is ./tmp-mri_motion_correct2-27002 -- mri_motion_correct2 logfile is ./mri_motion_correct2.log -- - Converting 001 Fri Jun 17 16:16:54 EDT 2005 mri_convert 001 /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-1.mnc ^[[B^[[A^[[B^[[B^[[B^[[Breading from 001... TR=273.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, -0) j_ras = (-0, 0, -1) k_ras = (-0, 1, -0) writing to /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-1.mnc... - Converting 002 Fri Jun 17 16:17:06 EDT 2005 mri_convert 002 /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-2.mnc reading from 002... TR=273.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, -0) j_ras = (-0, 0, -1) k_ras = (-0, 1, -0) writing to /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-2.mnc... - Motion Correcting /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-2.mnc Fri Jun 17 16:17:17 EDT 2005 COG of v1: 4.496311 15.253652 -23.867643 COG of v2: 4.493972 15.296473 -24.011532 [trans] = -0.002339 0.042821 -0.143888 Initial objective function val = 0.01666989 Final objective function value = 0.01148322 successful write - Resampling /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-2.mnc Fri Jun 17 16:18:21 EDT 2005 Transforming slices:Done - Averaging Fri Jun 17 16:18:27 EDT 2005 Processing:Done - Converting Average to output Fri Jun 17 16:18:32 EDT 2005 mri_convert /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/avgvol.mnc . -tr 2.73e+06 -te 0 -TI 0 -flip_angle 0 reading from /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/avgvol.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, -0) j_ras = (-0, 0, -1) k_ras = (-0, 1, -0) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions writing to Started at: Fri Jun 17 16:16:54 EDT 2005 Ended at: Fri Jun 17 16:18:41 EDT 20
Re: [Freesurfer] ERROR: nu_correct
Try it now. I have recently rebuilt the MINC toolkit, but it seems I overlooked its dependencies, and just now reverted the path back to where it was (and will leave it that way). Sorry for the hassle. On Fri, 2005-06-17 at 16:32 -0400, Margaret Duff wrote: > Hi, I have just recently gotten an error when running recon-all-nmr. I > am on the computer troy and my command line is recon-all-nmr -stage1 > -subjid SM2S2 and my SUBJECTS_DIR is /space/troy/1/users/FREESURFER. > I tried resetting my LANG to C and en_US and neither made a difference. > It seems like it can't find a start up file, which I found in > /usr/lib/perl5/5.8.5/MNI, but this doesn't seem to be one of the paths its > looking in. Is there anything I can do to prevent this error? I have > attached the error file from the terminal window below. Thanks, > Margaret > > > (nmr-std-env) recon-all-nmr -stage1 -subjid SM2S2 > > program versions used > $Id: recon-all-nmr,v 1.53 2004/12/08 20:45:06 greve Exp $ > $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ > mri_convert --version > stable2 > minctracc.c > $Id: talairach2,v 1.7 2004/08/31 18:07:37 tosa Exp $ > mri_convert --version > stable2 > # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ > # $Id: nu_estimate.in,v 1.1 2003/04/16 14:29:34 bert Exp $ > stable2 > stable2 > stable2 > stable2 > stable2 > stable2 > stable2 > stable2 > stable2 > stable2 > stable2 > stable2 > stable2 > stable2 > stable2 > stable2 > ### > INFO: SUBJECTS_DIR is /autofs/space/troy_001/users/FREESURFER > WARNING: current FREESURFER_HOME does not match that of previous > processing. > Current: /usr/local/freesurfer/beta > Previous: /usr/local/freesurfer/dev > - > MotionCor Fri Jun 17 16:16:50 EDT 2005 > /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig > mri_motion_correct2 -o . -i 001 -i 002 > tmpdir is ./tmp-mri_motion_correct2-27002 > -- > mri_motion_correct2 logfile is ./mri_motion_correct2.log > -- > - > Converting 001 > Fri Jun 17 16:16:54 EDT 2005 > mri_convert 001 > /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-1.mnc > ^[[B^[[A^[[B^[[B^[[B^[[Breading from 001... > TR=273.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, -0) > j_ras = (-0, 0, -1) > k_ras = (-0, 1, -0) > writing to > /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-1.mnc... > - > Converting 002 > Fri Jun 17 16:17:06 EDT 2005 > mri_convert 002 > /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-2.mnc > reading from 002... > TR=273.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, -0) > j_ras = (-0, 0, -1) > k_ras = (-0, 1, -0) > writing to > /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-2.mnc... > - > Motion Correcting > /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-2.mnc > Fri Jun 17 16:17:17 EDT 2005 > COG of v1: 4.496311 15.253652 -23.867643 > COG of v2: 4.493972 15.296473 -24.011532 > [trans] = -0.002339 0.042821 -0.143888 > Initial objective function val = 0.01666989 > Final objective function value = 0.01148322 > successful write > - > Resampling > /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-2.mnc > Fri Jun 17 16:18:21 EDT 2005 > Transforming > slices:Done > - > Averaging > Fri Jun 17 16:18:27 EDT 2005 > Processing:Done > - > Converting Average to output > Fri Jun 17 16:18:32 EDT 2005 > mri_convert > /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/avgvol.mnc > > . -tr 2.73e+06 -te 0 -TI 0 -flip_angle 0 > reading from > /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/avgvol.mnc... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, -0) > j_ras = (-0, 0, -1) > k_ras = (-0, 1, -0) > Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. > Data i
[Freesurfer] ERROR: nu_correct
Hi, I have just recently gotten an error when running recon-all-nmr. I am on the computer troy and my command line is recon-all-nmr -stage1 -subjid SM2S2 and my SUBJECTS_DIR is /space/troy/1/users/FREESURFER. I tried resetting my LANG to C and en_US and neither made a difference. It seems like it can't find a start up file, which I found in /usr/lib/perl5/5.8.5/MNI, but this doesn't seem to be one of the paths its looking in. Is there anything I can do to prevent this error? I have attached the error file from the terminal window below. Thanks, Margaret (nmr-std-env) recon-all-nmr -stage1 -subjid SM2S2 program versions used $Id: recon-all-nmr,v 1.53 2004/12/08 20:45:06 greve Exp $ $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ mri_convert --version stable2 minctracc.c $Id: talairach2,v 1.7 2004/08/31 18:07:37 tosa Exp $ mri_convert --version stable2 # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ # $Id: nu_estimate.in,v 1.1 2003/04/16 14:29:34 bert Exp $ stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 ### INFO: SUBJECTS_DIR is /autofs/space/troy_001/users/FREESURFER WARNING: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer/beta Previous: /usr/local/freesurfer/dev - MotionCor Fri Jun 17 16:16:50 EDT 2005 /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig mri_motion_correct2 -o . -i 001 -i 002 tmpdir is ./tmp-mri_motion_correct2-27002 -- mri_motion_correct2 logfile is ./mri_motion_correct2.log -- - Converting 001 Fri Jun 17 16:16:54 EDT 2005 mri_convert 001 /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-1.mnc ^[[B^[[A^[[B^[[B^[[B^[[Breading from 001... TR=273.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, -0) j_ras = (-0, 0, -1) k_ras = (-0, 1, -0) writing to /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-1.mnc... - Converting 002 Fri Jun 17 16:17:06 EDT 2005 mri_convert 002 /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-2.mnc reading from 002... TR=273.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, -0) j_ras = (-0, 0, -1) k_ras = (-0, 1, -0) writing to /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-2.mnc... - Motion Correcting /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-2.mnc Fri Jun 17 16:17:17 EDT 2005 COG of v1: 4.496311 15.253652 -23.867643 COG of v2: 4.493972 15.296473 -24.011532 [trans] = -0.002339 0.042821 -0.143888 Initial objective function val = 0.01666989 Final objective function value = 0.01148322 successful write - Resampling /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-2.mnc Fri Jun 17 16:18:21 EDT 2005 Transforming slices:Done - Averaging Fri Jun 17 16:18:27 EDT 2005 Processing:Done - Converting Average to output Fri Jun 17 16:18:32 EDT 2005 mri_convert /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/avgvol.mnc . -tr 2.73e+06 -te 0 -TI 0 -flip_angle 0 reading from /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/avgvol.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, -0) j_ras = (-0, 0, -1) k_ras = (-0, 1, -0) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions writing to Started at: Fri Jun 17 16:16:54 EDT 2005 Ended at: Fri Jun 17 16:18:41 EDT 2005 mri_motion_correct2: done - Nu Intensity Correction Fri Jun 17 16:18:41 EDT 2005 mri_convert orig nu0.mnc mri_convert orig nu0.mnc reading from orig... TR=273.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, -0) j_ras = (-0, 0, -1) k_ras = (-0, 1, -0) writing to nu0.mnc...
