[Freesurfer] recon_checker error
Opensuse 11.4 : Freesurfer 5.3 :QAtools_v1.1 I am trying to generate QC data from data generated using Freesurfer ver 5.3 and I'm getting the following error " Checking if all files exist...PASSED Checking actual file order...FAILED (read ../1006454_20216_2_0/scripts/recon_checker.log) ERROR: Actual file order disagrees with common file order for subject 1006454_20216_2_0" On checking the recon_checker.log it states This subject may have been processed with a different version of FreeSurfer other than the version used to create the common file order file (based on v5.1 by default if not specified by the user). Consider generating an output file order file for your specific dataset using the 'genoutputorderfile' flag. See the '-help' flag for details. I cannot find any details of this flag in any help file or any online help as to how to correct his problem Dave Liewald The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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] file error
OS Opensuse 13.2 Freesurfer 6 Dev Logfile Attached I have had no luck trying to get freesurfer to run. It is failing at the same point each time ( Please see log). I have tried with multiple datasets in multiple locations both on the local machine and across the network. I have also verified that the permissions of the dir are correct and I can manually read and write to the. I'm at a loss? Dave Liewald Wed Dec 9 11:37:57 GMT 2015 /UK_Biobank_MRI/FS_Output/1006924_20216_2_0 /UK_Biobank_MRI/freesurfer/bin/recon-all -i /UK_Biobank_MRI/WorkDir/1006924_20216_2_0/1.3.12.2.1107.5.2.19.45594.201507130826307583602667.dcm -s 1006924_20216_2_0 -sd /UK_Biobank_MRI/FS_Output -no-isrunning -all subjid 1006924_20216_2_0 setenv SUBJECTS_DIR /UK_Biobank_MRI/FS_Output FREESURFER_HOME /UK_Biobank_MRI/freesurfer Actual FREESURFER_HOME /UK_Biobank_MRI/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-dev-20151207 Linux CCACE-PROC01 3.16.7-24-desktop #1 SMP PREEMPT Mon Aug 3 14:37:06 UTC 2015 (ec183cc) x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize8192 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 193285 maxlocks unlimited maxsignal193285 maxmessage 819200 maxnice 0 maxrtprio0 maxrttimeunlimited total used free sharedbuffers cached Mem: 49495560 435314525964108 119680 242188 41644952 -/+ buffers/cache:1644312 47851248 Swap:314567668 1376 314566292 program versions used $Id: recon-all,v 1.555 2015/11/17 14:18:41 mreuter Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:57-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $Id: talairach_avi,v 1.11 2015/01/13 20:22:51 nicks Exp $ mri_convert --version dev build (use --all-info flag for full version info) ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: tkregister2.c,v 1.129 2014/02/26 21:31:58 greve Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mri_normalize.c,v 1.85 2015/08/05 19:24:14 fischl Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mri_watershed.cpp,v 1.101 2015/07/10 18:57:33 greve Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mri_segment.c,v 1.43 2015/02/05 23:34:40 zkaufman Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mri_label2label.c,v 1.47 2014/12/22 19:59:18 greve Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT
[Freesurfer] Path Problem
Environment : Opensuse 13.2 Freesurver Version 6 (Beta) Hi I hope you can help with this problem I'm using the version 6 Beta due to problems with license authentication. Freesurfer runs but bails out with a file not found error : Iteration 1 Fri Dec 4 09:38:57 GMT 2015 nu_correct -clobber ./tmp.mri_nu_correct.mni.24767/nu0.mnc ./tmp.mri_nu_correct.mni.24767/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.24767/0/ -iterations 1000 -stop 1e-4 -distance 200 -shrink 2 ERROR: file ./tmp.mri_nu_correct.mni.24767/nu1.mnc does not exist! Linux CCACE-PROC5 3.16.7-24-desktop #1 SMP PREEMPT Mon Aug 3 14:37:06 UTC 2015 (ec183cc) x86_64 x86_64 x86_64 GNU/Linux on examination of the file structure a directory named "tmp.mri_nu_correct.mni.24767" has been created under the "mri"directory and nothing has been created under the "tmp" directory in the subject root. I am guessing that this is the cause of the error. any advice on correcting this would be extremely useful Dave Liewald The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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] Path Problem
Hi Bruce here's the output CCACE-PROC5:/UK_Biobank_MRI/FS_Output/1493335_20216_2_0/mri # nu_correct -clobber ./tmp.mri_nu_correct.mni.24649/nu0.mnc ./tmp.mri_nu_correct.mni.24649/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.24649/0/ -iterations 1000 -stop 1e-4 -distance 200 -shrink 2 CCACE-PROC5:/UK_Biobank_MRI/FS_Output/1493335_20216_2_0/mri # nu_correct -version CCACE-PROC5:/UK_Biobank_MRI/FS_Output/1493335_20216_2_0/mri # which nu_correct/home/freesurfer/mni/bin/nu_correct CCACE-PROC5:/UK_Biobank_MRI/FS_Output/1493335_20216_2_0/mri # 1st command: No output 2nd command: No output 3rd Command : freesurfer has never been installed on this machine before and there is no freesurfer entries in the home directory thanks Dave From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fis...@nmr.mgh.harvard.edu> Sent: 04 December 2015 14:04 To: Freesurfer support list Subject: Re: [Freesurfer] Path Problem Hi Dave that is pretty puzzling. The nu1.mnc is the output of the command that is failing, so I don't see why it complains that it doesn't exist. The same command: nu_correct -clobber ./tmp.mri_nu_correct.mni.24649/nu0.mnc ./tmp.mri_nu_correct.mni.24649/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.24649/0/ -iterations 1000 -stop 1e-4 -distance 200 -shrink 2 works fine for me. Can you try it from the command line (from the mri dir)? If it fails, can you run: nu_correct -version and which nu_correct? cheers Bruce On Fri, 4 Dec 2015, LIEWALD David wrote: > Hi Bruce > > Yes the dir is writable and the echo command does create the test.dat in the > subdir. > > I have attached a recon-all log as requested > > Many Thanks > > Dave > > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl > <fis...@nmr.mgh.harvard.edu> > Sent: 04 December 2015 13:36 > To: Freesurfer support list > Subject: Re: [Freesurfer] Path Problem > > HI David > > can you write to that dir? For example, does > > echo test > ./tmp.mri_nu_correct.mni.24767/test.dat > > > work properly (from the mri dir)? Also, please send us the entire > recon-all.log so we can have a look > > cheers > Bruce > > On Fri, 4 Dec 2015, > LIEWALD > David wrote: > >> >> Environment : Opensuse 13.2 Freesurver Version 6 (Beta) >> >> >> Hi I hope you can help with this problem >> >> >> I'm using the version 6 Beta due to problems with license authentication. >> Freesurfer runs but bails >> out with a file not found error : >> >> >> >> Iteration 1 Fri Dec 4 09:38:57 GMT 2015 >> nu_correct -clobber ./tmp.mri_nu_correct.mni.24767/nu0.mnc >> ./tmp.mri_nu_correct.mni.24767/nu1.mnc >> -tmpdir ./tmp.mri_nu_correct.mni.24767/0/ -iterations 1000 -stop 1e-4 >> -distance 200 -shrink 2 >> >> >> >> ERROR: file ./tmp.mri_nu_correct.mni.24767/nu1.mnc does not exist! >> Linux CCACE-PROC5 3.16.7-24-desktop #1 SMP PREEMPT Mon Aug 3 14:37:06 UTC >> 2015 (ec183cc) x86_64 >> x86_64 x86_64 GNU/Linux >> >> >> >> on examination of the file structure a directory named >> "tmp.mri_nu_correct.mni.24767" has been >> created under the "mri"directory and nothing has been created under the >> "tmp" directory in the >> subject root. I am guessing that this is the cause of the error. >> >> >> any advice on correcting this would be extremely useful >> >> >> Dave Liewald >> >> >> > > ___ 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. -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Path Problem
Hi Bruce Just checked the actual location of the file is /UK_Biobank_MRI/freesurfer/mni/bin/nu_correct i.e. FREESURFER_HOME/mni/bin Dave From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fis...@nmr.mgh.harvard.edu> Sent: 04 December 2015 14:04 To: Freesurfer support list Subject: Re: [Freesurfer] Path Problem Hi Dave that is pretty puzzling. The nu1.mnc is the output of the command that is failing, so I don't see why it complains that it doesn't exist. The same command: nu_correct -clobber ./tmp.mri_nu_correct.mni.24649/nu0.mnc ./tmp.mri_nu_correct.mni.24649/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.24649/0/ -iterations 1000 -stop 1e-4 -distance 200 -shrink 2 works fine for me. Can you try it from the command line (from the mri dir)? If it fails, can you run: nu_correct -version and which nu_correct? cheers Bruce On Fri, 4 Dec 2015, LIEWALD David wrote: > Hi Bruce > > Yes the dir is writable and the echo command does create the test.dat in the > subdir. > > I have attached a recon-all log as requested > > Many Thanks > > Dave > > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl > <fis...@nmr.mgh.harvard.edu> > Sent: 04 December 2015 13:36 > To: Freesurfer support list > Subject: Re: [Freesurfer] Path Problem > > HI David > > can you write to that dir? For example, does > > echo test > ./tmp.mri_nu_correct.mni.24767/test.dat > > > work properly (from the mri dir)? Also, please send us the entire > recon-all.log so we can have a look > > cheers > Bruce > > On Fri, 4 Dec 2015, > LIEWALD > David wrote: > >> >> Environment : Opensuse 13.2 Freesurver Version 6 (Beta) >> >> >> Hi I hope you can help with this problem >> >> >> I'm using the version 6 Beta due to problems with license authentication. >> Freesurfer runs but bails >> out with a file not found error : >> >> >> >> Iteration 1 Fri Dec 4 09:38:57 GMT 2015 >> nu_correct -clobber ./tmp.mri_nu_correct.mni.24767/nu0.mnc >> ./tmp.mri_nu_correct.mni.24767/nu1.mnc >> -tmpdir ./tmp.mri_nu_correct.mni.24767/0/ -iterations 1000 -stop 1e-4 >> -distance 200 -shrink 2 >> >> >> >> ERROR: file ./tmp.mri_nu_correct.mni.24767/nu1.mnc does not exist! >> Linux CCACE-PROC5 3.16.7-24-desktop #1 SMP PREEMPT Mon Aug 3 14:37:06 UTC >> 2015 (ec183cc) x86_64 >> x86_64 x86_64 GNU/Linux >> >> >> >> on examination of the file structure a directory named >> "tmp.mri_nu_correct.mni.24767" has been >> created under the "mri"directory and nothing has been created under the >> "tmp" directory in the >> subject root. I am guessing that this is the cause of the error. >> >> >> any advice on correcting this would be extremely useful >> >> >> Dave Liewald >> >> >> > > ___ 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. -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Path Problem
Hi Bruce Yes the dir is writable and the echo command does create the test.dat in the subdir. I have attached a recon-all log as requested Many Thanks Dave From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fis...@nmr.mgh.harvard.edu> Sent: 04 December 2015 13:36 To: Freesurfer support list Subject: Re: [Freesurfer] Path Problem HI David can you write to that dir? For example, does echo test > ./tmp.mri_nu_correct.mni.24767/test.dat work properly (from the mri dir)? Also, please send us the entire recon-all.log so we can have a look cheers Bruce On Fri, 4 Dec 2015, LIEWALD David wrote: > > Environment : Opensuse 13.2 Freesurver Version 6 (Beta) > > > Hi I hope you can help with this problem > > > I'm using the version 6 Beta due to problems with license authentication. > Freesurfer runs but bails > out with a file not found error : > > > > Iteration 1 Fri Dec 4 09:38:57 GMT 2015 > nu_correct -clobber ./tmp.mri_nu_correct.mni.24767/nu0.mnc > ./tmp.mri_nu_correct.mni.24767/nu1.mnc > -tmpdir ./tmp.mri_nu_correct.mni.24767/0/ -iterations 1000 -stop 1e-4 > -distance 200 -shrink 2 > > > > ERROR: file ./tmp.mri_nu_correct.mni.24767/nu1.mnc does not exist! > Linux CCACE-PROC5 3.16.7-24-desktop #1 SMP PREEMPT Mon Aug 3 14:37:06 UTC > 2015 (ec183cc) x86_64 > x86_64 x86_64 GNU/Linux > > > > on examination of the file structure a directory named > "tmp.mri_nu_correct.mni.24767" has been > created under the "mri"directory and nothing has been created under the "tmp" > directory in the > subject root. I am guessing that this is the cause of the error. > > > any advice on correcting this would be extremely useful > > > Dave Liewald > > > -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Fri Dec 4 11:11:10 GMT 2015 /UK_Biobank_MRI/FS_Output/1493335_20216_2_0 /UK_Biobank_MRI/freesurfer/bin/recon-all -i /UK_Biobank_MRI/WorkDir/1493335_20216_2_0/1.3.12.2.1107.5.2.19.45594.2014102612140161812159407.dcm -s 1493335_20216_2_0 -sd /UK_Biobank_MRI/FS_Output -no-isrunning -all subjid 1493335_20216_2_0 setenv SUBJECTS_DIR /UK_Biobank_MRI/FS_Output FREESURFER_HOME /UK_Biobank_MRI/freesurfer Actual FREESURFER_HOME /UK_Biobank_MRI/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 Linux CCACE-PROC5 3.16.7-24-desktop #1 SMP PREEMPT Mon Aug 3 14:37:06 UTC 2015 (ec183cc) x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize8192 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 387206 maxlocks unlimited maxsignal387206 maxmessage 819200 maxnice 0 maxrtprio0 maxrttimeunlimited total used free sharedbuffers cached Mem: 99140516 53688556 45451960 95916 418652 51296424 -/+ buffers/cache:1973480 97167036 Swap:1258290761818048 124011028 program versions used $Id: recon-all,v 1.515.2.24 2015/10/01 21:23:52 greve Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_convert.c,v 1.221.2.2 2015/10/02 16:39:36 zkaufman Exp $ User: root Machine: CCACE-PROC5 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.11 2015/01/13 20:22:51 nicks Exp $ mri_convert --version dev build (use --all-info flag for full version info) ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: tkregister2.c,v 1.129 2014/02/26 21:31:58 greve Exp $ User: root Machine: CCACE-PROC5 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: root Machine: CCACE-PROC5 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_normalize.c,v 1.84.2.1 2015/08/13 17:12:10 zkaufman Exp $ User: root Mac
