Hello,
I’m new with FreeSurfer and I’m getting a really bad skull stripping (almost nothing) with mri_watershed –atlas in images converted from DICOM to .mgz with mri_convert. I lowered the threshold but did not improved considerably. I have tried with a subject from the tutorial dataset and it’s OK. What can be the problem?
Thank you very much!
Úrsula
Hi Arsula
are you running this through recon-all or outside of it? The skull stripping works better after the intensity normalization that is part of recon-all
cheers Bruce
On Fri, 29 Aug 2014, Úrsula Pérez Ramírez wrote:
Hello,
I’m new with FreeSurfer and I’m getting a really bad skull stripping (almost nothing) with mri_watershed –atlas in images converted from DICOM to .mgz with mri_convert. I lowered the threshold but did not improved considerably. I have tried with a subject from the tutorial dataset and it’s OK. What can be the problem?
Thank you very much!
Úrsula
Hi Bruce,
thank you very much for your fast answer. I'm running outside recon-all, only with mri_watershed. Thanks, that could help. Which are the options for recon-all if I have already the .mgz file?, I'm getting errors, appart from the warning for updating tcsh.
Cheers, Ursula
Date: Fri, 29 Aug 2014 11:23:06 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_watershed: really bad skull stripping
Hi Arsula
are you running this through recon-all or outside of it? The skull stripping works better after the intensity normalization that is part of recon-all
cheers Bruce
On Fri, 29 Aug 2014, Úrsula Pérez Ramírez wrote:
Hello,
I’m new with FreeSurfer and I’m getting a really bad skull stripping (almost nothing) with mri_watershed –atlas in images converted from DICOM to .mgz with mri_convert. I lowered the threshold but did not improved considerably. I have tried with a subject from the tutorial dataset and it’s OK. What can be the problem?
Thank you very much!
Úrsula
_______________________________________________ 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.
you can give any format we support to recon-all as the input, including .mgz
cheers Bruce On Fri, 29 Aug 2014, Úrsula Pérez Ramírez wrote:
Hi Bruce,
thank you very much for your fast answer. I'm running outside recon-all, only with mri_watershed. Thanks, that could help. Which are the options for recon-all if I have already the .mgz file?, I'm getting errors, appart from the warning for updating tcsh.
Cheers, Ursula
Date: Fri, 29 Aug 2014 11:23:06 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_watershed: really bad skull stripping
Hi Arsula
are you running this through recon-all or outside of it? The skull stripping works better after the intensity normalization that is part of recon-all
cheers Bruce
On Fri, 29 Aug 2014, Úrsula Pérez Ramírez wrote:
Hello,
I’m new with FreeSurfer and I’m getting a really bad skull stripping (almo
st
nothing) with mri_watershed –atlas in images converted from DICOM to .mgz with mri_convert. I lowered the threshold but did not improved considerabl
y.
I have tried with a subject from the tutorial dataset and it’s OK. What ca
n
be the problem?
Thank you very much!
Úrsula
_______________________________________________ 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.
Hi all, Thanks Bruce for your recommendation, with recon-all I obtain a much better skull stripping. Now I'm going to change thresholds because at the top and bottom slices the segmentation is inadequate: central segmentation is missing. Cheers, Úrsula
Date: Fri, 29 Aug 2014 11:48:51 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_watershed: really bad skull stripping
you can give any format we support to recon-all as the input, including .mgz
cheers Bruce On Fri, 29 Aug 2014, Úrsula Pérez Ramírez wrote:
Hi Bruce,
thank you very much for your fast answer. I'm running outside recon-all, only with mri_watershed. Thanks, that could help. Which are the options for recon-all if I have already the .mgz file?, I'm getting errors, appart from the warning for updating tcsh.
Cheers, Ursula
Date: Fri, 29 Aug 2014 11:23:06 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_watershed: really bad skull stripping
Hi Arsula
are you running this through recon-all or outside of it? The skull stripping works better after the intensity normalization that is part of recon-all
cheers Bruce
On Fri, 29 Aug 2014, Úrsula Pérez Ramírez wrote:
Hello,
I’m new with FreeSurfer and I’m getting a really bad skull stripping (almo
st
nothing) with mri_watershed –atlas in images converted from DICOM to .mgz with mri_convert. I lowered the threshold but did not improved considerabl
y.
I have tried with a subject from the tutorial dataset and it’s OK. What ca
n
be the problem?
Thank you very much!
Úrsula
_______________________________________________ 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 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.
I'm glad to hear it improved.
cheers Bruce
On Sat, 30 Aug 2014, Úrsula Pérez Ramírez wrote:
Hi all, Thanks Bruce for your recommendation, with recon-all I obtain a much better skull stripping. Now I'm going to change thresholds because at the top and bottom slices the segmentation is inadequate: central segmentation is missing.
Cheers,
Úrsula
Date: Fri, 29 Aug 2014 11:48:51 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_watershed: really bad skull stripping
you can give any format we support to recon-all as the input, including .mgz
cheers Bruce On Fri, 29 Aug 2014, Úrsula Pérez Ramírez wrote:
Hi Bruce,
thank you very much for your fast answer. I'm running outside recon-all, only with mri_watershed. Thanks, that could help. Which are the options fo
r
recon-all if I have already the .mgz file?, I'm getting errors, appart fro
m
the warning for updating tcsh.
Cheers, Ursula
Date: Fri, 29 Aug 2014 11:23:06 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_watershed: really bad skull stripping
Hi Arsula
are you running this through recon-all or outside of it? The skull stripping works better after the intensity normalization that is part of recon-all
cheers Bruce
On Fri, 29 Aug 2014, Úrsula Pérez Ramírez wrote:
Hello,
I’m new with FreeSurfer and I’m getting a really bad skull stripping (al
mo
st
nothing) with mri_watershed –atlas in images converted from DICOM to .mg
z
with mri_convert. I lowered the threshold but did not improved considera
bl
y.
I have tried with a subject from the tutorial dataset and it’s OK. What
ca
n
be the problem?
Thank you very much!
Úrsula
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The informati
on
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 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.
Hi all,
I am stuck with a license error in that freesurfer (after a simple recon-all call for segmentation) continues to interrupt the process soon after starting it, see complete copy of the error log file below.
I have freshly installed Freesurfer FROM SCRATCH and applied for a new licence file which lies at the appropriate location.
What does "INVALID LICENSE FILE" actually indicate, how can the file be invalid?
What can be done and why does the programm run absolutely smoothly on another Linux-64-bit system??
vG Philipp
Sat Aug 30 17:17:48 CEST 2014 /net/PE1/raid1/enigma-mdd/data/WG_989 /net/PE1/raid1/enigma-mdd/freesurfer/bin/recon-all -subjid WG_989 -all -hippo-subfields subjid WG_989 setenv SUBJECTS_DIR /net/PE1/raid1/enigma-mdd/data FREESURFER_HOME /net/PE1/raid1/enigma-mdd/freesurfer Actual FREESURFER_HOME /net/PE1/raid1/enigma-mdd/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux PE3 3.11.6-4-desktop #1 SMP PREEMPT Wed Oct 30 18:04:56 UTC 2013 (e6d4a27) x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 2066987 maxlocks unlimited maxsignal 2066987 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited
total used free shared buffers cached Mem: 264665936 263134184 1531752 0 194912 255250340 -/+ buffers/cache: 7688932 256977004 Swap: 20972820 4929156 16043664
######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks 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: stable5 $ TimeStamp: 2014/08/30-15:17:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400
======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $
ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /net/PE1/raid1/enigma-mdd/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /net/PE1/raid1/enigma-mdd/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# MotionCor Sat Aug 30 17:17:53 CEST 2014 Found 1 runs /net/PE1/raid1/enigma-mdd/data/WG_989/mri//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 /net/PE1/raid1/enigma-mdd/data/WG_989/mri//001.mgz /net/PE1/raid1/enigma-mdd/data/WG_989/mri/rawavg.mgz
/net/PE1/raid1/enigma-mdd/data/WG_989
mri_convert /net/PE1/raid1/enigma-mdd/data/WG_989/mri/rawavg.mgz /net/PE1/raid1/enigma-mdd/data/WG_989/mri/orig.mgz --conform
mri_convert /net/PE1/raid1/enigma-mdd/data/WG_989/mri/rawavg.mgz /net/PE1/raid1/enigma-mdd/data/WG_989/mri/orig.mgz --conform -------------------------------------------------------------------------- ERROR: Invalid FreeSurfer license key found in license file /net/PE1/raid1/enigma-mdd/freesurfer/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -------------------------------------------------------------------------- $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /net/PE1/raid1/enigma-mdd/data/WG_989/mri/rawavg.mgz... Linux PE3 3.11.6-4-desktop #1 SMP PREEMPT Wed Oct 30 18:04:56 UTC 2013 (e6d4a27) x86_64 x86_64 x86_64 GNU/Linux
recon-all -s WG_989 exited with ERRORS at Sat Aug 30 17:17:57 CEST 2014
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Philipp G. Sämann -
Úrsula Pérez Ramírez