Dear Matt,
Yes, recon-all has failed, I am not sure why, I am annexing the
recon-all.log file, I am using ubuntu 16.04, is it related to the default
version of perl i.e 5.22.03 in my computer, i verified some freesurfer
forums, but i did not get any answers, kindly review the log file.
Thanks
Vasudev
On 23 February 2017 at 22:23, Glasser, Matthew <[email protected]> wrote:
> You are showing errors from the PostFreeSurfer pipeline below.
>
> Peace,
>
> Matt.
>
> From: Dev vasu <[email protected]>
> Date: Thursday, February 23, 2017 at 3:21 PM
> To: Matt Glasser <[email protected]>
> Cc: "<[email protected]>" <[email protected]>, "
> [email protected]" <hcp-users-request@
> humanconnectome.org>
> Subject: Re: [HCP-Users] Freesurfer Non linear registration
>
> Dear Matt,
>
> Yes, I see the freesurfer pipeline fails, but i dont understand where
> exactly the problem occurs . In FS2CaretConvertRegisterNonlinear.sh ,
> The problem occurs at the following lines of code.
>
> #Find c_ras offset between FreeSurfer surface and volume and generate
> matrix to transform surfaces
> MatrixX=`mri_info "$FreeSurferFolder"/mri/brain.finalsurfs.mgz | grep
> "c_r" | cut -d "=" -f 5 | sed s/" "/""/g`
> MatrixY=`mri_info "$FreeSurferFolder"/mri/brain.finalsurfs.mgz | grep
> "c_a" | cut -d "=" -f 5 | sed s/" "/""/g`
> MatrixZ=`mri_info "$FreeSurferFolder"/mri/brain.finalsurfs.mgz | grep
> "c_s" | cut -d "=" -f 5 | sed s/" "/""/g`
> echo "1 0 0 ""$MatrixX" > "$FreeSurferFolder"/mri/c_ras.mat
> echo "0 1 0 ""$MatrixY" >> "$FreeSurferFolder"/mri/c_ras.mat
> echo "0 0 1 ""$MatrixZ" >> "$FreeSurferFolder"/mri/c_ras.mat
> echo "0 0 0 1" >> "$FreeSurferFolder"/mri/c_ras.mat
>
>
>
>
> Thanks
> Vasudev
>
> On 23 February 2017 at 22:16, Glasser, Matthew <[email protected]> wrote:
>
>> FreeSurfer failed to complete successfully.
>>
>> Peace,
>>
>> Matt.
>>
>> From: <[email protected]> on behalf of Dev vasu <
>> [email protected]>
>> Date: Thursday, February 23, 2017 at 3:14 PM
>> To: "<[email protected]>" <[email protected]>, "
>> [email protected]" <hcp-users-request@humanconnec
>> tome.org>
>> Subject: [HCP-Users] Freesurfer Non linear registration
>>
>> Dear all,
>>
>> When i tried to run Freesurfer Pipeline i am facing an error where the
>> pipeline could not generate brain.finalsurfs.mgz . Could you please let me
>> know the reason for this error?.
>>
>>
>> START: FS2CaretConvertRegisterNonlinear
>> FreeSurfer2CaretConvertAndRegisterNonLinear.sh: RegName: MSMSulc
>> mghRead(/media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/
>> T1w/KON2/mri/brain.finalsurfs.mgz, -1): could not open file
>> mghRead(/media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/
>> T1w/KON2/mri/brain.finalsurfs.mgz, -1): could not open file
>> mghRead(/media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/
>> T1w/KON2/mri/brain.finalsurfs.mgz, -1): could not open file
>> Cannot open volume /media/vasudev/vkirsch4/Projec
>> t_BLVP/HCP_Proj/KON2/T1w/wmparc_1mm for reading!
>>
>>
>> Thanks
>> Vasudev
>>
>> _______________________________________________
>> HCP-Users mailing list
>> [email protected]
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>
>>
>> ------------------------------
>>
>> The materials in this message are private and may contain Protected
>> Healthcare Information or other information of a sensitive nature. If you
>> are not the intended recipient, be advised that any unauthorized use,
>> disclosure, copying or the taking of any action in reliance on the contents
>> of this information is strictly prohibited. If you have received this email
>> in error, please immediately notify the sender via telephone or return mail.
>>
>
>
> ------------------------------
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
>
_______________________________________________
HCP-Users mailing list
[email protected]
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Fr 24. Feb 17:08:35 CET 2017
/media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w/KON2
/usr/local/bin/freesurfer/bin/recon-all
-i /media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w/T1w_acpc_dc_restore_1mm.nii.gz -subjid KON2 -sd /media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w -motioncor -talairach -nuintensitycor -normalization
subjid KON2
setenv SUBJECTS_DIR /media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w
FREESURFER_HOME /usr/local/bin/freesurfer
Actual FREESURFER_HOME /usr/local/bin/freesurfer
build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-HCP
Linux vasudev-OptiPlex-780 4.4.0-62-generic #83-Ubuntu SMP Wed Jan 18 14:10:15 UTC 2017 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 59733
maxlocks unlimited
maxsignal 59733
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 15332320 4702420 2413652 249004 8216248 9996944
Swap: 0 0 0
########################################
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: 2017/02/24-16:08:35-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
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: 2017/02/24-16:08:35-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
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: 2017/02/24-16:08:35-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/24-16:08:35-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/24-16:08:35-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/24-16:08:35-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/24-16:08:35-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/24-16:08:35-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/24-16:08:35-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/24-16:08:35-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/24-16:08:35-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/24-16:08:36-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/24-16:08:36-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/24-16:08:36-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/24-16:08:36-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/24-16:08:36-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/24-16:08:36-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/24-16:08:36-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/24-16:08:36-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/24-16:08:36-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/24-16:08:36-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/24-16:08:36-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/24-16:08:36-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/24-16:08:36-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/24-16:08:36-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/02/24-16:08:36-GMT BuildTimeStamp: Feb 1 2014 05:44:06 CVS: $Id: mris_make_surfaces.c,v 1.147 2014/01/29 20:42:02 fischl Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/24-16:08:37-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/24-16:08:37-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/24-16:08:37-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/24-16:08:37-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/24-16:08:37-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/24-16:08:37-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
$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: 2017/02/24-16:08:37-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
$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: 2017/02/24-16:08:37-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/24-16:08:37-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/24-16:08:37-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/24-16:08:37-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/24-16:08:37-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400
#######################################
GCADIR /usr/local/bin/freesurfer/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /usr/local/bin/freesurfer/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
#######################################
/media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w/KON2
mri_convert /media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w/T1w_acpc_dc_restore_1mm.nii.gz /media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w/KON2/mri/orig/001.mgz
mri_convert /media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w/T1w_acpc_dc_restore_1mm.nii.gz /media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w/KON2/mri/orig/001.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w/T1w_acpc_dc_restore_1mm.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
writing to /media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w/KON2/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Fr 24. Feb 17:08:40 CET 2017
Found 1 runs
/media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w/KON2/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.
cp /media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w/KON2/mri/orig/001.mgz /media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w/KON2/mri/rawavg.mgz
/media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w/KON2
mri_convert /media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w/KON2/mri/rawavg.mgz /media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w/KON2/mri/orig.mgz --conform
mri_convert /media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w/KON2/mri/rawavg.mgz /media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w/KON2/mri/orig.mgz --conform
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w/KON2/mri/rawavg.mgz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
Original Data has (1, 1, 1) mm size and (182, 217, 182) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w/KON2/mri/orig.mgz...
mri_add_xform_to_header -c /media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w/KON2/mri/transforms/talairach.xfm /media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w/KON2/mri/orig.mgz /media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w/KON2/mri/orig.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Talairach Fr 24. Feb 17:08:51 CET 2017
/media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w/KON2/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
Linux vasudev-OptiPlex-780 4.4.0-62-generic #83-Ubuntu SMP Wed Jan 18 14:10:15 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s KON2 exited with ERRORS at Fr 24. Feb 17:08:55 CET 2017
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
