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
stacksize 8192 kbytes
coredumpsize 0 kbytes
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 64 kbytes
maxproc 387206
maxlocks unlimited
maxsignal 387206
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buffers cached
Mem: 99140516 53688556 45451960 95916 418652 51296424
-/+ buffers/cache: 1973480 97167036
Swap: 125829076 1818048 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 Machine: CCACE-PROC5 Platform: Linux PlatformVersion: 3.16.7-24-desktop
CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name:
stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15 2015
01:03:13 CVS: $Id: mri_watershed.cpp,v 1.100.2.1 2015/07/10 18:57:54 greve Exp
$ User: root Machine: CCACE-PROC5 Platform: Linux PlatformVersion:
3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name:
stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15 2015
01:03:13 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User:
root Machine: CCACE-PROC5 Platform: Linux PlatformVersion: 3.16.7-24-desktop
CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name:
stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15 2015
01:03:13 CVS: $Id: mri_segment.c,v 1.43 2015/02/05 23:34:40 zkaufman Exp $
User: root Machine: CCACE-PROC5 Platform: Linux PlatformVersion:
3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion:
$Name: stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15
2015 01:03:13 CVS: $Id: mri_label2label.c,v 1.47 2014/12/22 19:59:18 greve Exp
$ User: root Machine: CCACE-PROC5 Platform: Linux PlatformVersion:
3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion:
$Name: stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15
2015 01:03:13 CVS: $Id: mri_em_register.c,v 1.101.2.1 2015/06/24 20:18:26
nicks Exp $ User: root Machine: CCACE-PROC5 Platform: Linux
PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion:
$Name: stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15
2015 01:03:13 CVS: $Id: mri_ca_normalize.c,v 1.62.2.1 2015/06/24 20:18:24
nicks Exp $ User: root Machine: CCACE-PROC5 Platform: Linux
PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion:
$Name: stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15
2015 01:03:13 CVS: $Id: mri_ca_register.c,v 1.92.2.1 2015/06/24 20:18:25 nicks
Exp $ User: root Machine: CCACE-PROC5 Platform: Linux PlatformVersion:
3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name:
stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15 2015
01:03:13 CVS: $Id: mri_ca_label.c,v 1.108 2014/11/24 20:09:20 greve Exp $
User: root Machine: CCACE-PROC5 Platform: Linux PlatformVersion:
3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name:
stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15 2015
01:03:13 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $
User: root Machine: CCACE-PROC5 Platform: Linux PlatformVersion:
3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name:
stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15 2015
01:03:13 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User:
root Machine: CCACE-PROC5 Platform: Linux PlatformVersion: 3.16.7-24-desktop
CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion:
$Name: stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15
2015 01:03:13 CVS: $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp
$ User: root Machine: CCACE-PROC5 Platform: Linux PlatformVersion:
3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion:
$Name: stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15
2015 01:03:13 CVS: $Id: mri_concatenate_lta.c,v 1.13.2.2 2015/08/19 16:36:35
greve Exp $ User: root Machine: CCACE-PROC5 Platform: Linux
PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion:
$Name: stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15
2015 01:03:13 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks
Exp $ User: root Machine: CCACE-PROC5 Platform: Linux PlatformVersion:
3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name:
stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15 2015
01:03:13 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $
User: root Machine: CCACE-PROC5 Platform: Linux PlatformVersion:
3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name:
stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15 2015
01:03:13 CVS: $Id: mris_inflate.c,v 1.44 2012/01/05 18:36:17 greve Exp $
User: root Machine: CCACE-PROC5 Platform: Linux PlatformVersion:
3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion:
$Name: stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15
2015 01:03:13 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp
$ User: root Machine: CCACE-PROC5 Platform: Linux PlatformVersion:
3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name:
stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15 2015
01:03:13 CVS: $Id: mris_sphere.c,v 1.59 2014/11/06 01:38:58 nicks Exp $ User:
root Machine: CCACE-PROC5 Platform: Linux PlatformVersion: 3.16.7-24-desktop
CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion:
$Name: stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15
2015 01:03:13 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks
Exp $ User: root Machine: CCACE-PROC5 Platform: Linux PlatformVersion:
3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion:
$Name: stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15
2015 01:03:13 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks
Exp $ User: root Machine: CCACE-PROC5 Platform: Linux PlatformVersion:
3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name:
stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15 2015
01:03:13 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $
User: root Machine: CCACE-PROC5 Platform: Linux PlatformVersion:
3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion:
$Name: stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15
2015 01:03:13 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve
Exp $ User: root Machine: CCACE-PROC5 Platform: Linux PlatformVersion:
3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15 2015
01:03:13 CVS: $Id: mris_make_surfaces.c,v 1.154.2.5 2015/08/13 17:10:46
zkaufman Exp $ User: root Machine: CCACE-PROC5 Platform: Linux
PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name:
stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15 2015
01:03:13 CVS: $Id: mris_register.c,v 1.61 2013/01/15 17:19:03 greve Exp $
User: root Machine: CCACE-PROC5 Platform: Linux PlatformVersion:
3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name:
stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15 2015
01:03:13 CVS: $Id: mris_volmask.cpp,v 1.26 2014/11/06 03:40:22 nicks Exp $
User: root Machine: CCACE-PROC5 Platform: Linux PlatformVersion:
3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info
ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT
BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_anatomical_stats.c,v
1.76.2.2 2015/07/06 21:59:22 greve Exp $ User: root Machine: CCACE-PROC5
Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC
CompilerVersion: 40400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name:
stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15 2015
01:03:13 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User:
root Machine: CCACE-PROC5 Platform: Linux PlatformVersion: 3.16.7-24-desktop
CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion:
$Name: stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15
2015 01:03:13 CVS: $Id: mris_curvature_stats.c,v 1.64.4.1 2015/06/04 21:12:38
nicks Exp $ User: root Machine: CCACE-PROC5 Platform: Linux
PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name:
stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15 2015
01:03:13 CVS: $Id: mris_calc.c,v 1.51.2.2 2015/06/04 21:12:37 nicks Exp $
User: root Machine: CCACE-PROC5 Platform: Linux PlatformVersion:
3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400
$Id: mri_robust_register.cpp,v 1.75 2014/11/18 16:14:42 mreuter Exp $
ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion:
$Name: stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15
2015 01:03:13 CVS: $Id: mri_robust_register.cpp,v 1.75 2014/11/18 16:14:42
mreuter Exp $ User: root Machine: CCACE-PROC5 Platform: Linux
PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400
$Id: mri_robust_template.cpp,v 1.48 2013/05/21 18:03:15 mreuter Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion:
$Name: stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15
2015 01:03:13 CVS: $Id: mri_robust_template.cpp,v 1.48 2013/05/21 18:03:15
mreuter Exp $ User: root Machine: CCACE-PROC5 Platform: Linux
PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name:
stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15 2015
01:03:13 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: root
Machine: CCACE-PROC5 Platform: Linux PlatformVersion: 3.16.7-24-desktop
CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name:
stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15 2015
01:03:13 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User:
root Machine: CCACE-PROC5 Platform: Linux PlatformVersion: 3.16.7-24-desktop
CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info
ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT
BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_fuse_segmentations.c,v 1.8
2011/03/02 00:04:15 nicks Exp $ User: root Machine: CCACE-PROC5 Platform:
Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion:
40400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name:
stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT BuildTimeStamp: Oct 15 2015
01:03:13 CVS: $Id: mri_segstats.c,v 1.110.2.5 2015/10/06 18:46:28 greve Exp $
User: root Machine: CCACE-PROC5 Platform: Linux PlatformVersion:
3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info
ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/04-11:11:10-GMT
BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_relabel_hypointensities.c,v
1.11.2.1 2015/05/15 18:45:54 nicks Exp $ User: root Machine: CCACE-PROC5
Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC
CompilerVersion: 40400
#######################################
GCADIR /UK_Biobank_MRI/freesurfer/average
GCA RB_all_2015-08-04.gca
GCASkull RB_all_withskull_2014-08-21.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /UK_Biobank_MRI/freesurfer/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
#######################################
/UK_Biobank_MRI/FS_Output/1493335_20216_2_0
mri_convert
/UK_Biobank_MRI/WorkDir/1493335_20216_2_0/1.3.12.2.1107.5.2.19.45594.2014102612140161812159407.dcm
/UK_Biobank_MRI/FS_Output/1493335_20216_2_0/mri/orig/001.mgz
mri_convert
/UK_Biobank_MRI/WorkDir/1493335_20216_2_0/1.3.12.2.1107.5.2.19.45594.2014102612140161812159407.dcm
/UK_Biobank_MRI/FS_Output/1493335_20216_2_0/mri/orig/001.mgz
$Id: mri_convert.c,v 1.221.2.2 2015/10/02 16:39:36 zkaufman Exp $
reading from
/UK_Biobank_MRI/WorkDir/1493335_20216_2_0/1.3.12.2.1107.5.2.19.45594.2014102612140161812159407.dcm...
Getting Series No
INFO: Found 419 files in /UK_Biobank_MRI/WorkDir/1493335_20216_2_0
INFO: Scanning for Series Number 6
Scanning Directory
INFO: found 208 files in series
INFO: loading series header info.
RunNo = 5
INFO: sorting.
INFO: (256 256 208), nframes = 1, ismosaic=0
PE Dir ROW ROW
AutoAlign matrix detected
AutoAlign Matrix ---------------------
0.99968 0.01491 -0.02031 0.79577;
-0.01936 0.97018 -0.24066 18.85196;
0.01612 0.24098 0.97016 -63.17948;
0.00000 0.00000 0.00000 1.00000;
FileName
/UK_Biobank_MRI/WorkDir/1493335_20216_2_0/1.3.12.2.1107.5.2.19.45594.2014102612135645375058671.dcm
Identification
NumarisVer syngo MR D13
ScannerModel Skyra
PatientName CY N8 Y8 63
Date and time
StudyDate 20141026
StudyTime 120714.065000
SeriesTime 121403.993000
AcqTime 120902.250000
Acquisition parameters
PulseSeq *tfl3d1_16ns
Protocol T1_p2_1mm_fov256_sag_TI_880
PhEncDir ROW
EchoNo 1
FlipAngle 8
EchoTime 2.01
InversionTime 880
RepetitionTime 2000
PhEncFOV 256
ReadoutFOV 256
Image information
RunNo 5
SeriesNo 6
ImageNo 1
NImageRows 256
NImageCols 256
NFrames 1
SliceArraylSize 1
IsMosaic 0
ImgPos 107.1797 134.1671 28.5086
VolRes 1.0000 1.0000 1.0000
VolDim 256 256 208
Vc -0.0149 -0.9704 0.2410
Vr -0.0203 -0.2407 -0.9704
Vs -0.9997 0.0194 0.0161
VolCenter -1.2956 -18.8423 -63.1714
TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
IsDWI = 0
INFO: no Siemens slice order reversal detected (good!).
TR=2000.00, TE=2.01, TI=880.00, flip angle=8.00
i_ras = (-0.0149096, -0.970402, 0.241034)
j_ras = (-0.0203119, -0.240717, -0.970383)
k_ras = (-0.999682, 0.0193639, 0.0161217)
writing to /UK_Biobank_MRI/FS_Output/1493335_20216_2_0/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Fri Dec 4 11:11:58 GMT 2015
Found 1 runs
/UK_Biobank_MRI/FS_Output/1493335_20216_2_0/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 /UK_Biobank_MRI/FS_Output/1493335_20216_2_0/mri/orig/001.mgz
/UK_Biobank_MRI/FS_Output/1493335_20216_2_0/mri/rawavg.mgz
/UK_Biobank_MRI/FS_Output/1493335_20216_2_0
mri_convert /UK_Biobank_MRI/FS_Output/1493335_20216_2_0/mri/rawavg.mgz
/UK_Biobank_MRI/FS_Output/1493335_20216_2_0/mri/orig.mgz --conform
mri_convert /UK_Biobank_MRI/FS_Output/1493335_20216_2_0/mri/rawavg.mgz
/UK_Biobank_MRI/FS_Output/1493335_20216_2_0/mri/orig.mgz --conform
$Id: mri_convert.c,v 1.221.2.2 2015/10/02 16:39:36 zkaufman Exp $
reading from /UK_Biobank_MRI/FS_Output/1493335_20216_2_0/mri/rawavg.mgz...
TR=2000.00, TE=2.01, TI=880.00, flip angle=8.00
i_ras = (-0.0149096, -0.970402, 0.241034)
j_ras = (-0.0203119, -0.240717, -0.970383)
k_ras = (-0.999682, 0.0193639, 0.0161217)
changing data type from short to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /UK_Biobank_MRI/FS_Output/1493335_20216_2_0/mri/orig.mgz...
mri_add_xform_to_header -c
/UK_Biobank_MRI/FS_Output/1493335_20216_2_0/mri/transforms/talairach.xfm
/UK_Biobank_MRI/FS_Output/1493335_20216_2_0/mri/orig.mgz
/UK_Biobank_MRI/FS_Output/1493335_20216_2_0/mri/orig.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Talairach Fri Dec 4 11:12:12 GMT 2015
/UK_Biobank_MRI/FS_Output/1493335_20216_2_0/mri
mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1
--proto-iters 1000 --distance 200 --stop 1e-4 --shrink 2
/UK_Biobank_MRI/FS_Output/1493335_20216_2_0/mri
/UK_Biobank_MRI/freesurfer/bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance
200 --stop 1e-4 --shrink 2
nIters 1
$Id: mri_nu_correct.mni,v 1.20.2.3 2015/06/18 00:23:55 nicks Exp $
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
Fri Dec 4 11:12:12 GMT 2015
tmpdir is ./tmp.mri_nu_correct.mni.24649
/UK_Biobank_MRI/FS_Output/1493335_20216_2_0/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.24649/nu0.mnc -odt float
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.24649/nu0.mnc -odt float
$Id: mri_convert.c,v 1.221.2.2 2015/10/02 16:39:36 zkaufman Exp $
reading from orig.mgz...
TR=2000.00, TE=2.01, TI=880.00, flip angle=8.00
i_ras = (-1, 1.86265e-09, 0)
j_ras = (-1.86265e-09, -1.54832e-08, -1)
k_ras = (1.86265e-09, 1, -2.03727e-10)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.24649/nu0.mnc...
--------------------------------------------------------
Iteration 1 Fri Dec 4 11:12:14 GMT 2015
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
ERROR: file ./tmp.mri_nu_correct.mni.24649/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
recon-all -s 1493335_20216_2_0 exited with ERRORS at Fri Dec 4 11:12:14 GMT
2015
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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