Hi Bruce,
I attached the recon-all.log!
Thanks in advance for taking a look!
Darko
Message: 3
Date: Sat, 31 Mar 2018 06:47:12 -0400
From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_watershed Error: indices out of bounds
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <23b23889-c042-4a04-9316-4c8ed5468...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=utf-8
Can you send us the recon-all.log?
> On Mar 30, 2018, at 11:32 AM, Darko Komneni? <komnen...@gmail.com> wrote:
>
> Dear experts,
> while running recon-all on FreeSurfer 5.1.0 I encountered the following error:
> mri_watershed Error: indices out of bounds
>
> I searched the email archive and found this thread:
> https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22\[Freesurfer\]+mri_watershed+Error\%3A+indices+out+of+bounds%22&o=newest&f=1
> My problem seems identical to the one described by initial poster.
> The suggestion was to try the following command:
> set mdir=$SUBJECTS_DIR/$subject/mri
> mri_add_xform_to_header $mdir/transforms/talairach.xfm $mdir/nu.mgz
> $mir/nu.mgz
>
> When I tried it, the message I got was:
> mri_add_xform_to_header: could not open source file /nu.mgz
> No such file or directory
> And indeed such file does not exist in the mri subfolder of my
> current subject's folder.
>
> Any further suggestions on how to fix this? Like the person asking
> originally, this is the only participant where it happened, for
> others, recon-all finished without error and all the images were
> acquired in the same scanner.
> Thanks in advance!
> Best,
> Darko
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
Thu Mar 29 20:04:50 CEST 2018
/media/fmriDATA_4/Darko/Freesurfer_subjects/NMO_0008_3
/usr/local/freesurfer/bin/recon-all
-i /media/fmriDATA_4/Darko/newNMO_T1s/NMO_0008_3/NMO_0008.MR.PAUL_120_NMO.6.1.20151102.075821.yulj3m.dcm -subject NMO_0008_3 -all -hippo-subfields
subjid NMO_0008_3
setenv SUBJECTS_DIR /media/fmriDATA_4/Darko/Freesurfer_subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
Linux carsten-ubuntu 2.6.32-55-generic #117-Ubuntu SMP Tue Dec 3 17:31:12 UTC 2013 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 unlimited
total used free shared buffers cached
Mem: 32956180 8139844 24816336 0 613156 1753872
-/+ buffers/cache: 5772816 27183364
Swap: 19530744 0 19530744
########################################
program versions used
$Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 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: 2018/03/29-18:04:50-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-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: 2018/03/29-18:04:50-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-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: 2018/03/29-18:04:50-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/03/29-18:04:50-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/03/29-18:04:50-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/03/29-18:04:50-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/03/29-18:04:50-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/03/29-18:04:50-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/03/29-18:04:51-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/03/29-18:04:51-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/03/29-18:04:51-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/03/29-18:04:51-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/03/29-18:04:51-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/03/29-18:04:51-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/03/29-18:04:51-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/03/29-18:04:51-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/03/29-18:04:51-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/03/29-18:04:51-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/03/29-18:04:51-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/03/29-18:04:52-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/03/29-18:04:52-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/03/29-18:04:52-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/03/29-18:04:52-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/03/29-18:04:52-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/03/29-18:04:52-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/03/29-18:04:52-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/03/29-18:04:52-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/03/29-18:04:52-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/03/29-18:04:52-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/03/29-18:04:52-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/03/29-18:04:52-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/03/29-18:04:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
$Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $
ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/03/29-18:04:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
$Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/03/29-18:04:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/03/29-18:04:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/03/29-18:04:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/03/29-18:04:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/03/29-18:04:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: darko Machine: carsten-ubuntu Platform: Linux PlatformVersion: 2.6.32-55-generic CompilerName: GCC CompilerVersion: 30400
#######################################
GCADIR /usr/local/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/freesurfer/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
#######################################
/media/fmriDATA_4/Darko/Freesurfer_subjects/NMO_0008_3
mri_convert /media/fmriDATA_4/Darko/newNMO_T1s/NMO_0008_3/NMO_0008.MR.PAUL_120_NMO.6.1.20151102.075821.yulj3m.dcm /media/fmriDATA_4/Darko/Freesurfer_subjects/NMO_0008_3/mri/orig/001.mgz
mri_convert /media/fmriDATA_4/Darko/newNMO_T1s/NMO_0008_3/NMO_0008.MR.PAUL_120_NMO.6.1.20151102.075821.yulj3m.dcm /media/fmriDATA_4/Darko/Freesurfer_subjects/NMO_0008_3/mri/orig/001.mgz
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from /media/fmriDATA_4/Darko/newNMO_T1s/NMO_0008_3/NMO_0008.MR.PAUL_120_NMO.6.1.20151102.075821.yulj3m.dcm...
Getting Series No
INFO: Found 178 files in /media/fmriDATA_4/Darko/newNMO_T1s/NMO_0008_3
INFO: Scanning for Series Number 6
Scanning Directory
INFO: found 176 files in series
INFO: loading series header info.
RunNo = 5
INFO: sorting.
INFO: (256 256 176), nframes = 1, ismosaic=0
PE Dir ROW ROW
AutoAlign matrix detected
AutoAlign Matrix ---------------------
0.992 0.029 -0.123 -10.261;
-0.089 0.850 -0.520 -52.559;
0.089 0.527 0.845 20.007;
0.000 0.000 0.000 1.000;
FileName /media/fmriDATA_4/Darko/newNMO_T1s/NMO_0008_3/NMO_0008.MR.PAUL_120_NMO.6.1.20151102.075821.yulj3m.dcm
Identification
NumarisVer syngo MR B17
ScannerModel TrioTim
PatientName NMO^0008
Date and time
StudyDate 20151102
StudyTime 075821.906000
SeriesTime 081737.078000
AcqTime 081309.177500
Acquisition parameters
PulseSeq *tfl3d1_ns
Protocol MPRAGE_31082011_JW_AC-PC
PhEncDir ROW
EchoNo 1
FlipAngle 9
EchoTime 3.03
InversionTime 900
RepetitionTime 1900
PhEncFOV 256
ReadoutFOV 256
Image information
RunNo 5
SeriesNo 6
ImageNo 1
NImageRows 256
NImageCols 256
NFrames 1
SliceArraylSize 1
IsMosaic 0
ImgPos 116.4439 220.0831 52.9482
VolRes 1.0000 1.0000 1.0000
VolDim 256 256 176
Vc -0.0286 -0.8495 0.5268
Vr -0.1228 -0.5200 -0.8453
Vs -0.9920 0.0889 0.0894
VolCenter 9.7654 52.6032 20.0512
TransferSyntaxUID 1.2.840.10008.1.2.1
INFO: no Siemens slice order reversal detected (good!).
TR=1900.00, TE=3.03, TI=900.00, flip angle=9.00
i_ras = (-0.0286323, -0.849509, 0.526797)
j_ras = (-0.122779, -0.520034, -0.845275)
k_ras = (-0.992021, 0.0888818, 0.089412)
writing to /media/fmriDATA_4/Darko/Freesurfer_subjects/NMO_0008_3/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Thu Mar 29 20:05:18 CEST 2018
Found 1 runs
/media/fmriDATA_4/Darko/Freesurfer_subjects/NMO_0008_3/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/fmriDATA_4/Darko/Freesurfer_subjects/NMO_0008_3/mri/orig/001.mgz /media/fmriDATA_4/Darko/Freesurfer_subjects/NMO_0008_3/mri/rawavg.mgz
/media/fmriDATA_4/Darko/Freesurfer_subjects/NMO_0008_3
mri_convert /media/fmriDATA_4/Darko/Freesurfer_subjects/NMO_0008_3/mri/rawavg.mgz /media/fmriDATA_4/Darko/Freesurfer_subjects/NMO_0008_3/mri/orig.mgz --conform
mri_convert /media/fmriDATA_4/Darko/Freesurfer_subjects/NMO_0008_3/mri/rawavg.mgz /media/fmriDATA_4/Darko/Freesurfer_subjects/NMO_0008_3/mri/orig.mgz --conform
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from /media/fmriDATA_4/Darko/Freesurfer_subjects/NMO_0008_3/mri/rawavg.mgz...
TR=1900.00, TE=3.03, TI=900.00, flip angle=9.00
i_ras = (-0.0286323, -0.849509, 0.526797)
j_ras = (-0.122779, -0.520034, -0.845275)
k_ras = (-0.992021, 0.0888818, 0.089412)
Original Data has (1, 1, 1) mm size and (256, 256, 176) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from short to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /media/fmriDATA_4/Darko/Freesurfer_subjects/NMO_0008_3/mri/orig.mgz...
mri_add_xform_to_header -c /media/fmriDATA_4/Darko/Freesurfer_subjects/NMO_0008_3/mri/transforms/talairach.xfm /media/fmriDATA_4/Darko/Freesurfer_subjects/NMO_0008_3/mri/orig.mgz /media/fmriDATA_4/Darko/Freesurfer_subjects/NMO_0008_3/mri/orig.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Talairach Thu Mar 29 20:05:35 CEST 2018
/media/fmriDATA_4/Darko/Freesurfer_subjects/NMO_0008_3/mri
talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#--------------------------------------------
#@# Talairach Failure Detection Thu Mar 29 20:06:19 CEST 2018
/media/fmriDATA_4/Darko/Freesurfer_subjects/NMO_0008_3/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.4301, pval=0.1049 >= threshold=0.0050)
awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /media/fmriDATA_4/Darko/Freesurfer_subjects/NMO_0008_3/mri/transforms/talairach_avi.log
TalAviQA: 0.96691
z-score: -2
#--------------------------------------------
#@# Nu Intensity Correction Thu Mar 29 20:06:20 CEST 2018
mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
/media/fmriDATA_4/Darko/Freesurfer_subjects/NMO_0008_3/mri
/usr/local/freesurfer/bin/mri_nu_correct.mni
--i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
nIters 2
$Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $
Linux carsten-ubuntu 2.6.32-55-generic #117-Ubuntu SMP Tue Dec 3 17:31:12 UTC 2013 x86_64 GNU/Linux
Thu Mar 29 20:06:20 CEST 2018
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
tmpdir is ./tmp.mri_nu_correct.mni.9476
/media/fmriDATA_4/Darko/Freesurfer_subjects/NMO_0008_3/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9476/nu0.mnc -odt float
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9476/nu0.mnc -odt float
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from orig.mgz...
TR=1900.00, TE=3.03, TI=900.00, flip angle=9.00
i_ras = (-1, -5.96046e-08, 1.49012e-08)
j_ras = (1.19209e-07, -5.4948e-08, -1)
k_ras = (-5.21541e-08, 1, 1.32248e-07)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.9476/nu0.mnc...
--------------------------------------------------------
Iteration 1 Thu Mar 29 20:06:23 CEST 2018
nu_correct -clobber ./tmp.mri_nu_correct.mni.9476/nu0.mnc ./tmp.mri_nu_correct.mni.9476/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.9476/0/
[darko@carsten-ubuntu:/media/fmriDATA_4/Darko/Freesurfer_subjects/NMO_0008_3/mri/] [2018-03-29 20:06:24] running:
/usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.9476/0/ ./tmp.mri_nu_correct.mni.9476/nu0.mnc ./tmp.mri_nu_correct.mni.9476/nu1.imp
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 50
CV of field change: 0.00173761
[darko@carsten-ubuntu:/media/fmriDATA_4/Darko/Freesurfer_subjects/NMO_0008_3/mri/] [2018-03-29 20:06:59] running:
/usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.9476/nu0.mnc ./tmp.mri_nu_correct.mni.9476/0//template.mnc
Transforming slices:......................................................................................Done
Transforming slices:................................................................................................................................................................................................................................................................Done
--------------------------------------------------------
Iteration 2 Thu Mar 29 20:07:02 CEST 2018
nu_correct -clobber ./tmp.mri_nu_correct.mni.9476/nu1.mnc ./tmp.mri_nu_correct.mni.9476/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.9476/1/
[darko@carsten-ubuntu:/media/fmriDATA_4/Darko/Freesurfer_subjects/NMO_0008_3/mri/] [2018-03-29 20:07:02] running:
/usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.9476/1/ ./tmp.mri_nu_correct.mni.9476/nu1.mnc ./tmp.mri_nu_correct.mni.9476/nu2.imp
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 42
CV of field change: 0.000978601
[darko@carsten-ubuntu:/media/fmriDATA_4/Darko/Freesurfer_subjects/NMO_0008_3/mri/] [2018-03-29 20:07:34] running:
/usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.9476/nu1.mnc ./tmp.mri_nu_correct.mni.9476/1//template.mnc
Transforming slices:......................................................................................Done
Transforming slices:................................................................................................................................................................................................................................................................Done
mri_binarize --i ./tmp.mri_nu_correct.mni.9476/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.9476/ones.mgz
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /media/fmriDATA_4/Darko/Freesurfer_subjects/NMO_0008_3/mri
cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.9476/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.9476/ones.mgz
sysname Linux
hostname carsten-ubuntu
machine x86_64
user darko
input ./tmp.mri_nu_correct.mni.9476/nu2.mnc
frame 0
nErode3d 0
nErode2d 0
output ./tmp.mri_nu_correct.mni.9476/ones.mgz
Binarizing based on threshold
min -1
max +infinity
binval 1
binvalnot 0
Found 16777216 values in range
Counting number of voxels
Found 16777216 voxels in final mask
mri_binarize done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.9476/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.9476/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9476/input.mean.dat
$Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $
cwd
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.9476/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.9476/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9476/input.mean.dat
sysname Linux
hostname carsten-ubuntu
machine x86_64
user darko
Loading ./tmp.mri_nu_correct.mni.9476/ones.mgz
Loading orig.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 1 segmentations
Computing statistics for each segmentation
0 1 16777216 1.67772e+07
Reporting on 1 segmentations
Computing spatial average of each frame
0
Writing to ./tmp.mri_nu_correct.mni.9476/input.mean.dat
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.9476/ones.mgz --i ./tmp.mri_nu_correct.mni.9476/nu2.mnc --sum ./tmp.mri_nu_correct.mni.9476/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9476/output.mean.dat
$Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $
cwd
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.9476/ones.mgz --i ./tmp.mri_nu_correct.mni.9476/nu2.mnc --sum ./tmp.mri_nu_correct.mni.9476/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9476/output.mean.dat
sysname Linux
hostname carsten-ubuntu
machine x86_64
user darko
Loading ./tmp.mri_nu_correct.mni.9476/ones.mgz
Loading ./tmp.mri_nu_correct.mni.9476/nu2.mnc
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 1 segmentations
Computing statistics for each segmentation
0 1 16777216 1.67772e+07
Reporting on 1 segmentations
Computing spatial average of each frame
0
Writing to ./tmp.mri_nu_correct.mni.9476/output.mean.dat
mris_calc -o ./tmp.mri_nu_correct.mni.9476/nu2.mnc ./tmp.mri_nu_correct.mni.9476/nu2.mnc mul 1.01904212889407552174
Saving result to './tmp.mri_nu_correct.mni.9476/nu2.mnc' (type = MINC ) [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.9476/nu2.mnc nu.mgz --like orig.mgz
mri_convert ./tmp.mri_nu_correct.mni.9476/nu2.mnc nu.mgz --like orig.mgz
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from ./tmp.mri_nu_correct.mni.9476/nu2.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -5.96046e-08, 1.49012e-08)
j_ras = (1.19209e-07, -5.4948e-08, -1)
k_ras = (-5.21541e-08, 1, 1.32248e-07)
INFO: transform src into the like-volume: orig.mgz
Reslicing using trilinear interpolation
writing to nu.mgz...
mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
type change took 0 minutes and 10 seconds.
mapping ( 8, 94) to ( 3, 110)
Thu Mar 29 20:08:31 CEST 2018
mri_nu_correct.mni done
#--------------------------------------------
#@# Intensity Normalization Thu Mar 29 20:08:31 CEST 2018
/media/fmriDATA_4/Darko/Freesurfer_subjects/NMO_0008_3/mri
mri_normalize -g 1 nu.mgz T1.mgz
using max gradient = 1.000
reading from nu.mgz...
normalizing image...
building Voronoi diagram...
performing soap bubble smoothing...
3d normalization pass 1 of 2
building Voronoi diagram...
performing soap bubble smoothing...
3d normalization pass 2 of 2
building Voronoi diagram...
performing soap bubble smoothing...
writing output to T1.mgz
3D bias adjustment took 3 minutes and 32 seconds.
MRIsplineNormalize(): npeaks = 10
Starting OpenSpline(): npoints = 10
white matter peak found at 111
white matter peak found at 106
gm peak at 49 (49), valley at 0 (-1)
csf peak at 24, setting threshold to 40
white matter peak found at 111
white matter peak found at 110
gm peak at 47 (47), valley at 0 (-1)
csf peak at 23, setting threshold to 39
#--------------------------------------------
#@# Skull Stripping Thu Mar 29 20:12:04 CEST 2018
/media/fmriDATA_4/Darko/Freesurfer_subjects/NMO_0008_3/mri
mri_em_register -skull nu.mgz /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta
aligning to atlas containing skull, setting unknown_nbr_spacing = 5
reading 1 input volumes...
logging results to talairach_with_skull.log
reading '/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca'...
gcaAllocMax: node dims 64 64 64
gcaAllocMax: prior dims 128 128 128
gcaAllocMax: max_labels 0
average std = 23.1 using min determinant for regularization = 53.4
0 singular and 5702 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
bounding unknown intensity as < 20.2 or > 943.7
total sample mean = 92.0 (1443 zeros)
************************************************
spacing=8, using 3481 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 3481, passno 0, spacing 8
resetting wm mean[0]: 117 --> 126
resetting gm mean[0]: 74 --> 74
input volume #1 is the most T1-like
using real data threshold=11.0
skull bounding box = (48, 0, 27) --> (210, 255, 217)
using (102, 85, 122) as brain centroid...
mean wm in atlas = 126, using box (82,53,99) --> (121, 116,145) to find MRI wm
before smoothing, mri peak at 105
after smoothing, mri peak at 105, scaling input intensities by 1.200
scaling channel 0 by 1.2
initial log_p = -10409.5
************************************************
First Search limited to translation only.
************************************************
Found translation: (4.0, 23.3, -15.3): log p = -10351.526
****************************************
Nine parameter search. iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-10351.5, old_max_log_p =-10351.5 (thresh=-10341.2)
1.000 0.000 0.000 3.977;
0.000 1.000 0.000 23.295;
0.000 0.000 1.000 -15.341;
0.000 0.000 0.000 1.000;
reducing scale to 0.2500
****************************************
Nine parameter search. iteration 1 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-10338.1, old_max_log_p =-10351.5 (thresh=-10341.2)
1.030 -0.066 0.101 -7.617;
0.070 0.996 -0.063 23.188;
-0.099 0.069 1.050 -21.618;
0.000 0.000 0.000 1.000;
****************************************
Nine parameter search. iteration 2 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-10338.1, old_max_log_p =-10338.1 (thresh=-10327.7)
1.030 -0.066 0.101 -7.617;
0.070 0.996 -0.063 23.188;
-0.099 0.069 1.050 -21.618;
0.000 0.000 0.000 1.000;
reducing scale to 0.0625
****************************************
Nine parameter search. iteration 3 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-10336.3, old_max_log_p =-10338.1 (thresh=-10327.7)
1.030 -0.066 0.101 -7.617;
0.069 0.993 -0.063 23.418;
-0.099 0.069 1.051 -21.768;
0.000 0.000 0.000 1.000;
min search scale 0.025000 reached
***********************************************
Computing MAP estimate using 3481 samples...
***********************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
1.03043 -0.06568 0.10148 -7.61733;
0.06940 0.99339 -0.06329 23.41759;
-0.09915 0.06879 1.05113 -21.76763;
0.00000 0.00000 0.00000 1.00000;
nsamples 3481
Quasinewton: input matrix
1.03043 -0.06568 0.10148 -7.61733;
0.06940 0.99339 -0.06329 23.41759;
-0.09915 0.06879 1.05113 -21.76763;
0.00000 0.00000 0.00000 1.00000;
IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 006: -log(p) = 10336.3 tol 0.000010
Resulting transform:
1.030 -0.066 0.101 -7.617;
0.069 0.993 -0.063 23.418;
-0.099 0.069 1.051 -21.768;
0.000 0.000 0.000 1.000;
pass 1, spacing 8: log(p) = -10336.3 (old=-10409.5)
transform before final EM align:
1.030 -0.066 0.101 -7.617;
0.069 0.993 -0.063 23.418;
-0.099 0.069 1.051 -21.768;
0.000 0.000 0.000 1.000;
**************************************************
EM alignment process ...
Computing final MAP estimate using 382743 samples.
**************************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
1.03043 -0.06568 0.10148 -7.61733;
0.06940 0.99339 -0.06329 23.41759;
-0.09915 0.06879 1.05113 -21.76763;
0.00000 0.00000 0.00000 1.00000;
nsamples 382743
Quasinewton: input matrix
1.03043 -0.06568 0.10148 -7.61733;
0.06940 0.99339 -0.06329 23.41759;
-0.09915 0.06879 1.05113 -21.76763;
0.00000 0.00000 0.00000 1.00000;
IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = 1146132.5 tol 0.000000
final transform:
1.030 -0.066 0.101 -7.617;
0.069 0.993 -0.063 23.418;
-0.099 0.069 1.051 -21.768;
0.000 0.000 0.000 1.000;
writing output transformation to transforms/talairach_with_skull.lta...
registration took 27 minutes and 38 seconds.
mri_watershed -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz
Mode: T1 normalized volume
Mode: Use the information of atlas (default parms, --help for details)
gcaAllocMax: node dims 64 64 64
gcaAllocMax: prior dims 128 128 128
gcaAllocMax: max_labels 0
*********************************************************
The input file is T1.mgz
The output file is brainmask.auto.mgz
Weighting the input with atlas information before watershed
*************************WATERSHED**************************
Sorting...
first estimation of the COG coord: x=132 y=111 z=155 r=98
first estimation of the main basin volume: 3967288 voxels
mri_watershed Error: indices out of bounds
Linux carsten-ubuntu 2.6.32-55-generic #117-Ubuntu SMP Tue Dec 3 17:31:12 UTC 2013 x86_64 GNU/Linux
recon-all -s NMO_0008_3 exited with ERRORS at Thu Mar 29 20:39:47 CEST 2018
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
_______________________________________________
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.
