External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to recon_all my subjects which is .nii file. But I
usually meet this error.
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0.0079, pval=0.0000 < threshold=0.0050)
Command exited with non-zero status 1
@#@FSTIME 2019:04:04:10:30:25 talairach_afd N 4 e 0.00 S 0.00 U 0.00
P 50% M 6252 F 7 R 243 W 0 c 1 w 8 I 1384 O 0 L 1.11 0.48 0.21
@#@FSLOADPOST 2019:04:04:10:30:25 talairach_afd N 4 1.11 0.48 0.21
Manual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test,
making sure the -notal-check flag follows -all
or -autorecon1 in the command string.
See:http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
ERROR: Talairach failed!
Linux abby-virtual-machine 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6
09:33:07 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 0306A_T1_w4 exited with ERRORS at Thu Apr 4 10:30:25 CST 2019
For more details, see the log file
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
I've searched the list and they advised to check with this website
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview.
however,my subject's recon_all folder doesn't have T1.mgz and
brainmask.mgz. it just has mri_nu_correct.mni.log orig
orig_nu.mgz transforms mri_nu_correct.mni.log.bak orig.mgz
rawavg.mgz
I run ten files, and almost all of them go wrong, which is very
strange.I need your help. please give some advises with program
statements in detail.
I really appreciate your help
1) FreeSurfer version: freesurfer-linux-centos7_x86_64-dev.tar.gz
2) Platform: ubuntu 18
3) recon-all.log:see attached
Thu Apr 4 10:27:46 CST 2019
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4
/usr/local/freesurfer/bin/recon-all
-i 0306A_T1_w4.nii -s 0306A_T1_w4 -all
subjid 0306A_T1_w4
setenv SUBJECTS_DIR /home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-linux-centos7_x86_64-dev-20190402-8622e54
Linux abby-virtual-machine 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07
UTC 2019 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 16384 kbytes
maxproc 15449
maxlocks unlimited
maxsignal 15449
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 4015684 1296860 900516 12656 1818308 2447140
Swap: 3999740 435200 3564540
########################################
program versions used
$Id: recon-all,v 1.601 2017/02/08 21:17:33 greve Exp $
$Id: lta_convert.cpp,v 1.10 2016/08/09 02:11:11 zkaufman Exp $
ProgramName: lta_convert ProgramArguments: -all-info ProgramVersion: $Name:
$ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02
Id: $Id: lta_convert.cpp,v 1.10 2016/08/09 02:11:11 zkaufman Exp $ User: abby
Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: $
TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02 Id:
$Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: abby Machine:
abby-virtual-machine Platform: Linux PlatformVersion: 4.15.0-46-generic
CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_annotation2label ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019
12:06:02 Id: $Id: mri_annotation2label.c,v 1.32 2016/08/02 21:20:27 nicks Exp
$ User: abby Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_aparc2aseg ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019
12:06:02 Id: $Id: mri_aparc2aseg.c,v 1.54 2016/12/26 15:29:30 fischl Exp $
User: abby Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_aparc2wmseg ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019
12:06:02 Id: $Id: mri_aparc2wmseg.c,v 1.6 2011/03/02 00:04:13 nicks Exp $
User: abby Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_binarize ProgramArguments: -all-info ProgramVersion: $Name:
$ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02
Id: $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ User: abby
Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name:
$ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02
Id: $Id: mri_ca_label.c,v 1.115 2016/10/22 17:31:36 fischl Exp $ User: abby
Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019
12:06:02 Id: $Id: mri_ca_normalize.c,v 1.69 2016/10/22 17:30:57 fischl Exp $
User: abby Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019
12:06:02 Id: $Id: mri_ca_register.c,v 1.99 2016/10/22 17:31:24 fischl Exp $
User: abby Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_cc ProgramArguments: -all-info ProgramVersion: $Name: $
TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02 Id:
$Id: mri_cc.c,v 1.39 2015/12/04 13:59:56 fischl Exp $ User: abby Machine:
abby-virtual-machine Platform: Linux PlatformVersion: 4.15.0-46-generic
CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_compute_overlap ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019
12:06:02 Id: $Id: mri_compute_overlap.c,v 1.19 2015/10/20 20:07:19 fischl Exp
$ User: abby Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_compute_seg_overlap ProgramArguments: -all-info
ProgramVersion: $Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp:
Apr 2 2019 12:06:02 Id: $Id: mri_compute_seg_overlap.c,v 1.18 2015/08/28
18:05:30 greve Exp $ User: abby Machine: abby-virtual-machine Platform:
Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion:
40800
ProgramName: mri_concat ProgramArguments: -all-info ProgramVersion: $Name: $
TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02 Id:
$Id: mri_concat.c,v 1.67 2017/02/16 19:49:35 greve Exp $ User: abby Machine:
abby-virtual-machine Platform: Linux PlatformVersion: 4.15.0-46-generic
CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019
12:06:02 Id: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $
User: abby Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name:
$ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02
Id: $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ User: abby
Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_diff ProgramArguments: -all-info ProgramVersion: $Name: $
TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02 Id:
$Id: mri_diff.c,v 1.37 2017/01/11 18:15:33 greve Exp $ User: abby Machine:
abby-virtual-machine Platform: Linux PlatformVersion: 4.15.0-46-generic
CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_edit_wm_with_aseg ProgramArguments: -all-info
ProgramVersion: $Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp:
Apr 2 2019 12:06:02 Id: $Id: mri_edit_wm_with_aseg.c,v 1.25 2012/03/29
13:17:38 fischl Exp $ User: abby Machine: abby-virtual-machine Platform:
Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion:
40800
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019
12:06:02 Id: $Id: mri_em_register.c,v 1.106 2016/10/22 17:31:12 fischl Exp $
User: abby Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $
TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02 Id:
$Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: abby Machine:
abby-virtual-machine Platform: Linux PlatformVersion: 4.15.0-46-generic
CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info
ProgramVersion: $Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp:
Apr 2 2019 12:06:02 Id: $Id: mri_fuse_segmentations.cpp,v 1.8 2011/03/02
00:04:15 nicks Exp $ User: abby Machine: abby-virtual-machine Platform:
Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion:
40800
ProgramName: mri_fwhm ProgramArguments: -all-info ProgramVersion: $Name: $
TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02 Id:
$Id: mri_fwhm.c,v 1.35 2016/11/01 20:25:24 greve Exp $ User: abby Machine:
abby-virtual-machine Platform: Linux PlatformVersion: 4.15.0-46-generic
CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: $
TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02 Id:
$Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: abby Machine:
abby-virtual-machine Platform: Linux PlatformVersion: 4.15.0-46-generic
CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_info ProgramArguments: -all-info ProgramVersion: $Name: $
TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02 Id:
$Id: mri_info.c,v 1.87 2014/11/20 23:46:54 greve Exp $ User: abby Machine:
abby-virtual-machine Platform: Linux PlatformVersion: 4.15.0-46-generic
CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019
12:06:02 Id: $Id: mri_label2label.c,v 1.50 2016/12/10 22:57:43 fischl Exp $
User: abby Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_label2vol ProgramArguments: -all-info ProgramVersion: $Name:
$ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02
Id: $Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $ User: abby
Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_log_likelihood ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019
12:06:02 Id: $Id: mri_log_likelihood.c,v 1.4 2011/03/02 00:04:22 nicks Exp $
User: abby Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_mask ProgramArguments: -all-info ProgramVersion: $Name: $
TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02 Id:
$Id: mri_mask.c,v 1.24 2016/11/28 20:30:57 fischl Exp $ User: abby Machine:
abby-virtual-machine Platform: Linux PlatformVersion: 4.15.0-46-generic
CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_matrix_multiply ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019
12:06:02 Id: $Id: mri_matrix_multiply.c,v 1.13 2011/03/02 00:04:23 nicks Exp $
User: abby Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name:
$ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02
Id: $Id: mri_normalize.c,v 1.92 2017/01/27 22:31:34 ah221 Exp $ User: abby
Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019
12:06:02 Id: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $
User: abby Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: $
TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02 Id:
$Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: abby Machine:
abby-virtual-machine Platform: Linux PlatformVersion: 4.15.0-46-generic
CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info
ProgramVersion: $Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp:
Apr 2 2019 12:06:02 Id: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15
18:44:10 nicks Exp $ User: abby Machine: abby-virtual-machine Platform:
Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion:
40800
ProgramName: mri_relabel_nonwm_hypos ProgramArguments: -all-info
ProgramVersion: $Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp:
Apr 2 2019 12:06:02 Id: $Id: mri_relabel_nonwm_hypos.c,v 1.2 2014/04/17
18:03:22 greve Exp $ User: abby Machine: abby-virtual-machine Platform:
Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion:
40800
ProgramName: mri_remove_neck ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019
12:06:02 Id: $Id: mri_remove_neck.c,v 1.10 2011/03/02 00:04:24 nicks Exp $
User: abby Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
$Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $
ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019
12:06:02 Id: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp
$ User: abby Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
$Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019
12:06:02 Id: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter
Exp $ User: abby Machine: abby-virtual-machine Platform: Linux
PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mris_anatomical_stats ProgramArguments: -all-info
ProgramVersion: $Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp:
Apr 2 2019 12:06:02 Id: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14
15:15:34 greve Exp $ User: abby Machine: abby-virtual-machine Platform:
Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion:
40800
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name:
$ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02
Id: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: abby
Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: $
TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02 Id:
$Id: mris_calc.c,v 1.55 2016/09/27 18:50:16 greve Exp $ User: abby Machine:
abby-virtual-machine Platform: Linux PlatformVersion: 4.15.0-46-generic
CompilerName: GCC CompilerVersion: 40800
ProgramName: mris_convert ProgramArguments: -all-info ProgramVersion: $Name:
$ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02
Id: $Id$ User: abby Machine: abby-virtual-machine Platform: Linux
PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019
12:06:02 Id: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $
User: abby Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019
12:06:02 Id: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp
$ User: abby Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mris_diff ProgramArguments: -all-info ProgramVersion: $Name: $
TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02 Id:
$Id: mris_diff.c,v 1.20 2014/03/21 23:57:48 greve Exp $ User: abby Machine:
abby-virtual-machine Platform: Linux PlatformVersion: 4.15.0-46-generic
CompilerName: GCC CompilerVersion: 40800
ProgramName: mris_divide_parcellation ProgramArguments: -all-info
ProgramVersion: $Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp:
Apr 2 2019 12:06:02 Id: $Id: mris_divide_parcellation.c,v 1.12 2012/10/24
19:50:06 maritza Exp $ User: abby Machine: abby-virtual-machine Platform:
Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion:
40800
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name:
$ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02
Id: $Id: mri_segment.c,v 1.44 2016/10/22 17:29:37 fischl Exp $ User: abby
Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name:
$ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02
Id: $Id: mri_segstats.c,v 1.122 2017/01/23 18:23:14 greve Exp $ User: abby
Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019
12:06:02 Id: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $
User: abby Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019
12:06:02 Id: $Id: mris_fix_topology.c,v 1.51 2016/10/27 19:43:58 fischl Exp $
User: abby Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019
12:06:02 Id: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $
User: abby Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mris_jacobian ProgramArguments: -all-info ProgramVersion: $Name:
$ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02
Id: $Id: mris_jacobian.c,v 1.11 2015/02/05 23:34:40 zkaufman Exp $ User: abby
Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mris_label2annot ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019
12:06:02 Id: $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $
User: abby Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mris_left_right_register ProgramArguments: -all-info
ProgramVersion: $Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp:
Apr 2 2019 12:06:02 Id: $Id: mris_left_right_register.c,v 1.2 2011/12/16
20:49:37 greve Exp $ User: abby Machine: abby-virtual-machine Platform:
Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion:
40800
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019
12:06:02 Id: $Id: mris_make_surfaces.c,v 1.172 2017/02/16 19:42:36 fischl Exp
$ User: abby Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name:
$ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02
Id: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: abby
Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name:
$ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02
Id: $Id: mris_register.c,v 1.64 2017/02/07 19:04:44 fischl Exp $ User: abby
Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name:
$ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02
Id: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: abby
Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name:
$ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02
Id: $Id: mris_sphere.c,v 1.62 2017/02/07 19:04:37 fischl Exp $ User: abby
Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mris_surface_stats ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019
12:06:02 Id: $Id: mris_surface_stats.c,v 1.10 2011/03/02 00:04:34 nicks Exp $
User: abby Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_stats2seg ProgramArguments: -all-info ProgramVersion: $Name:
$ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02
Id: $Id: mri_stats2seg.c,v 1.9 2011/03/02 00:04:24 nicks Exp $ User: abby
Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mris_thickness ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019
12:06:02 Id: $Id: mris_thickness.c,v 1.28 2012/11/27 17:41:26 fischl Exp $
User: abby Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mris_thickness_diff ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019
12:06:02 Id: $Id: mris_thickness_diff.c,v 1.16 2011/03/02 00:04:34 nicks Exp $
User: abby Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019
12:06:02 Id: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $
User: abby Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_surf2surf ProgramArguments: -all-info ProgramVersion: $Name:
$ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02
Id: $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ User: abby
Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_surf2vol ProgramArguments: -all-info ProgramVersion: $Name:
$ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02
Id: $Id: mri_surf2vol.c,v 1.28 2014/12/08 19:49:02 greve Exp $ User: abby
Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_surfcluster ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019
12:06:02 Id: $Id: mri_surfcluster.c,v 1.60 2016/11/01 19:49:22 greve Exp $
User: abby Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mris_volmask ProgramArguments: -all-info ProgramVersion: $Name:
$ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02
Id: $Id: mris_volmask.cpp,v 1.28 2016/11/18 19:19:29 fischl Exp $ User: abby
Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019
12:06:02 Id: $Id: mri_tessellate.c,v 1.39 2016/07/20 21:05:04 zkaufman Exp $
User: abby Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_vol2surf ProgramArguments: -all-info ProgramVersion: $Name:
$ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02
Id: $Id: mri_vol2surf.c,v 1.68 2014/05/30 20:58:47 greve Exp $ User: abby
Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_vol2vol ProgramArguments: -all-info ProgramVersion: $Name:
$ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02
Id: $Id: mri_vol2vol.c,v 1.89 2016/06/22 22:33:40 fischl Exp $ User: abby
Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_voldiff ProgramArguments: -all-info ProgramVersion: $Name:
$ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02
Id: $Id: mri_voldiff.c,v 1.6 2011/03/02 00:04:25 nicks Exp $ User: abby
Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name:
$ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02
Id: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User:
abby Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
ProgramName: tkregister2_cmdl ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019
12:06:02 Id: $Id: tkregister2.c,v 1.133 2016/08/02 21:17:11 greve Exp $ User:
abby Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
$Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name:
$ TimeStamp: 2019/04/04-02:27:46-GMT BuildTimeStamp: Apr 2 2019 12:06:02
Id: $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ User: abby
Machine: abby-virtual-machine Platform: Linux PlatformVersion:
4.15.0-46-generic CompilerName: GCC CompilerVersion: 40800
FLIRT version 6.0
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier
(x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
#######################################
GCADIR /usr/local/freesurfer/average
GCA RB_all_2016-05-10.vc700.gca
GCASkull RB_all_withskull_2016-05-10.vc700.gca
AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
GCSDIR /usr/local/freesurfer/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
#######################################
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4
mri_convert
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4.nii
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4/mri/orig/001.mgz
mri_convert
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4.nii
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4/mri/orig/001.mgz
$Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
reading from
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4.nii...
TR=5.99, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.988005, 0.10751, -0.110851)
j_ras = (-0.147426, -0.443073, 0.884281)
k_ras = (-0.0459542, -0.890016, -0.453608)
writing to
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4/mri/orig/001.mgz...
@#@FSTIME 2019:04:04:10:27:46 mri_convert N 2 e 2.42 S 0.20 U 2.07 P 94% M
56396 F 1 R 12815 W 0 c 148 w 120 I 48872 O 22816 L 0.00 0.00 0.03
@#@FSLOADPOST 2019:04:04:10:27:48 mri_convert N 2 0.08 0.02 0.04
#--------------------------------------------
#@# MotionCor Thu Apr 4 10:27:49 CST 2019
Found 1 runs
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
Only one run found so motion
correction will not be performed. I'll
copy the run to rawavg and continue.
cp
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4/mri/orig/001.mgz
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4/mri/rawavg.mgz
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4
mri_convert
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4/mri/rawavg.mgz
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4/mri/orig.mgz
--conform
mri_convert
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4/mri/rawavg.mgz
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4/mri/orig.mgz
--conform
$Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
reading from
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4/mri/rawavg.mgz...
TR=5.99, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.988005, 0.10751, -0.110851)
j_ras = (-0.147426, -0.443073, 0.884281)
k_ras = (-0.0459542, -0.890016, -0.453608)
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 0 2539.48 1000, flo=0, fhi=0.999, dest_type=0
Reslicing using trilinear interpolation
writing to
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4/mri/orig.mgz...
@#@FSTIME 2019:04:04:10:27:52 mri_convert N 3 e 3.63 S 0.05 U 3.57 P 99% M
68636 F 1 R 20209 W 0 c 124 w 2 I 56 O 11208 L 0.08 0.02 0.04
@#@FSLOADPOST 2019:04:04:10:27:56 mri_convert N 3 0.15 0.03 0.04
mri_add_xform_to_header -c
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4/mri/transforms/talairach.xfm
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4/mri/orig.mgz
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4/mri/orig.mgz
INFO: extension is mgz
@#@FSTIME 2019:04:04:10:27:56 mri_add_xform_to_header N 4 e 0.64 S 0.03 U 0.60
P 99% M 23196 F 11 R 4575 W 0 c 35 w 14 I 2664 O 11208 L 0.15 0.03 0.04
@#@FSLOADPOST 2019:04:04:10:27:57 mri_add_xform_to_header N 4 0.15 0.03 0.04
#--------------------------------------------
#@# Talairach Thu Apr 4 10:27:57 CST 2019
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4/mri
mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1
--proto-iters 1000 --distance 50
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4/mri
/usr/local/freesurfer/bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
nIters 1
$Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
Linux abby-virtual-machine 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07
UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
Thu Apr 4 10:27:57 CST 2019
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier
(x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
/usr/bin/bc
Found /dev/shm , will use for temp dir
tmpdir is /dev/shm/tmp.mri_nu_correct.mni.62553
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4/mri
mri_convert orig.mgz /dev/shm/tmp.mri_nu_correct.mni.62553/nu0.mnc -odt float
mri_convert orig.mgz /dev/shm/tmp.mri_nu_correct.mni.62553/nu0.mnc -odt float
$Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
reading from orig.mgz...
TR=5.99, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 1.86265e-09)
j_ras = (0, 0, -1)
k_ras = (-3.72529e-09, 1, 0)
changing data type from uchar to float (noscale = 0)...
writing to /dev/shm/tmp.mri_nu_correct.mni.62553/nu0.mnc...
--------------------------------------------------------
Iteration 1 Thu Apr 4 10:27:58 CST 2019
nu_correct -clobber /dev/shm/tmp.mri_nu_correct.mni.62553/nu0.mnc
/dev/shm/tmp.mri_nu_correct.mni.62553/nu1.mnc -tmpdir
/dev/shm/tmp.mri_nu_correct.mni.62553/0/ -iterations 1000 -distance 50
[abby@abby-virtual-machine:/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4/mri/]
[2019-04-04 10:27:58] running:
/usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen
0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline
1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir
/dev/shm/tmp.mri_nu_correct.mni.62553/0/
/dev/shm/tmp.mri_nu_correct.mni.62553/nu0.mnc
/dev/shm/tmp.mri_nu_correct.mni.62553/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
Number of iterations: 35
CV of field change: 0.00099329
mri_convert /dev/shm/tmp.mri_nu_correct.mni.62553/nu1.mnc orig_nu.mgz --like
orig.mgz --conform
mri_convert /dev/shm/tmp.mri_nu_correct.mni.62553/nu1.mnc orig_nu.mgz --like
orig.mgz --conform
$Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
reading from /dev/shm/tmp.mri_nu_correct.mni.62553/nu1.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 1.86265e-09)
j_ras = (0, 0, -1)
k_ras = (-3.72529e-09, 1, 0)
INFO: transform src into the like-volume: orig.mgz
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 0 257.063 1000, flo=0, fhi=0.999, dest_type=0
writing to orig_nu.mgz...
Thu Apr 4 10:28:30 CST 2019
mri_nu_correct.mni done
@#@FSTIME 2019:04:04:10:27:57 mri_nu_correct.mni N 11 e 33.65 S 2.52 U 30.85 P
99% M 168820 F 3 R 428955 W 0 c 3946 w 3422 I 1304 O 220128 L 0.15 0.03 0.04
@#@FSLOADPOST 2019:04:04:10:28:30 mri_nu_correct.mni N 11 0.65 0.17 0.09
talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
talairach_avi log file is transforms/talairach_avi.log...
Started at Thu Apr 4 10:28:30 CST 2019
Ended at Thu Apr 4 10:28:49 CST 2019
talairach_avi done
@#@FSTIME 2019:04:04:10:28:30 talairach_avi N 4 e 18.70 S 0.87 U 11.77 P 67% M
255872 F 11 R 396454 W 0 c 549 w 175 I 271016 O 295272 L 0.65 0.17 0.09
@#@FSLOADPOST 2019:04:04:10:28:49 talairach_avi N 4 0.67 0.21 0.11
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#--------------------------------------------
#@# Talairach Failure Detection Thu Apr 4 10:28:51 CST 2019
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0.0738, pval=0.0034 < threshold=0.0050)
Command exited with non-zero status 1
@#@FSTIME 2019:04:04:10:28:51 talairach_afd N 4 e 0.00 S 0.00 U 0.00 P 50% M
5612 F 7 R 198 W 0 c 3 w 13 I 1960 O 0 L 0.67 0.21 0.11
@#@FSLOADPOST 2019:04:04:10:28:51 talairach_afd N 4 0.67 0.21 0.11
Manual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test,
making sure the -notal-check flag follows -all
or -autorecon1 in the command string.
See:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
INFO: Retrying Talairach align using 3T-based atlas...
#--------------------------------------------
#@# Talairach Thu Apr 4 10:28:51 CST 2019
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4/mri
mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1
--proto-iters 1000 --distance 50
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4/mri
/usr/local/freesurfer/bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
nIters 1
$Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
Linux abby-virtual-machine 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07
UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
Thu Apr 4 10:28:51 CST 2019
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier
(x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
/usr/bin/bc
Found /dev/shm , will use for temp dir
tmpdir is /dev/shm/tmp.mri_nu_correct.mni.63274
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4/mri
mri_convert orig.mgz /dev/shm/tmp.mri_nu_correct.mni.63274/nu0.mnc -odt float
mri_convert orig.mgz /dev/shm/tmp.mri_nu_correct.mni.63274/nu0.mnc -odt float
$Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
reading from orig.mgz...
TR=5.99, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 1.86265e-09)
j_ras = (0, 0, -1)
k_ras = (-3.72529e-09, 1, 0)
changing data type from uchar to float (noscale = 0)...
writing to /dev/shm/tmp.mri_nu_correct.mni.63274/nu0.mnc...
--------------------------------------------------------
Iteration 1 Thu Apr 4 10:28:52 CST 2019
nu_correct -clobber /dev/shm/tmp.mri_nu_correct.mni.63274/nu0.mnc
/dev/shm/tmp.mri_nu_correct.mni.63274/nu1.mnc -tmpdir
/dev/shm/tmp.mri_nu_correct.mni.63274/0/ -iterations 1000 -distance 50
[abby@abby-virtual-machine:/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4/mri/]
[2019-04-04 10:28:52] running:
/usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen
0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline
1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir
/dev/shm/tmp.mri_nu_correct.mni.63274/0/
/dev/shm/tmp.mri_nu_correct.mni.63274/nu0.mnc
/dev/shm/tmp.mri_nu_correct.mni.63274/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
Number of iterations: 35
CV of field change: 0.00099329
mri_convert /dev/shm/tmp.mri_nu_correct.mni.63274/nu1.mnc orig_nu.mgz --like
orig.mgz --conform
mri_convert /dev/shm/tmp.mri_nu_correct.mni.63274/nu1.mnc orig_nu.mgz --like
orig.mgz --conform
$Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
reading from /dev/shm/tmp.mri_nu_correct.mni.63274/nu1.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 1.86265e-09)
j_ras = (0, 0, -1)
k_ras = (-3.72529e-09, 1, 0)
INFO: transform src into the like-volume: orig.mgz
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 0 257.063 1000, flo=0, fhi=0.999, dest_type=0
writing to orig_nu.mgz...
Thu Apr 4 10:29:24 CST 2019
mri_nu_correct.mni done
@#@FSTIME 2019:04:04:10:28:51 mri_nu_correct.mni N 11 e 33.07 S 1.84 U 31.08 P
99% M 168828 F 0 R 430771 W 0 c 3308 w 3405 I 0 O 220120 L 0.67 0.21 0.11
@#@FSLOADPOST 2019:04:04:10:29:24 mri_nu_correct.mni N 11 0.87 0.31 0.15
talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm --atlas
3T18yoSchwartzReactN32_as_orig
talairach_avi log file is transforms/talairach_avi.log...
Started at Thu Apr 4 10:29:24 CST 2019
Ended at Thu Apr 4 10:29:43 CST 2019
talairach_avi done
@#@FSTIME 2019:04:04:10:29:24 talairach_avi N 6 e 19.16 S 0.68 U 12.45 P 68% M
255828 F 2 R 396598 W 0 c 580 w 150 I 131848 O 295272 L 0.87 0.31 0.15
@#@FSLOADPOST 2019:04:04:10:29:43 talairach_avi N 6 0.91 0.36 0.17
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#--------------------------------------------
#@# Talairach Failure Detection Thu Apr 4 10:29:45 CST 2019
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0.0603, pval=0.0034 < threshold=0.0050)
Command exited with non-zero status 1
@#@FSTIME 2019:04:04:10:29:45 talairach_afd N 4 e 0.00 S 0.00 U 0.00 P 100% M
5536 F 0 R 202 W 0 c 0 w 1 I 0 O 0 L 0.91 0.36 0.17
@#@FSLOADPOST 2019:04:04:10:29:45 talairach_afd N 4 0.91 0.36 0.17
Manual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test,
making sure the -notal-check flag follows -all
or -autorecon1 in the command string.
See:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
INFO: Trying MINC mritotal to perform Talairach align...
#--------------------------------------------
#@# Talairach Thu Apr 4 10:29:45 CST 2019
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4/mri
mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1
--proto-iters 1000 --distance 50
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4/mri
/usr/local/freesurfer/bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
nIters 1
$Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
Linux abby-virtual-machine 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07
UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
Thu Apr 4 10:29:45 CST 2019
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier
(x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
/usr/bin/bc
Found /dev/shm , will use for temp dir
tmpdir is /dev/shm/tmp.mri_nu_correct.mni.63985
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4/mri
mri_convert orig.mgz /dev/shm/tmp.mri_nu_correct.mni.63985/nu0.mnc -odt float
mri_convert orig.mgz /dev/shm/tmp.mri_nu_correct.mni.63985/nu0.mnc -odt float
$Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
reading from orig.mgz...
TR=5.99, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 1.86265e-09)
j_ras = (0, 0, -1)
k_ras = (-3.72529e-09, 1, 0)
changing data type from uchar to float (noscale = 0)...
writing to /dev/shm/tmp.mri_nu_correct.mni.63985/nu0.mnc...
--------------------------------------------------------
Iteration 1 Thu Apr 4 10:29:47 CST 2019
nu_correct -clobber /dev/shm/tmp.mri_nu_correct.mni.63985/nu0.mnc
/dev/shm/tmp.mri_nu_correct.mni.63985/nu1.mnc -tmpdir
/dev/shm/tmp.mri_nu_correct.mni.63985/0/ -iterations 1000 -distance 50
[abby@abby-virtual-machine:/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4/mri/]
[2019-04-04 10:29:47] running:
/usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen
0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline
1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir
/dev/shm/tmp.mri_nu_correct.mni.63985/0/
/dev/shm/tmp.mri_nu_correct.mni.63985/nu0.mnc
/dev/shm/tmp.mri_nu_correct.mni.63985/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
Number of iterations: 35
CV of field change: 0.00099329
mri_convert /dev/shm/tmp.mri_nu_correct.mni.63985/nu1.mnc orig_nu.mgz --like
orig.mgz --conform
mri_convert /dev/shm/tmp.mri_nu_correct.mni.63985/nu1.mnc orig_nu.mgz --like
orig.mgz --conform
$Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
reading from /dev/shm/tmp.mri_nu_correct.mni.63985/nu1.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 1.86265e-09)
j_ras = (0, 0, -1)
k_ras = (-3.72529e-09, 1, 0)
INFO: transform src into the like-volume: orig.mgz
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 0 257.063 1000, flo=0, fhi=0.999, dest_type=0
writing to orig_nu.mgz...
Thu Apr 4 10:30:18 CST 2019
mri_nu_correct.mni done
@#@FSTIME 2019:04:04:10:29:45 mri_nu_correct.mni N 11 e 33.15 S 1.74 U 31.22 P
99% M 168908 F 0 R 430005 W 0 c 3852 w 3476 I 0 O 220128 L 0.91 0.36 0.17
@#@FSLOADPOST 2019:04:04:10:30:18 mri_nu_correct.mni N 11 0.95 0.43 0.20
talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4/mri
/usr/local/freesurfer/bin/talairach
--i orig_nu.mgz --xfm transforms/talairach.auto.xfm
$Id: talairach,v 1.8 2016/02/16 17:17:20 zkaufman Exp $
Linux abby-virtual-machine 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07
UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
Thu Apr 4 10:30:19 CST 2019
tmpdir is transforms/tmp.talairach.64531
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4/mri
mri_convert orig_nu.mgz transforms/tmp.talairach.64531/src.mnc
mri_convert orig_nu.mgz transforms/tmp.talairach.64531/src.mnc
$Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
reading from orig_nu.mgz...
TR=5.99, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 1.86265e-09)
j_ras = (0, 0, -1)
k_ras = (-3.72529e-09, 1, 0)
writing to transforms/tmp.talairach.64531/src.mnc...
--------------------------------------------
mritotal -verbose -debug -clobber -modeldir
/usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm
transforms/tmp.talairach.64531/src.mnc transforms/talairach.auto.xfm
Transforming
slices:................................................................................................................................Done
Copying
chunks:......................................................................................................................................................Done.
Copying
chunks:..........................................................................................................Done.
Transforming
slices:......................................................................................................................................................Done
Copying
chunks:....................................................................................................................Done.
Copying
chunks:....................................................................................................................Done.
Source volume size: 74 by 106 by 106
Source voxel size = 2.000 2.000 2.000
Source min/max real range = -0.000 152.009
Source min/max voxel= -0.000 152.009
Target volume size: 58 by 110 by 86
Target voxel = 2.000 2.000 2.000
Target min/max real range= 0.970 123.710
Target min/max voxel = -0.000 123.710
AFTER init_params()
Transform matrix = 1.0000 0.0000 0.0000 -9.0714
0.0000 1.0000 0.0000 -25.6183
0.0000 0.0000 1.0000 35.7644
Transform center = 9.399 8.027 -26.310
Transform rotations = 0.000 0.000 0.000
Transform trans = -9.071 -25.618 35.764
Transform scale = 1.000 1.000 1.000
Transform shear = 0.000 0.000 0.000
Target volume is smallest
Lattice step size = 4.000 4.000 4.000
Lattice start = -85.095 -125.510 -47.250
Lattice count = 43 55 29
Source volume size: 84 by 116 by 116
Source voxel size = 2.000 2.000 2.000
Source min/max real range = -0.000 214.594
Source min/max voxel= -0.000 214.594
Target volume size: 68 by 110 by 86
Target voxel = 2.000 2.000 2.000
Target min/max real range= -0.000 144.070
Target min/max voxel = -0.000 144.070
AFTER init_params()
Transform matrix = 0.8254 -0.3634 -0.1516 -3.8159
0.0441 0.4352 -0.8031 -37.4822
0.3912 0.7175 0.4103 9.7114
Transform center = 9.399 8.027 -26.310
Transform rotations = 1.051 -0.442 0.053
Transform trans = -4.386 -20.472 34.663
Transform scale = 0.914 0.914 0.914
Transform shear = 0.000 0.000 0.000
Target volume is smallest
Lattice step size = 4.000 4.000 4.000
Lattice start = -85.095 -125.510 -57.250
Lattice count = 43 55 34
Source volume size: 84 by 116 by 116
Source voxel size = 2.000 2.000 2.000
Source min/max real range = 0.076 25.009
Source min/max voxel= 0.076 25.009
Target volume size: 68 by 110 by 86
Target voxel = 2.000 2.000 2.000
Target min/max real range= 0.037 11.652
Target min/max voxel = 0.037 11.652
AFTER init_params()
Transform matrix = 0.8014 -0.3884 -0.1272 -1.1167
0.0882 0.4376 -0.7810 -37.0761
0.3991 0.6833 0.4279 11.8727
Transform center = 9.399 8.027 -26.310
Transform rotations = 1.011 -0.460 0.110
Transform trans = -2.755 -20.213 36.160
Transform scale = 0.900 0.900 0.900
Transform shear = -0.000 -0.000 0.000
Target volume is smallest
Lattice step size = 4.000 4.000 4.000
Lattice start = -65.095 -105.510 -57.250
Lattice count = 35 46 34
Source volume size: 84 by 116 by 116
Source voxel size = 2.000 2.000 2.000
Source min/max real range = 0.076 25.009
Source min/max voxel= 0.076 25.009
Target volume size: 68 by 110 by 86
Target voxel = 2.000 2.000 2.000
Target min/max real range= 0.037 11.652
Target min/max voxel = 0.037 11.652
AFTER init_params()
Transform matrix = 0.7768 -0.2727 -0.1409 -8.3705
0.1295 0.6389 -0.5223 -17.8589
0.2783 0.4639 0.6364 22.4157
Transform center = 9.399 8.027 -26.310
Transform rotations = 0.630 -0.340 0.165
Transform trans = -8.949 -5.800 38.321
Transform scale = 0.835 0.835 0.835
Transform shear = 0.000 -0.000 -0.000
Target volume is smallest
Lattice step size = 4.000 4.000 4.000
Lattice start = -65.095 -105.510 -57.250
Lattice count = 35 46 34
Source volume size: 84 by 116 by 116
Source voxel size = 2.000 2.000 2.000
Source min/max real range = 0.076 25.009
Source min/max voxel= 0.076 25.009
Target volume size: 68 by 110 by 86
Target voxel = 2.000 2.000 2.000
Target min/max real range= 0.037 11.652
Target min/max voxel = 0.037 11.652
AFTER init_params()
Transform matrix = 0.8192 -0.2863 -0.1524 -10.8446
0.1001 0.5251 -0.4486 -16.7363
0.2677 0.4523 0.5891 24.9254
Transform center = 9.399 8.027 -26.310
Transform rotations = 0.655 -0.346 0.153
Transform trans = -10.832 -7.806 41.883
Transform scale = 0.881 0.698 0.789
Transform shear = 0.000 0.000 0.000
Target volume is smallest
Lattice step size = 4.000 4.000 4.000
Lattice start = -65.095 -105.510 -57.250
Lattice count = 35 46 34
Source volume size: 84 by 116 by 116
Source voxel size = 2.000 2.000 2.000
Source min/max real range = 0.076 25.009
Source min/max voxel= 0.076 25.009
Target volume size: 68 by 110 by 86
Target voxel = 2.000 2.000 2.000
Target min/max real range= 0.037 11.652
Target min/max voxel = 0.037 11.652
AFTER init_params()
Transform matrix = 0.8184 -0.2963 -0.1621 -11.1426
0.0974 0.5136 -0.4467 -16.3752
0.3232 0.5243 0.6732 22.7897
Transform center = 9.399 8.027 -26.310
Transform rotations = 0.662 -0.362 0.152
Transform trans = -10.962 -7.611 38.634
Transform scale = 0.885 0.688 0.912
Transform shear = -0.000 0.000 -0.000
Target volume is smallest
Lattice step size = 4.000 4.000 4.000
Lattice start = -65.095 -105.510 -57.250
Lattice count = 35 46 34
lta_convert --src orig_nu.mgz --trg
/usr/local/freesurfer/mni/bin/../share/mni_autoreg/average_305.mnc --inxfm
transforms/talairach.auto.xfm --outlta transforms/talairach.auto.xfm.lta
--subject fsaverage
Thu Apr 4 10:30:23 CST 2019
talairach done
@#@FSTIME 2019:04:04:10:30:19 talairach N 4 e 4.82 S 0.21 U 4.49 P 97% M 40288
F 3 R 71881 W 0 c 1081 w 217 I 640 O 99288 L 0.95 0.43 0.20
@#@FSLOADPOST 2019:04:04:10:30:23 talairach N 4 1.11 0.48 0.21
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#--------------------------------------------
#@# Talairach Failure Detection Thu Apr 4 10:30:25 CST 2019
/home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0.0079, pval=0.0000 < threshold=0.0050)
Command exited with non-zero status 1
@#@FSTIME 2019:04:04:10:30:25 talairach_afd N 4 e 0.00 S 0.00 U 0.00 P 50% M
6252 F 7 R 243 W 0 c 1 w 8 I 1384 O 0 L 1.11 0.48 0.21
@#@FSLOADPOST 2019:04:04:10:30:25 talairach_afd N 4 1.11 0.48 0.21
Manual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test,
making sure the -notal-check flag follows -all
or -autorecon1 in the command string.
See:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
ERROR: Talairach failed!
Linux abby-virtual-machine 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07
UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 0306A_T1_w4 exited with ERRORS at Thu Apr 4 10:30:25 CST 2019
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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