External Email - Use Caution
Hello FreeSurfer Developers,
I'm trying to compute volumetric data from MPRAGE images by using recon-all as
decribed athttps://surfer.nmr.mgh.harvard.edu/fswiki/recon-all
I've got the following message:
mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n
2
ERROR: flag --uchar not recognized
Does anyone have any thoughts on how to trouble-shoot this problem? Also, I've
attached the recon-all.log in case it's of any use.
FreeSurfer version: freesurfer-darwin-macOS-7.1.1
(freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0)
macOS high Sierra 10.13.6, x86_64
XQuartz 2.7.11 (xorg-server 1.18.4)
recon-all.log: see attached
Sincerely,
Nurhan Erbil
Thu Oct 22 12:44:03 +03 2020
/Applications/freesurfer/subjects/nr
/Applications/freesurfer/bin/recon-all
-s nr -i /Applications/freesurfer/subjects/s1.mgz -all -qcache
subjid nr
setenv SUBJECTS_DIR /Applications/freesurfer/subjects
FREESURFER_HOME /Applications/freesurfer
Actual FREESURFER_HOME /Applications/freesurfer
build-stamp.txt: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
Darwin Nurhans-MacBook-Pro.local 17.7.0 Darwin Kernel Version 17.7.0: Mon Aug
31 22:11:23 PDT 2020; root:xnu-4570.71.82.6~1/RELEASE_X86_64 x86_64
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 8192 kbytes
coredumpsize 0 kbytes
memoryuse unlimited
descriptors 256
memorylocked unlimited
maxproc 709
PhysMem: 7245M used (1515M wired), 944M unused.
########################################
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: 2020/10/22-09:44:05-GMT BuildTimeStamp: May 25 2011
22:32:58 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
User: nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform: Darwin
PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
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: 2020/10/22-09:44:05-GMT BuildTimeStamp: May 25
2011 22:32:58 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve
Exp $ User: nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform: Darwin
PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nschmans@W0084482
(i686-apple-darwin8.8.1) on 2006-10-03 at 21:43:56
ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2020/10/22-09:44:06-GMT BuildTimeStamp: May 25
2011 22:32:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $
User: nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform: Darwin
PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2020/10/22-09:44:07-GMT BuildTimeStamp: May 25 2011
22:32:58 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $
User: nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform: Darwin
PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2020/10/22-09:44:07-GMT BuildTimeStamp: May 25 2011
22:32:58 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $
User: nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform: Darwin
PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2020/10/22-09:44:07-GMT BuildTimeStamp: May 25 2011
22:32:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User:
nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform: Darwin
PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2020/10/22-09:44:07-GMT BuildTimeStamp: May 25 2011
22:32:58 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User:
nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform: Darwin
PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2020/10/22-09:44:07-GMT BuildTimeStamp: May 25
2011 22:32:58 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve
Exp $ User: nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform: Darwin
PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2020/10/22-09:44:08-GMT BuildTimeStamp: May 25
2011 22:32:58 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp
$ User: nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform: Darwin
PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2020/10/22-09:44:08-GMT BuildTimeStamp: May 25
2011 22:32:58 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks
Exp $ User: nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform: Darwin
PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2020/10/22-09:44:08-GMT BuildTimeStamp: May 25
2011 22:32:58 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl
Exp $ User: nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform: Darwin
PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2020/10/22-09:44:08-GMT BuildTimeStamp: May 25 2011
22:32:58 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $
User: nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform: Darwin
PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2020/10/22-09:44:09-GMT BuildTimeStamp: May 25 2011
22:32:58 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User:
nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform: Darwin
PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2020/10/22-09:44:09-GMT BuildTimeStamp: May 25 2011
22:32:58 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User:
nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform: Darwin
PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2020/10/22-09:44:09-GMT BuildTimeStamp: May 25
2011 22:32:58 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp
$ User: nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform: Darwin
PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2020/10/22-09:44:09-GMT BuildTimeStamp: May 25
2011 22:32:58 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks
Exp $ User: nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform: Darwin
PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2020/10/22-09:44:10-GMT BuildTimeStamp: May 25
2011 22:32:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks
Exp $ User: nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform: Darwin
PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2020/10/22-09:44:10-GMT BuildTimeStamp: May 25 2011
22:32:58 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User:
nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform: Darwin
PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2020/10/22-09:44:10-GMT BuildTimeStamp: May 25 2011
22:32:58 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $
User: nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform: Darwin
PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2020/10/22-09:44:10-GMT BuildTimeStamp: May 25
2011 22:32:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp
$ User: nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform: Darwin
PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2020/10/22-09:44:10-GMT BuildTimeStamp: May 25 2011
22:32:58 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User:
nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform: Darwin
PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2020/10/22-09:44:10-GMT BuildTimeStamp: May 25
2011 22:32:58 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks
Exp $ User: nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform: Darwin
PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2020/10/22-09:44:10-GMT BuildTimeStamp: May 25
2011 22:32:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks
Exp $ User: nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform: Darwin
PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2020/10/22-09:44:10-GMT BuildTimeStamp: May 25 2011
22:32:58 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
User: nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform: Darwin
PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2020/10/22-09:44:10-GMT BuildTimeStamp: May 25
2011 22:32:58 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks
Exp $ User: nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform: Darwin
PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2020/10/22-09:44:10-GMT BuildTimeStamp: May 25
2011 22:32:58 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks
Exp $ User: nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform: Darwin
PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2020/10/22-09:44:10-GMT BuildTimeStamp: May 25 2011
22:32:58 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $
User: nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform: Darwin
PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2020/10/22-09:44:10-GMT BuildTimeStamp: May 25 2011
22:32:58 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $
User: nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform: Darwin
PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
ProgramName: mris_anatomical_stats ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp: 2020/10/22-09:44:11-GMT
BuildTimeStamp: May 25 2011 22:32:58 CVS: $Id: mris_anatomical_stats.c,v 1.72
2011/03/02 00:04:26 nicks Exp $ User: nurhanerbil Machine:
Nurhans-MacBook-Pro.local Platform: Darwin PlatformVersion: 17.7.0
CompilerName: GCC CompilerVersion: 40000
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2020/10/22-09:44:11-GMT BuildTimeStamp: May 25 2011
22:32:58 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User:
nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform: Darwin
PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2020/10/22-09:44:11-GMT BuildTimeStamp: May 25
2011 22:32:58 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30
nicks Exp $ User: nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform:
Darwin PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2020/10/22-09:44:11-GMT BuildTimeStamp: May 25 2011
22:32:58 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $
User: nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform: Darwin
PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
$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: 2020/10/22-09:44:12-GMT BuildTimeStamp: May 25
2011 22:32:58 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49
nicks Exp $ User: nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform:
Darwin PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
$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: 2020/10/22-09:44:12-GMT BuildTimeStamp: May 25
2011 22:32:58 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24
nicks Exp $ User: nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform:
Darwin PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2020/10/22-09:44:12-GMT BuildTimeStamp: May 25 2011
22:32:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User:
nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform: Darwin
PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2020/10/22-09:44:13-GMT BuildTimeStamp: May 25 2011
22:32:58 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User:
nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform: Darwin
PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp: 2020/10/22-09:44:13-GMT
BuildTimeStamp: May 25 2011 22:32:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8
2011/03/02 00:04:15 nicks Exp $ User: nurhanerbil Machine:
Nurhans-MacBook-Pro.local Platform: Darwin PlatformVersion: 17.7.0
CompilerName: GCC CompilerVersion: 40000
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2020/10/22-09:44:13-GMT BuildTimeStamp: May 25 2011
22:32:58 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $
User: nurhanerbil Machine: Nurhans-MacBook-Pro.local Platform: Darwin
PlatformVersion: 17.7.0 CompilerName: GCC CompilerVersion: 40000
#######################################
GCADIR /Applications/freesurfer/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /Applications/freesurfer/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
#######################################
/Applications/freesurfer/subjects/nr
\n mri_convert /Applications/freesurfer/subjects/s1.mgz
/Applications/freesurfer/subjects/nr/mri/orig/001.mgz \n
mri_convert /Applications/freesurfer/subjects/s1.mgz
/Applications/freesurfer/subjects/nr/mri/orig/001.mgz
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from /Applications/freesurfer/subjects/s1.mgz...
TR=1900.00, TE=2.52, TI=900.00, flip angle=9.00
i_ras = (-0, -1, 0)
j_ras = (-0, -0, -1)
k_ras = (-1, 0, 0)
writing to /Applications/freesurfer/subjects/nr/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Thu Oct 22 12:44:19 +03 2020
Found 1 runs
/Applications/freesurfer/subjects/nr/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.
\n cp /Applications/freesurfer/subjects/nr/mri/orig/001.mgz
/Applications/freesurfer/subjects/nr/mri/rawavg.mgz \n
/Applications/freesurfer/subjects/nr
\n mri_convert /Applications/freesurfer/subjects/nr/mri/rawavg.mgz
/Applications/freesurfer/subjects/nr/mri/orig.mgz --conform \n
mri_convert /Applications/freesurfer/subjects/nr/mri/rawavg.mgz
/Applications/freesurfer/subjects/nr/mri/orig.mgz --conform
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from /Applications/freesurfer/subjects/nr/mri/rawavg.mgz...
TR=1900.00, TE=2.52, TI=900.00, flip angle=9.00
i_ras = (-0, -1, 0)
j_ras = (-0, -0, -1)
k_ras = (-1, 0, 0)
Original Data has (0.976562, 0.976562, 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 /Applications/freesurfer/subjects/nr/mri/orig.mgz...
\n mri_add_xform_to_header -c
/Applications/freesurfer/subjects/nr/mri/transforms/talairach.xfm
/Applications/freesurfer/subjects/nr/mri/orig.mgz
/Applications/freesurfer/subjects/nr/mri/orig.mgz \n
INFO: extension is mgz
#--------------------------------------------
#@# Talairach Thu Oct 22 12:44:34 +03 2020
/Applications/freesurfer/subjects/nr/mri
\n talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm \n
\n cp transforms/talairach.auto.xfm transforms/talairach.xfm \n
#--------------------------------------------
#@# Talairach Failure Detection Thu Oct 22 12:45:13 +03 2020
/Applications/freesurfer/subjects/nr/mri
\n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n
talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7807,
pval=0.8469 >= threshold=0.0050)
\n awk -f /Applications/freesurfer/bin/extract_talairach_avi_QA.awk
/Applications/freesurfer/subjects/nr/mri/transforms/talairach_avi.log \n
TalAviQA: 0.97719
z-score: 0
#--------------------------------------------
#@# Nu Intensity Correction Thu Oct 22 12:45:14 +03 2020
\n mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm
--n 2 \n
ERROR: flag --uchar not recognized
Darwin Nurhans-MacBook-Pro.local 17.7.0 Darwin Kernel Version 17.7.0: Mon Aug
31 22:11:23 PDT 2020; root:xnu-4570.71.82.6~1/RELEASE_X86_64 x86_64
recon-all -s nr exited with ERRORS at Thu Oct 22 12:45:14 +03 2020
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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