Try using this one instead

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/reg-feat2anat

doug

On 6/19/13 8:48 PM, 王志伟 wrote:
Dear Sir or Madam, 
 I am trying to apply FreeSurfer Tools to FSL fMRI Analysis (FEAT) as your tutorial. But there were many errors and I cannot figure them out. 
Could you help me deal with them?  
Thank you so much!

The log files are attached.

The details are as follows:

the version of Linux: rhel6.2;

the version of freesurfer:  freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0

SUBJECTS_DIR: /usr/local/freesurfer/subjects

working directory /usr/local/freesurfer/subjects/fbert-feat

command: reg-feat2anat --feat fbert1.feat --subject bert

there is no ERROR in  anat2std.register.dat.fslregister.log
the first ERROR in  anat2exf.register.dat.fslregister.log   is 

'' /usr/local/freesurfer/subjects/fbert-feat
mri_convert ERROR: could not determine file for /usr/local/freesurfer/subjects/bert/mri/ERROR: fbert1.feat/reg/freesurfer/tmp/refvol.fslregister.nii
mri_convert ERROR: could not determine file for /usr/local/freesurfer/subjects/bert/mri/ERROR: fbert1.feat/reg/freesurfer/tmp/refvol.fslregister.nii'' 

the reg-feat2anat.log is as follow:

Wed Jun 19 20:41:16 CST 2013
/usr/local/freesurfer/subjects/fbert-feat
/usr/local/freesurfer/bin/reg-feat2anat
--feat fbert1.feat --subject bert
Linux T7600-3 2.6.32-220.el6.x86_64 #1 SMP Wed Nov 9 08:03:13 EST 2011 x86_64 x86_64 x86_64 GNU/Linux
example_func ras_good_flag 1
-------------------------------------------------------
Initializing exf2anat with header
tkregister2_cmdl --targ /usr/local/freesurfer/subjects/bert/mri/brainmask.mgz --mov fbert1.feat/example_func.nii.gz --reg fbert1.feat/reg/freesurfer/anat2exf.register.dat.init --fslregout fbert1.feat/reg/freesurfer/exf2anat.init.fsl.mat --regheader --noedit
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
target  volume /usr/local/freesurfer/subjects/bert/mri/brainmask.mgz
movable volume fbert1.feat/example_func.nii.gz
reg file       fbert1.feat/reg/freesurfer/anat2exf.register.dat.init
LoadVol        0
ZeroCRAS       0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
INFO: loading target /usr/local/freesurfer/subjects/bert/mri/brainmask.mgz
Ttarg: --------------------
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
INFO: loading movable fbert1.feat/example_func.nii.gz
Tmov: --------------------
-3.438   0.000   0.000   110.000;
 0.000   0.000   4.000  -70.000;
 0.000  -3.438   0.000   110.000;
 0.000   0.000   0.000   1.000;
mkheaderreg = 1, float2int = 0
Computing reg from header (and possibly input matrix)
---- Input registration matrix (computed) --------
 1.000   0.000   0.000   5.400;
 0.000   0.000   1.000   0.000;
 0.000  -1.000   0.000  -18.000;
 0.000   0.000   0.000   1.000;
---------------------------------------
---- Input registration matrix --------
 1.000   0.000   0.000   5.400;
 0.000   0.000   1.000   0.000;
 0.000  -1.000   0.000  -18.000;
 0.000   0.000   0.000   1.000;
Determinant 1
subject = subject-unknown
RegMat ---------------------------
 1.000   0.000   0.000   5.400;
 0.000   0.000   1.000   0.000;
 0.000  -1.000   0.000  -18.000;
 0.000   0.000   0.000   1.000;
FSLOUTPUTTYPE NIFTI_GZ 
tkreg2FSL: mov det = -47.2656, ref det = -1

fslregister --s bert --reg fbert1.feat/reg/freesurfer/anat2exf.register.dat --mov fbert1.feat/example_func.nii.gz --dof 6 --bins 256 --cost corratio --fslmat fbert1.feat/reg/freesurfer/exf2anat.fsl.mat --fsvol brainmask --maxangle 90 --initfslmat fbert1.feat/reg/freesurfer/exf2anat.init.fsl.mat --tmp fbert1.feat/reg/freesurfer/tmp --out fbert1.feat/reg/freesurfer/tmp/exf-in-anat.nii.gz

Log file is fbert1.feat/reg/freesurfer/anat2exf.register.dat.fslregister.log

Wed Jun 19 20:41:18 CST 2013
--s bert --reg fbert1.feat/reg/freesurfer/anat2exf.register.dat --mov fbert1.feat/example_func.nii.gz --dof 6 --bins 256 --cost corratio --fslmat fbert1.feat/reg/freesurfer/exf2anat.fsl.mat --fsvol brainmask --maxangle 90 --initfslmat fbert1.feat/reg/freesurfer/exf2anat.init.fsl.mat --tmp fbert1.feat/reg/freesurfer/tmp --out fbert1.feat/reg/freesurfer/tmp/exf-in-anat.nii.gz
$Id: fslregister,v 1.34.2.1 2011/03/28 20:35:36 greve Exp $
T7600-3
Linux T7600-3 2.6.32-220.el6.x86_64 #1 SMP Wed Nov 9 08:03:13 EST 2011 x86_64 x86_64 x86_64 GNU/Linux
nIters 1
--------------------------------------
/usr/local/freesurfer/subjects/fbert-feat
mri_convert ERROR: could not determine file for /usr/local/freesurfer/subjects/bert/mri/ERROR: fbert1.feat/reg/freesurfer/tmp/refvol.fslregister.nii
mri_convert ERROR: could not determine file for /usr/local/freesurfer/subjects/bert/mri/ERROR: fbert1.feat/reg/freesurfer/tmp/refvol.fslregister.nii 

mri_convert: extra arguments ("not" and following)

type mri_convert -u for usage

--------------------------------------
/usr/local/freesurfer/subjects/fbert-feat
mri_convert fbert1.feat/example_func.nii.gz fbert1.feat/reg/freesurfer/tmp/movvol.fslregister.nii --frame 0
mri_convert fbert1.feat/example_func.nii.gz fbert1.feat/reg/freesurfer/tmp/movvol.fslregister.nii --frame 0 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from fbert1.feat/example_func.nii.gz...
TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
keeping frame 0
writing to fbert1.feat/reg/freesurfer/tmp/movvol.fslregister.nii...
Mov determinant is -47.2656
Wed Jun 19 20:41:18 CST 2013
/usr/local/freesurfer/subjects/fbert-feat
flirt.fsl -ref fbert1.feat/reg/freesurfer/tmp/refvol.fslregister.nii -in fbert1.feat/reg/freesurfer/tmp/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat fbert1.feat/reg/freesurfer/tmp/fslmat0.trans.mat -schedule /usr/local/fsl/etc/flirtsch/xyztrans.sch -init fbert1.feat/reg/freesurfer/exf2anat.init.fsl.mat
** ERROR (nifti_image_read): failed to find header file for 'fbert1.feat/reg/freesurfer/tmp/refvol.fslregister'
** ERROR: nifti_image_open(fbert1.feat/reg/freesurfer/tmp/refvol.fslregister): bad header info
Error: failed to open file fbert1.feat/reg/freesurfer/tmp/refvol.fslregister
ERROR: Could not open image fbert1.feat/reg/freesurfer/tmp/refvol.fslregister
Image Exception : #22 :: Failed to read volume fbert1.feat/reg/freesurfer/tmp/refvol.fslregister.nii
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Abort (core dumped) 
Wed Jun 19 20:41:18 CST 2013
/usr/local/freesurfer/subjects/fbert-feat
flirt.fsl -ref fbert1.feat/reg/freesurfer/tmp/refvol.fslregister.nii -in fbert1.feat/reg/freesurfer/tmp/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat fbert1.feat/reg/freesurfer/exf2anat.fsl.mat -init fbert1.feat/reg/freesurfer/tmp/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch -o fbert1.feat/reg/freesurfer/tmp/outvol.fslregister.nii
** ERROR (nifti_image_read): failed to find header file for 'fbert1.feat/reg/freesurfer/tmp/refvol.fslregister'
** ERROR: nifti_image_open(fbert1.feat/reg/freesurfer/tmp/refvol.fslregister): bad header info
Error: failed to open file fbert1.feat/reg/freesurfer/tmp/refvol.fslregister
ERROR: Could not open image fbert1.feat/reg/freesurfer/tmp/refvol.fslregister
Image Exception : #22 :: Failed to read volume fbert1.feat/reg/freesurfer/tmp/refvol.fslregister.nii
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Abort (core dumped) 
Wed Jun 19 20:41:18 CST 2013
/usr/local/freesurfer/subjects/fbert-feat
mri_convert fbert1.feat/reg/freesurfer/tmp/outvol.fslregister.nii fbert1.feat/reg/freesurfer/tmp/exf-in-anat.nii.gz
mri_convert fbert1.feat/reg/freesurfer/tmp/outvol.fslregister.nii fbert1.feat/reg/freesurfer/tmp/exf-in-anat.nii.gz 
niiRead(): error opening file fbert1.feat/reg/freesurfer/tmp/outvol.fslregister.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from fbert1.feat/reg/freesurfer/tmp/outvol.fslregister.nii...
tkregister2_cmdl --s bert --mov fbert1.feat/example_func.nii.gz --reg fbert1.feat/reg/freesurfer/anat2exf.register.dat --fslreg fbert1.feat/reg/freesurfer/exf2anat.fsl.mat --noedit
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
ERROR: cannot open fbert1.feat/reg/freesurfer/exf2anat.fsl.mat
 
Started at Wed Jun 19 20:41:18 CST 2013 
Ended   at Wed Jun 19 20:41:18 CST 2013
 
fslregister Done
 
To check results, run:
tkregister2 --mov fbert1.feat/example_func.nii.gz --reg fbert1.feat/reg/freesurfer/anat2exf.register.dat --surf orig
 

bbregister --mov fbert1.feat/example_func.nii.gz --bold --6 --init-reg fbert1.feat/reg/freesurfer/anat2exf.register.dat --reg fbert1.feat/reg/freesurfer/anat2exf.register.dat
ERROR: cannot find fbert1.feat/reg/freesurfer/anat2exf.register.dat
fslregister --mov fbert1.feat/reg/standard.nii.gz --s bert --reg fbert1.feat/reg/freesurfer/anat2std.register.dat --dof 12

Log file is fbert1.feat/reg/freesurfer/anat2std.register.dat.fslregister.log

Wed Jun 19 20:41:18 CST 2013
--mov fbert1.feat/reg/standard.nii.gz --s bert --reg fbert1.feat/reg/freesurfer/anat2std.register.dat --dof 12
$Id: fslregister,v 1.34.2.1 2011/03/28 20:35:36 greve Exp $
T7600-3
Linux T7600-3 2.6.32-220.el6.x86_64 #1 SMP Wed Nov 9 08:03:13 EST 2011 x86_64 x86_64 x86_64 GNU/Linux
nIters 1
--------------------------------------
/usr/local/freesurfer/subjects/fbert-feat
mri_convert /usr/local/freesurfer/subjects/bert/mri/brainmask.mgz fbert1.feat/reg/tmp.fslregister.17828/refvol.fslregister.nii
mri_convert /usr/local/freesurfer/subjects/bert/mri/brainmask.mgz fbert1.feat/reg/tmp.fslregister.17828/refvol.fslregister.nii 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /usr/local/freesurfer/subjects/bert/mri/brainmask.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to fbert1.feat/reg/tmp.fslregister.17828/refvol.fslregister.nii...
--------------------------------------
/usr/local/freesurfer/subjects/fbert-feat
mri_convert fbert1.feat/reg/standard.nii.gz fbert1.feat/reg/tmp.fslregister.17828/movvol.fslregister.nii --frame 0
mri_convert fbert1.feat/reg/standard.nii.gz fbert1.feat/reg/tmp.fslregister.17828/movvol.fslregister.nii --frame 0 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from fbert1.feat/reg/standard.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
keeping frame 0
writing to fbert1.feat/reg/tmp.fslregister.17828/movvol.fslregister.nii...
Mov determinant is -8
/usr/local/freesurfer/subjects/fbert-feat
tkregister2_cmdl --mov fbert1.feat/reg/tmp.fslregister.17828/movvol.fslregister.nii --reg fbert1.feat/reg/tmp.fslregister.17828/reg0.17828.dat --regheader --fslregout fbert1.feat/reg/freesurfer/anat2std.register.dat.fsl.mat0 --s bert --noedit
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume fbert1.feat/reg/tmp.fslregister.17828/movvol.fslregister.nii
reg file       fbert1.feat/reg/tmp.fslregister.17828/reg0.17828.dat
LoadVol        0
ZeroCRAS       0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
INFO: loading target /usr/local/freesurfer/subjects/bert/mri/orig.mgz
Ttarg: --------------------
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
INFO: loading movable fbert1.feat/reg/tmp.fslregister.17828/movvol.fslregister.nii
Tmov: --------------------
-2.000   0.000   0.000   91.000;
 0.000   0.000   2.000  -91.000;
 0.000  -2.000   0.000   109.000;
 0.000   0.000   0.000   1.000;
mkheaderreg = 1, float2int = 0
Computing reg from header (and possibly input matrix)
---- Input registration matrix (computed) --------
 1.000   0.000   0.000   6.400;
 0.000   0.000   1.000  -19.000;
 0.000  -1.000   0.000  -35.000;
 0.000   0.000   0.000   1.000;
---------------------------------------
---- Input registration matrix --------
 1.000   0.000   0.000   6.400;
 0.000   0.000   1.000  -19.000;
 0.000  -1.000   0.000  -35.000;
 0.000   0.000   0.000   1.000;
Determinant 1
subject = bert
RegMat ---------------------------
 1.000   0.000   0.000   6.400;
 0.000   0.000   1.000  -19.000;
 0.000  -1.000   0.000  -35.000;
 0.000   0.000   0.000   1.000;
FSLOUTPUTTYPE NIFTI 
tkreg2FSL: mov det = -8, ref det = -1
Wed Jun 19 20:41:20 CST 2013
/usr/local/freesurfer/subjects/fbert-feat
flirt.fsl -ref fbert1.feat/reg/tmp.fslregister.17828/refvol.fslregister.nii -in fbert1.feat/reg/tmp.fslregister.17828/movvol.fslregister.nii -bins 256 -cost corratio -dof 12 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat fbert1.feat/reg/tmp.fslregister.17828/fslmat0.trans.mat -schedule /usr/local/fsl/etc/flirtsch/xyztrans.sch -init fbert1.feat/reg/freesurfer/anat2std.register.dat.fsl.mat0
Wed Jun 19 20:41:27 CST 2013
/usr/local/freesurfer/subjects/fbert-feat
flirt.fsl -ref fbert1.feat/reg/tmp.fslregister.17828/refvol.fslregister.nii -in fbert1.feat/reg/tmp.fslregister.17828/movvol.fslregister.nii -bins 256 -cost corratio -dof 12 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat fbert1.feat/reg/freesurfer/anat2std.register.dat.fsl.mat -init fbert1.feat/reg/tmp.fslregister.17828/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch
tkregister2_cmdl --s bert --mov fbert1.feat/reg/standard.nii.gz --reg fbert1.feat/reg/freesurfer/anat2std.register.dat --fslreg fbert1.feat/reg/freesurfer/anat2std.register.dat.fsl.mat --noedit
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
---- FSL registration matrix --------
 0.905   0.003   0.033   43.546;
 0.039  -0.091  -0.903   197.762;
 0.008   1.050  -0.080   4.971;
 0.000   0.000   0.000   1.000;
---------------------------------------
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume fbert1.feat/reg/standard.nii.gz
reg file       fbert1.feat/reg/freesurfer/anat2std.register.dat
LoadVol        0
ZeroCRAS       0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
INFO: loading target /usr/local/freesurfer/subjects/bert/mri/orig.mgz
Ttarg: --------------------
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
INFO: loading movable fbert1.feat/reg/standard.nii.gz
Tmov: --------------------
-2.000   0.000   0.000   91.000;
 0.000   0.000   2.000  -91.000;
 0.000  -2.000   0.000   109.000;
 0.000   0.000   0.000   1.000;
mkheaderreg = 0, float2int = 0
FSLOUTPUTTYPE NIFTI 
fsl2TkReg: mov det = -8, ref det = -1
---- Input registration matrix (computed) --------
 1.103  -0.001   0.040   0.610;
-0.048  -0.095   1.097  -22.130;
-0.005  -0.945  -0.084  -12.686;
 0.000   0.000   0.000   1.000;
---------------------------------------
---- Input registration matrix --------
 1.103  -0.001   0.040   0.610;
-0.048  -0.095   1.097  -22.130;
-0.005  -0.945  -0.084  -12.686;
 0.000   0.000   0.000   1.000;
Determinant 1.15433
subject = bert
RegMat ---------------------------
 1.103  -0.001   0.040   0.610;
-0.048  -0.095   1.097  -22.130;
-0.005  -0.945  -0.084  -12.686;
 0.000   0.000   0.000   1.000;
Cleaning up
 
Started at Wed Jun 19 20:41:18 CST 2013 
Ended   at Wed Jun 19 20:41:48 CST 2013
 
fslregister Done
 
To check results, run:
tkregister2 --mov fbert1.feat/reg/standard.nii.gz --reg fbert1.feat/reg/freesurfer/anat2std.register.dat --surf orig
 
mri_matrix_multiply -im fbert1.feat/reg/freesurfer/anat2exf.register.dat -iim fbert1.feat/reg/freesurfer/anat2std.register.dat -om fbert1.feat/reg/freesurfer/exf2std.register.dat
tkregister2_cmdl --targ fbert1.feat/reg/standard.nii.gz --mov fbert1.feat/example_func.nii.gz --reg fbert1.feat/reg/freesurfer/exf2std.register.dat --fslregout fbert1.feat/reg/freesurfer/example_func2standard.mat --noedit
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
target  volume fbert1.feat/reg/standard.nii.gz
movable volume fbert1.feat/example_func.nii.gz
reg file       fbert1.feat/reg/freesurfer/exf2std.register.dat
LoadVol        0
ZeroCRAS       0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
ERROR: reading fbert1.feat/reg/freesurfer/exf2std.register.dat
mri_matrix_multiply -im fbert1.feat/reg/freesurfer/anat2std.register.dat -iim fbert1.feat/reg/freesurfer/anat2exf.register.dat -om fbert1.feat/reg/freesurfer/std2exf.register.dat
-------------------------------------------------------
tkregister2_cmdl --s bert --targ /usr/local/freesurfer/subjects/bert/mri/brainmask.mgz --mov fbert1.feat/reg/standard.nii.gz --reg fbert1.feat/reg/freesurfer/anat2std.register.dat --fslregout fbert1.feat/reg/freesurfer/std2anat.fsl.mat --noedit
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
target  volume /usr/local/freesurfer/subjects/bert/mri/brainmask.mgz
movable volume fbert1.feat/reg/standard.nii.gz
reg file       fbert1.feat/reg/freesurfer/anat2std.register.dat
LoadVol        0
ZeroCRAS       0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
---- Input registration matrix --------
 1.103  -0.001   0.040   0.610;
-0.048  -0.095   1.097  -22.130;
-0.005  -0.945  -0.084  -12.686;
 0.000   0.000   0.000   1.000;
float2int = 0
---------------------------------------
INFO: loading target /usr/local/freesurfer/subjects/bert/mri/brainmask.mgz
Ttarg: --------------------
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
INFO: loading movable fbert1.feat/reg/standard.nii.gz
Tmov: --------------------
-2.000   0.000   0.000   91.000;
 0.000   0.000   2.000  -91.000;
 0.000  -2.000   0.000   109.000;
 0.000   0.000   0.000   1.000;
mkheaderreg = 0, float2int = 0
---- Input registration matrix --------
 1.103  -0.001   0.040   0.610;
-0.048  -0.095   1.097  -22.130;
-0.005  -0.945  -0.084  -12.686;
 0.000   0.000   0.000   1.000;
Determinant 1.15433
subject = bert
RegMat ---------------------------
 1.103  -0.001   0.040   0.610;
-0.048  -0.095   1.097  -22.130;
-0.005  -0.945  -0.084  -12.686;
 0.000   0.000   0.000   1.000;
FSLOUTPUTTYPE NIFTI_GZ 
tkreg2FSL: mov det = -8, ref det = -1
To visually check your results, run:
tkregister2 --s bert --mov fbert1.feat/example_func.nii.gz --reg fbert1.feat/reg/freesurfer/anat2exf.register.dat --fslreg fbert1.feat/reg/freesurfer/exf2anat.fsl.mat --surf orig --tag
Wed Jun 19 20:41:50 CST 2013
reg-feat2anat done


--
Zhiwei Wang（王志伟）, Graduate Student
Laboratory of Brain Imaging
Institute of Neuroscience
Chinese Academy of Sciences
320 Yue-Yang Road， ION Building 313
Shanghai 200031,China








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