On Wed, Mar 27, 2013 at 3:32 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu> wrote:
Hi Corinna, are you sure that the mri-in-hardi.nii.reg registration is accurate? the following should look in register:
tkregister2 --reg mri-in-hardi.nii.reg --mov mri-in-hardi.nii --surfs
doug
On 03/25/2013 06:09 PM, Corinna Bauer wrote:
I am trying to get the V1 label to map onto my HARDI data, however, the mri_label2vol registration is off. The label ends up in the brainstem rather than V1. the V1 labels are in the proper location when I use orig.mgz, but when I used the output from mri_vol2vol as the mri-in-hardi or the hardi itself as the temp image, the location of the label is off.
mri_label2vol --label label/rh.V1.label --label label/lh.V1.label --temp mri-in-hardi.nii --reg mri-in-hardi.nii.reg --o lindsay_v1.nii
On Mon, Mar 25, 2013 at 4:05 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
yep, looks right
On 03/25/2013 03:12 PM, Corinna Bauer wrote:
Also, I now want to apply the inverse transform to move the T1
into the HARDI space. Did I do this correctly? It looks good
in tkregister.
mri_vol2vol --mov hardi/ffiltered_func_data_01.nii.gz --targ
mri/orig.mgz --reg register.dat --inv --o mri-in-hardi.nii
On Mon, Mar 25, 2013 at 1:47 PM, Corinna Bauer
<corinnab83@gmail.com <mailto:corinnab83@gmail.com>
<mailto:corinnab83@gmail.com <mailto:corinnab83@gmail.com>>>
wrote:
ahhh, yes, that's it. sorry my oversight.
On Mon, Mar 25, 2013 at 1:45 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>> wrote:
Are you sure you made the right edit? It should be
"--fsvol
$fsvol.mgz" It looks like you might have changed it to
"--fsvol.mgz $fsvol"
On 03/25/2013 01:30 PM, Corinna Bauer wrote:
Ok I adjusted the bbregister file to say fsvol.mgz
in the
location you specified and got this error a bit
later on
in the bbregister output:
setenv SUBJECTS_DIR
/usr/local/freesurfer/subjects/symmetry
cd /usr/local/freesurfer/subjects/symmetry/lindsay
/usr/local/freesurfer/bin/bbregister --s lindsay --mov
hardi/ffiltered_func_data_01.nii.gz --dti
--init-fsl --reg
register.dat
$Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22
mreuter Exp $
Linux lotfi 3.2.0-38-generic #61-Ubuntu SMP Tue Feb 19
12:18:21 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /usr/local/freesurfer
mri_convert hardi/ffiltered_func_data_01.nii.gz
./tmp.bbregister.15807/template.nii
mri_convert hardi/ffiltered_func_data_01.nii.gz
./tmp.bbregister.15807/template.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16
mreuter
Exp $
reading from hardi/ffiltered_func_data_01.nii.gz...
TR=17843.91, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.991204, -0.025762, 0.129811)
j_ras = (-0.0259819, 0.999662, 0)
k_ras = (0.129768, 0.00337275, 0.991539)
writing to ./tmp.bbregister.15807/template.nii...
fslregister --s lindsay --mov
./tmp.bbregister.15807/template.nii --reg
./tmp.bbregister.15807/reg.init.dat --niters 1
--maxangle
90 --nobetmov --tmp ./tmp.bbregister.15807/fslregister
--dof 6 --fsvol.mgz brainmask
ERROR: Flag --fsvol.mgz unrecognized.
--s lindsay --mov ./tmp.bbregister.15807/template.nii
--reg ./tmp.bbregister.15807/reg.init.dat --niters 1
--maxangle 90 --nobetmov --tmp
./tmp.bbregister.15807/fslregister --dof 6 --fsvol.mgz
brainmask
mri_segreg --mov ./tmp.bbregister.15807/template.nii
--init-reg ./tmp.bbregister.15807/reg.init.dat
--out-reg
./tmp.bbregister.15807/bbr.pass1.dat
--subsamp-brute 100
--subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4
--surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5
regio_read_register(): No such file or directory
Could not open ./tmp.bbregister.15807/reg.init.dat
mri_segreg --mov ./tmp.bbregister.15807/template.nii
--init-reg ./tmp.bbregister.15807/bbr.pass1.dat
--out-reg
register.dat --brute -0.1 0.1 0.1 --interp trilinear
--wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0
--mincost
register.dat.mincost --dof 6 --nmax 36 --param
register.dat.param --surf white --cur-reg
./tmp.bbregister.15807/reg.curopt.dat
--gm-proj-frac 0.5
--nsub 1 --gm-gt-wm 0.5
regio_read_register(): No such file or directory
Could not open ./tmp.bbregister.15807/bbr.pass1.dat
Cleaning up
Started at Mon Mar 25 13:24:53 EDT 2013
Ended at Mon Mar 25 13:25:00 EDT 2013
BBR-Run-Time-Sec 7
bbregister Done
To check results, run:
tkregister2 --mov hardi/ffiltered_func_data_01.nii.gz
--reg register.dat --surf
On Mon, Mar 25, 2013 at 1:22 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>> wrote:
Corinna, can you edit
$FREESURFER_HOME/bin/bbregister?
If so,
change the following line
From
set cmd = (fslregister --s $subject --mov
$regvol
--reg $InitReg \
--niters 1 --maxangle 90 --tmp
$tmpdir/fslregister \
--dof $FSLDOF --fsvol $fsvol)
To
set cmd = (fslregister --s $subject --mov
$regvol
--reg $InitReg \
--niters 1 --maxangle 90 --tmp
$tmpdir/fslregister \
--dof $FSLDOF --fsvol $fsvol.mgz)
It is just the very last part that is changed
where I
added ".mgz"
to $fsvol
Re-run bbregister and let me know if this works.
doug
On 03/25/2013 01:11 PM, Corinna Bauer wrote:
yes, this file exists.
On Mon, Mar 25, 2013 at 1:10 PM, Douglas N
Greve
<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>>> wrote:
Can you verify that
/usr/local/freesurfer/subjects/symmetry/lindsay/mri/brainmask.mgz
exists?
doug
On 03/25/2013 12:55 PM, Corinna Bauer
wrote:
sure. Here is the dng.log.
Corinna
On Mon, Mar 25, 2013 at 12:45 PM,
Douglas
N Greve
<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>>>> wrote:
Hi Corinna, can you run
fslregister --debug --s
lindsay --mov
hardi/ffiltered_func_data_01.nii.gz --reg fsl.reg.dat
--niters 1
--maxangle 90 --nobetmov --tmp
./tmp.fslregister
--dof 6
--fsvol
brainmask |& tee dng.log
and send me the dng.log?
doug
On 03/25/2013 12:39 PM,
Corinna Bauer
wrote:
> Hello all,
>
> I am attempting to run
bbregister on
4D HARDI
data that
has already
> been motion, eddy, and
epi-distortion corrected
in fsl.
I run
the command:
> bbregister --s lindsay --mov
hardi/ffiltered_func_data_01.nii.gz
--dti
> --init-fsl --reg
register.dat and
get a number
of errors
that
seem to
> begin in the mri_convert
section as
seen below.
> Any insight?
>
> Cheers,
> Corinna
>
> FREESURFER_HOME
/usr/local/freesurfer
> mri_convert
hardi/ffiltered_func_data_01.nii.gz
>
./tmp.bbregister.15356/template.nii
> mri_convert
hardi/ffiltered_func_data_01.nii.gz
>
./tmp.bbregister.15356/template.nii
> $Id: mri_convert.c,v 1.179.2.7
2012/09/05 21:55:16
mreuter Exp $
> reading from
hardi/ffiltered_func_data_01.nii.gz...
> TR=17843.91, TE=0.00,
TI=0.00, flip
angle=0.00
> i_ras = (-0.991204,
-0.025762, 0.129811)
> j_ras = (-0.0259819,
0.999662, 0)
> k_ras = (0.129768,
0.00337275, 0.991539)
> writing to
./tmp.bbregister.15356/template.nii...
> fslregister --s lindsay --mov
./tmp.bbregister.15356/template.nii
> --reg
./tmp.bbregister.15356/reg.init.dat --niters 1
--maxangle 90
> --nobetmov --tmp
./tmp.bbregister.15356/fslregister
--dof 6 --fsvol
> brainmask
>
> Log file is
./tmp.bbregister.15356/reg.init.dat.fslregister.log
>
> Mon Mar 25 12:22:23 EDT 2013
> --s lindsay --mov
./tmp.bbregister.15356/template.nii --reg
>
./tmp.bbregister.15356/reg.init.dat
--niters 1
--maxangle 90
> --nobetmov --tmp
./tmp.bbregister.15356/fslregister
--dof 6 --fsvol
> brainmask
> $Id: fslregister,v 1.34.2.2
2012/11/08 16:18:56
greve Exp $
> lotfi
> Linux lotfi 3.2.0-38-generic
#61-Ubuntu SMP Tue
Feb 19
12:18:21 UTC
> 2013 x86_64 x86_64 x86_64
GNU/Linux
> nIters 1
>
--------------------------------------
>
/usr/local/freesurfer/subjects/symmetry/lindsay
> mri_convert ERROR: could not
determine file for
>
/usr/local/freesurfer/subjects/symmetry/lindsay/mri/ERROR:
>
./tmp.bbregister.15356/fslregister/refvol.fslregister.nii
> mri_convert ERROR: could not
determine file for
>
/usr/local/freesurfer/subjects/symmetry/lindsay/mri/ERROR:
>
./tmp.bbregister.15356/fslregister/refvol.fslregister.nii
>
> mri_convert: extra arguments
("not"
and following)
>
> type mri_convert -u for usage
>
>
--------------------------------------
>
/usr/local/freesurfer/subjects/symmetry/lindsay
> mri_convert
./tmp.bbregister.15356/template.nii
>
./tmp.bbregister.15356/fslregister/movvol.fslregister.nii
--frame 0
> mri_convert
./tmp.bbregister.15356/template.nii
>
./tmp.bbregister.15356/fslregister/movvol.fslregister.nii
--frame 0
> $Id: mri_convert.c,v 1.179.2.7
2012/09/05 21:55:16
mreuter Exp $
> reading from
./tmp.bbregister.15356/template.nii...
> TR=17843.91, TE=0.00,
TI=0.00, flip
angle=0.00
> i_ras = (-0.991204,
-0.025762, 0.129811)
> j_ras = (-0.0259819,
0.999662, 0)
> k_ras = (0.129768,
0.00337275, 0.991539)
> keeping frame 0
> writing to
./tmp.bbregister.15356/fslregister/movvol.fslregister.nii...
> Mov determinant is -6.125
>
/usr/local/freesurfer/subjects/symmetry/lindsay
> tkregister2_cmdl --mov
>
./tmp.bbregister.15356/fslregister/movvol.fslregister.nii
--reg
>
./tmp.bbregister.15356/fslregister/reg0.15393.dat
--regheader
> --fslregout
./tmp.bbregister.15356/reg.init.dat.fsl.mat0
--s lindsay
> --noedit
> tkregister_tcl
/usr/local/freesurfer/tktools/tkregister2.tcl
> INFO: no target volume
specified,
assuming
FreeSurfer
orig volume.
> target volume orig
> movable volume
./tmp.bbregister.15356/fslregister/movvol.fslregister.nii
> reg file
./tmp.bbregister.15356/fslregister/reg0.15393.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/symmetry/lindsay/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
>
./tmp.bbregister.15356/fslregister/movvol.fslregister.nii
> Tmov: --------------------
> -1.750 0.000 0.000 112.000;
> 0.000 0.000 2.000 -60.000;
> 0.000 -1.750 0.000 112.000;
> 0.000 0.000 0.000 1.000;
> mkheaderreg = 1, float2int = 0
> Computing reg from header (and
possibly input
matrix)
> ---- Input registration matrix
(computed) --------
> 0.991 0.026 -0.130 2.508;
> 0.130 0.003 0.992 -30.941;
> 0.026 -1.000 -0.000 1.279;
> 0.000 0.000 0.000 1.000;
>
---------------------------------------
> ---- Input registration
matrix --------
> 0.991 0.026 -0.130 2.508;
> 0.130 0.003 0.992 -30.941;
> 0.026 -1.000 -0.000 1.279;
> 0.000 0.000 0.000 1.000;
> Determinant 1
> subject = lindsay
> RegMat
---------------------------
> 0.991 0.026 -0.130 2.508;
> 0.130 0.003 0.992 -30.941;
> 0.026 -1.000 -0.000 1.279;
> 0.000 0.000 0.000 1.000;
> FSLOUTPUTTYPE NIFTI
> tkreg2FSL: mov det = -6.125,
ref det
= -1
> Mon Mar 25 12:22:34 EDT 2013
>
/usr/local/freesurfer/subjects/symmetry/lindsay
> flirt.fsl -ref
>
./tmp.bbregister.15356/fslregister/refvol.fslregister.nii -in
>
./tmp.bbregister.15356/fslregister/movvol.fslregister.nii
-bins 256
> -cost corratio -dof 6
-searchrx -90
90 -searchry
-90 90
-searchrz -90
> 90 -verbose 0 -omat
>
./tmp.bbregister.15356/fslregister/fslmat0.trans.mat
-schedule
>
/usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init
>
./tmp.bbregister.15356/reg.init.dat.fsl.mat0
> ** ERROR (nifti_image_read):
failed
to find
header file for
>
'./tmp.bbregister.15356/fslregister/refvol.fslregister'
> ** ERROR:
>
nifti_image_open(./tmp.bbregister.15356/fslregister/refvol.fslregister):
> bad header info
> ERROR: failed to open file
>
./tmp.bbregister.15356/fslregister/refvol.fslregister
> ERROR: Could not open image
>
./tmp.bbregister.15356/fslregister/refvol.fslregister
> Image Exception : #22 ::
Failed to
read volume
>
./tmp.bbregister.15356/fslregister/refvol.fslregister.nii
> terminate called after
throwing an
instance of
'RBD_COMMON::BaseException'
> Abort (core dumped)
> Mon Mar 25 12:22:34 EDT 2013
>
/usr/local/freesurfer/subjects/symmetry/lindsay
> flirt.fsl -ref
>
./tmp.bbregister.15356/fslregister/refvol.fslregister.nii -in
>
./tmp.bbregister.15356/fslregister/movvol.fslregister.nii
-bins 256
> -cost corratio -dof 6
-searchrx -90
90 -searchry
-90 90
-searchrz -90
> 90 -verbose 0 -omat
./tmp.bbregister.15356/reg.init.dat.fsl.mat
-init
>
./tmp.bbregister.15356/fslregister/fslmat0.trans.mat
-schedule
>
/usr/local/freesurfer/bin/flirt.newdefault.20080811.sch
> ** ERROR (nifti_image_read):
failed
to find
header file for
>
'./tmp.bbregister.15356/fslregister/refvol.fslregister'
> ** ERROR:
>
nifti_image_open(./tmp.bbregister.15356/fslregister/refvol.fslregister):
> bad header info
> ERROR: failed to open file
>
./tmp.bbregister.15356/fslregister/refvol.fslregister
> ERROR: Could not open image
>
./tmp.bbregister.15356/fslregister/refvol.fslregister
> Image Exception : #22 ::
Failed to
read volume
>
./tmp.bbregister.15356/fslregister/refvol.fslregister.nii
> terminate called after
throwing an
instance of
'RBD_COMMON::BaseException'
> Abort (core dumped)
> tkregister2_cmdl --s lindsay
--mov
./tmp.bbregister.15356/template.nii
> --reg
./tmp.bbregister.15356/reg.init.dat --fslreg
>
./tmp.bbregister.15356/reg.init.dat.fsl.mat --noedit
> tkregister_tcl
/usr/local/freesurfer/tktools/tkregister2.tcl
> ERROR: cannot open
./tmp.bbregister.15356/reg.init.dat.fsl.mat
> cat:
./tmp.bbregister.15356/reg.init.dat: No
such file
or directory
> tmp: Subscript out of range.
>
> Started at Mon Mar 25
12:22:23 EDT 2013
> Ended at Mon Mar 25
12:22:34 EDT 2013
>
> fslregister Done
>
> To check results, run:
> tkregister2 --mov
./tmp.bbregister.15356/template.nii --reg
>
./tmp.bbregister.15356/reg.init.dat
--surf orig
>
> mri_segreg --mov
./tmp.bbregister.15356/template.nii
--init-reg
>
./tmp.bbregister.15356/reg.init.dat
--out-reg
>
./tmp.bbregister.15356/bbr.pass1.dat
--subsamp-brute 100
--subsamp 100
> --tol 1e-4 --tol1d 1e-3
--brute -4 4
4 --surf white
--gm-proj-frac 0.5
> --gm-gt-wm 0.5
> regio_read_register(): No
such file
or directory
> Could not open
./tmp.bbregister.15356/reg.init.dat
> mri_segreg --mov
./tmp.bbregister.15356/template.nii
--init-reg
>
./tmp.bbregister.15356/bbr.pass1.dat
--out-reg
register.dat --brute
> -0.1 0.1 0.1 --interp trilinear
--wm-proj-abs 2
--tol
1e-8 --tol1d
> 1e-3 --c0 0 --mincost
register.dat.mincost --dof 6
--nmax 36 --param
> register.dat.param --surf white
--cur-reg
>
./tmp.bbregister.15356/reg.curopt.dat
--gm-proj-frac 0.5
--nsub 1
> --gm-gt-wm 0.5
> regio_read_register(): No
such file
or directory
> Could not open
./tmp.bbregister.15356/bbr.pass1.dat
> Cleaning up
>
> Started at Mon Mar 25
12:22:16 EDT 2013
> Ended at Mon Mar 25
12:22:34 EDT 2013
> BBR-Run-Time-Sec 18
>
> bbregister Done
> To check results, run:
> tkregister2 --mov
hardi/ffiltered_func_data_01.nii.gz --reg
> register.dat --surf
>
>
>
>
>
>
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>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
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<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>>>
Phone Number: 617-724-2358
<tel:617-724-2358>
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<tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358
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<tel:617-724-2358 <tel:617-724-2358>>
<tel:617-724-2358 <tel:617-724-2358>
<tel:617-724-2358 <tel:617-724-2358>>>>
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<tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>
<tel:617-724-2358 <tel:617-724-2358>
<tel:617-724-2358 <tel:617-724-2358>>> <tel:617-724-2358
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<tel:617-724-2358 <tel:617-724-2358>>
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<tel:617-724-2358 <tel:617-724-2358>>>>>
Fax: 617-726-7422
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<tel:617-726-7422 <tel:617-726-7422>
<tel:617-726-7422 <tel:617-726-7422>>>> <tel:617-726-7422
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<tel:617-726-7422 <tel:617-726-7422>>
<tel:617-726-7422 <tel:617-726-7422>
<tel:617-726-7422 <tel:617-726-7422>>>
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<tel:617-726-7422 <tel:617-726-7422>
<tel:617-726-7422 <tel:617-726-7422>>>>>