Hi All,
I have a similar error, which I traced back (I think!) to bbregister
failing to write FLAIRraw.lta. My only solution was to download the subject
directories from our linux (RedHat) cluster and run the registration on an
OSX binary. This then creates the .lta file and I upload it back to the
linux cluster to run -FLAIRpial which creates the FLAIR.mgz volume. Weird,
I know!
Kind regards,
- Charles
On 18 April 2013 03:15, Nick Schmansky <ni...@nmr.mgh.harvard.edu> wrote:
> Eduard,
>
> Can you send the whole recon-all.log file? The error show below is a
> strange one. It appears as if the string "ERROR: could not determine
> file" is the input to mri_convert, and I'm not sure how that can happen.
>
> Also double check (by viewing in freeview) that T2raw.mgz is a valid
> file (ie, looks like a T2-space brain).
>
> and perhaps send output of:
>
> mri_info b0_mricron_20120529_152032DTI32DirSENSEs601a1000.nii
>
> Nick
>
>
> On Wed, 2013-04-17 at 13:04 +0000, Eduard Vilaplana Martinez wrote:
> > Dear FreeSurfer experts,
> >
> > First of all, congrats for this new 5.2 stable version.
> >
> > My name is Eduard, and I'm trying to perform de T2 pial refinement in a
> pre-processed subject with the B0 image from a DTI. I used that command:
> >
> >
> > recon-all -autorecon3 -T2pial -s ACC019/ -T2
> /home/linux/Escritorio/COHORTE_T2/b0_mricron_20120529_152032DTI32DirSENSEs601a1000.nii
> >
> > Being "ACC019" the subject ID and
> "/home/linux/Escritorio/COHORTE_T2/b0_mricron_20120529_152032DTI32DirSENSEs601a1000.nii"
> the path to the T2 nifti.
> >
> > Whatever I do, it always return me the following error. Any suggestions
> would be greatly appreciated. Thanks in advance.
> >
> >
> > @# Refine Pial Surfs w/ T2/FLAIR Wed Apr 17 14:37:42 CEST 2013
> >
> > bbregister --s ACC019 --mov
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz --lta
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta
> --init-fsl --T2
> >
> > Log file is
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat.log
> > Wed Apr 17 14:37:42 CEST 2013
> >
> > setenv SUBJECTS_DIR /home/linux/Escritorio/COHORTE_T2
> > cd /home/linux/Escritorio/COHORTE_T2/ACC019/scripts
> > /usr/local/freesurfer/bin/bbregister --s ACC019 --mov
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz --lta
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta
> --init-fsl --T2
> >
> > $Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $
> > Linux linux-To-be-filled-by-O-E-M 3.2.0-40-generic #64-Ubuntu SMP Mon
> Mar 25 21:22:10 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
> > FREESURFER_HOME /usr/local/freesurfer
> > mri_convert /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii
> > mri_convert /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii
> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> > reading from
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz...
> > TR=10800.00, TE=0.00, TI=0.00, flip angle=0.00
> > i_ras = (-0.996796, 0.0725774, -0.0336276)
> > j_ras = (0.065149, 0.980551, 0.185135)
> > k_ras = (-0.0464102, -0.182351, 0.982138)
> > writing to
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii...
> > fslregister --s ACC019 --mov
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii
> --reg
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat
> --niters 1 --maxangle 90 --nobetmov --tmp
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister
> --dof 6 --fsvol brainmask
> >
> > Log file is
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fslregister.log
> >
> > Wed Apr 17 14:37:42 CEST 2013
> > --s ACC019 --mov
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii
> --reg
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat
> --niters 1 --maxangle 90 --nobetmov --tmp
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister
> --dof 6 --fsvol brainmask
> > $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
> > linux-To-be-filled-by-O-E-M
> > Linux linux-To-be-filled-by-O-E-M 3.2.0-40-generic #64-Ubuntu SMP Mon
> Mar 25 21:22:10 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
> > nIters 1
> > --------------------------------------
> > /home/linux/Escritorio/COHORTE_T2/ACC019/scripts
> > mri_convert ERROR: could not determine file for
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/ERROR:
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii
> > mri_convert ERROR: could not determine file for
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/ERROR:
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii
> >
> > mri_convert: extra arguments ("not" and following)
> >
> > type mri_convert -u for usage
> >
> > --------------------------------------
> > /home/linux/Escritorio/COHORTE_T2/ACC019/scripts
> > mri_convert
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii
> --frame 0
> > mri_convert
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/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
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii...
> > TR=10800.00, TE=0.00, TI=0.00, flip angle=0.00
> > i_ras = (-0.996796, 0.0725774, -0.0336276)
> > j_ras = (0.065149, 0.980551, 0.185135)
> > k_ras = (-0.0464102, -0.182351, 0.982138)
> > keeping frame 0
> > writing to
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii...
> > Mov determinant is -5.12001
> > /home/linux/Escritorio/COHORTE_T2/ACC019/scripts
> > tkregister2_cmdl --mov
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii
> --reg
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/reg0.6003.dat
> --regheader --fslregout
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fsl.mat0
> --s ACC019 --noedit
> > tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
> > INFO: no target volume specified, assuming FreeSurfer orig volume.
> > target volume orig
> > movable volume
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii
> > reg file
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/reg0.6003.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
> /home/linux/Escritorio/COHORTE_T2/ACC019/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
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii
> > Tmov: --------------------
> > -1.600 0.000 0.000 128.000;
> > 0.000 0.000 2.000 -80.000;
> > 0.000 -1.600 0.000 128.000;
> > 0.000 0.000 0.000 1.000;
> > mkheaderreg = 1, float2int = 0
> > Computing reg from header (and possibly input matrix)
> > ---- Input registration matrix (computed) --------
> > 0.997 -0.073 0.034 0.214;
> > -0.046 -0.182 0.982 -30.911;
> > -0.065 -0.981 -0.185 1.512;
> > 0.000 0.000 0.000 1.000;
> > ---------------------------------------
> > ---- Input registration matrix --------
> > 0.997 -0.073 0.034 0.214;
> > -0.046 -0.182 0.982 -30.911;
> > -0.065 -0.981 -0.185 1.512;
> > 0.000 0.000 0.000 1.000;
> > Determinant 1
> > subject = ACC019
> > RegMat ---------------------------
> > 0.997 -0.073 0.034 0.214;
> > -0.046 -0.182 0.982 -30.911;
> > -0.065 -0.981 -0.185 1.512;
> > 0.000 0.000 0.000 1.000;
> > FSLOUTPUTTYPE NIFTI
> > tkreg2FSL: mov det = -5.12001, ref det = -1
> > Wed Apr 17 14:37:44 CEST 2013
> > /home/linux/Escritorio/COHORTE_T2/ACC019/scripts
> > flirt.fsl -ref
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii
> -in
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii
> -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz
> -90 90 -verbose 0 -omat
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/fslmat0.trans.mat
> -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fsl.mat0
> > ** ERROR (nifti_image_read): failed to find header file for
> '/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister'
> > ** ERROR:
> nifti_image_open(/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister):
> bad header info
> > ERROR: failed to open file
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister
> > ERROR: Could not open image
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister
> > Image Exception : #22 :: Failed to read volume
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii
> > terminate called after throwing an instance of
> 'RBD_COMMON::BaseException'
> > Abort (core dumped)
> > Wed Apr 17 14:37:44 CEST 2013
> > /home/linux/Escritorio/COHORTE_T2/ACC019/scripts
> > flirt.fsl -ref
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii
> -in
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii
> -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz
> -90 90 -verbose 0 -omat
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fsl.mat
> -init
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/fslmat0.trans.mat
> -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch
> > ** ERROR (nifti_image_read): failed to find header file for
> '/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister'
> > ** ERROR:
> nifti_image_open(/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister):
> bad header info
> > ERROR: failed to open file
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister
> > ERROR: Could not open image
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister
> > Image Exception : #22 :: Failed to read volume
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii
> > terminate called after throwing an instance of
> 'RBD_COMMON::BaseException'
> > Abort (core dumped)
> > tkregister2_cmdl --s ACC019 --mov
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii
> --reg
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat
> --fslreg
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fsl.mat
> --noedit
> > tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
> > ERROR: cannot open
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fsl.mat
> > cat:
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat:
> No such file or directory
> > tmp: Subscript out of range.
> >
> > Started at Wed Apr 17 14:37:42 CEST 2013
> > Ended at Wed Apr 17 14:37:44 CEST 2013
> >
> > fslregister Done
> >
> > To check results, run:
> > tkregister2 --mov
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii
> --reg
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat
> --surf orig
> >
> > mri_segreg --mov
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii
> --init-reg
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat
> --out-reg
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/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
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat
> > mri_segreg --mov
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii
> --init-reg
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/bbr.pass1.dat
> --out-reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat
> --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d
> 1e-3 --c0 0 --mincost
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat.mincost
> --dof 6 --nmax 36 --param
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat.param
> --surf white --cur-reg
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/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
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/bbr.pass1.dat
> > tkregister2_cmdl --mov
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz --reg
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat --noedit
> --ltaout /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta
> > regio_read_register(): No such file or directory
> > Could not open
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat
> > tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
> > INFO: no target volume specified, assuming FreeSurfer orig volume.
> > target volume orig
> > movable volume
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz
> > reg file
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.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
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat
> > Cleaning up
> >
> > Started at Wed Apr 17 14:37:42 CEST 2013
> > Ended at Wed Apr 17 14:37:45 CEST 2013
> > BBR-Run-Time-Sec 3
> >
> > bbregister Done
> > To check results, run:
> > tkregister2 --mov
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz --reg
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat --surf
> >
> >
> > mri_convert -at
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta -rl
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig.mgz
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/T2.mgz
> >
> > mri_convert -at
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta -rl
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig.mgz
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/T2.mgz
> >
> ltaReadFile(/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta):
> can't open file
> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> > reading from
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz...
> > TR=10800.00, TE=0.00, TI=0.00, flip angle=0.00
> > i_ras = (-0.996796, 0.0725774, -0.0336276)
> > j_ras = (0.065149, 0.980551, 0.185135)
> > k_ras = (-0.0464102, -0.182351, 0.982138)
> > INFO: Reading transformation from file
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta...
> > Reading transform with LTAreadEx()
> > No such file or directory
> > ERROR: Reading transform from file
> /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta
> > Linux linux-To-be-filled-by-O-E-M 3.2.0-40-generic #64-Ubuntu SMP Mon
> Mar 25 21:22:10 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
> >
> > recon-all -s ACC019 exited with ERRORS at Wed Apr 17 14:37:45 CEST 2013
> >
> > For more details, see the log file
> /home/linux/Escritorio/COHORTE_T2/ACC019/scripts/recon-all.log
> > To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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> but does not contain patient information, please contact the sender and
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>
>
--
*Charles Malpas *
Master of Psychology (Clinical Neuropsychology) / PhD Candidate
Melbourne School of Psychological Sciences & Department of Medicine (RMH)
The University of Melbourne 3010
*Melbourne Brain Centre @ RMH*
Neuropsychiatry Research Group* *
Level 4, Main Building, Royal Melbourne Hospital
Phone: 0451 116 434
Email: c.mal...@student.unimelb.edu.au
Skype: charles.malpas
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