Re: [Freesurfer] dcmunpack Error

[Maryam Tayebi]

External Email - Use Caution

Dear Greve,
Thank you so much. It s finally fixed and now is working properly.

Regards

On Fri, 9 Nov 2018 at 02:50, Greve, Douglas N.,Ph.D. 
wrote:

> It actually looks like it completed and created the desired output file.
> Did you check it? Those errors are generated because it is trying to
> figure out whether the file is a diffusion scan. You can turn it off by
> setting
> setenv FS_LOAD_DWI 0
> or for bash
> export FS_LOAD_DWI=0
>
>
> On 11/07/2018 09:55 PM, Maryam Tayebi wrote:
> >
> > External Email - Use Caution
> >
> > I tried this way, but I got lots of errors, as the attached file. What
> > is the problem? Is there anything wrong with my data? Because I am
> > using the online databases which I think it might be back to 2009 ish.
> >
> > Thanks
> >
> > On Thu, 8 Nov 2018 at 11:55, Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> > You have to specify an output directory with -targ and the runs
> > you want
> > to unpack with -run. See the help (ie, run dcmunpack with -help)
> >
> > On 11/07/2018 05:38 PM, Maryam Tayebi wrote:
> > >
> > > External Email - Use Caution
> > >
> > > Hello Freesurfer Developers,
> > > I was going to reconstruct MPRAGE images from GE 3T machine.
> > > First I used this command:
> > > /dcmunpack -src . -scanonly scan.log/
> > >
> > > It made just /scan.log/ file for me. Then I used this command:
> > > /unpacksdcmdir -src / -targ  > directory>
> > > -scanonly scan.log/
> > >
> > > However, it made 3 files for me; dicomdir.sumfile, parse.status and
> > > unpack.log, but they were 0 bites. Furthermore, the following
> > message
> > > also appeared on the terminal:
> > >
> > > /ERROR: parsing /hpc/mtay316/tutorial4/practice_with_data/dicoms/
> > > See logfile
> > /hpc/mtay316/tutorial4/practice_with_data//unpack.log for
> > > more details/
> > >
> > > I used this command for SIEMENS data and it worked. Apparently this
> > > code just works on SIEMENS data not GE. So now what is the code
> > that I
> > > can use for GE dcm images?
> > >
> > > 1) FREESURFER Version:
> > > freesurfer-x86_64-unknown-linux-gnu-stable6-20170118
> > > 2) Platform: Ubuntu 16.04 LTS
> > > 3) unpack.log : see attached
> > >
> > > Regards
> > >
> > >
> > > --
> > > *Maryam Tayebi*
> > >
> > > PhD Candidate of Bioengineering
> > > Auckland Bioengineering Institute, University of Auckland,
> > Auckland,
> > > New Zealand
> > >
> > >
> > >
> > > MSc of Medical Imaging
> > > University of Manchester, Manchester, UK
> > >
> > >
> > > ___
> > > 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  Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
> > --
> > *Maryam Tayebi*
> >
> > PhD Candidate of Bioengineering
> > Auckland Bioengineering Institute, University of Auckland, Auckland,
> > New Zealand
> >
> >
> >
> > MSc of Medical Imaging
> > University of Manchester, Manchester, UK
> >
> >
> > ___
> > 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



-- 
*Maryam Tayebi*

PhD Candidate of Bioengineering
Auckland Bioengineering Institute, University of Auckland, Auckland, New
Zealand



MSc of Medical Imaging
University of Manchester, Manchester, UK
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Re: [Freesurfer] dcmunpack Error

[Greve, Douglas N.,Ph.D.]

It actually looks like it completed and created the desired output file. 
Did you check it? Those errors are generated because it is trying to 
figure out whether the file is a diffusion scan. You can turn it off by 
setting
setenv FS_LOAD_DWI 0
or for bash
export FS_LOAD_DWI=0


On 11/07/2018 09:55 PM, Maryam Tayebi wrote:
>
> External Email - Use Caution
>
> I tried this way, but I got lots of errors, as the attached file. What 
> is the problem? Is there anything wrong with my data? Because I am 
> using the online databases which I think it might be back to 2009 ish.
>
> Thanks
>
> On Thu, 8 Nov 2018 at 11:55, Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> You have to specify an output directory with -targ and the runs
> you want
> to unpack with -run. See the help (ie, run dcmunpack with -help)
>
> On 11/07/2018 05:38 PM, Maryam Tayebi wrote:
> >
> > External Email - Use Caution
> >
> > Hello Freesurfer Developers,
> > I was going to reconstruct MPRAGE images from GE 3T machine.
> > First I used this command:
> > /dcmunpack -src . -scanonly scan.log/
> >
> > It made just /scan.log/ file for me. Then I used this command:
> > /unpacksdcmdir -src / -targ  directory>
> > -scanonly scan.log/
> >
> > However, it made 3 files for me; dicomdir.sumfile, parse.status and
> > unpack.log, but they were 0 bites. Furthermore, the following
> message
> > also appeared on the terminal:
> >
> > /ERROR: parsing /hpc/mtay316/tutorial4/practice_with_data/dicoms/
> > See logfile
> /hpc/mtay316/tutorial4/practice_with_data//unpack.log for
> > more details/
> >
> > I used this command for SIEMENS data and it worked. Apparently this
> > code just works on SIEMENS data not GE. So now what is the code
> that I
> > can use for GE dcm images?
> >
> > 1) FREESURFER Version:
> > freesurfer-x86_64-unknown-linux-gnu-stable6-20170118
> > 2) Platform: Ubuntu 16.04 LTS
> > 3) unpack.log : see attached
> >
> > Regards
> >
> >
> > --
> > *Maryam Tayebi*
> >
> > PhD Candidate of Bioengineering
> > Auckland Bioengineering Institute, University of Auckland,
> Auckland,
> > New Zealand
> >
> >
> >
> > MSc of Medical Imaging
> > University of Manchester, Manchester, UK
> >
> >
> > ___
> > 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
>
>
>
> -- 
> *Maryam Tayebi*
>
> PhD Candidate of Bioengineering
> Auckland Bioengineering Institute, University of Auckland, Auckland, 
> New Zealand
>
>
>
> MSc of Medical Imaging
> University of Manchester, Manchester, UK
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] dcmunpack Error

[Maryam Tayebi]

External Email - Use Caution

I tried this way, but I got lots of errors, as the attached file. What is
the problem? Is there anything wrong with my data? Because I am using the
online databases which I think it might be back to 2009 ish.

Thanks

On Thu, 8 Nov 2018 at 11:55, Greve, Douglas N.,Ph.D. 
wrote:

> You have to specify an output directory with -targ and the runs you want
> to unpack with -run. See the help (ie, run dcmunpack with -help)
>
> On 11/07/2018 05:38 PM, Maryam Tayebi wrote:
> >
> > External Email - Use Caution
> >
> > Hello Freesurfer Developers,
> > I was going to reconstruct MPRAGE images from GE 3T machine.
> > First I used this command:
> > /dcmunpack -src . -scanonly scan.log/
> >
> > It made just /scan.log/ file for me. Then I used this command:
> > /unpacksdcmdir -src / -targ 
> > -scanonly scan.log/
> >
> > However, it made 3 files for me; dicomdir.sumfile, parse.status and
> > unpack.log, but they were 0 bites. Furthermore, the following message
> > also appeared on the terminal:
> >
> > /ERROR: parsing /hpc/mtay316/tutorial4/practice_with_data/dicoms/
> > See logfile /hpc/mtay316/tutorial4/practice_with_data//unpack.log for
> > more details/
> >
> > I used this command for SIEMENS data and it worked. Apparently this
> > code just works on SIEMENS data not GE. So now what is the code that I
> > can use for GE dcm images?
> >
> > 1) FREESURFER Version:
> > freesurfer-x86_64-unknown-linux-gnu-stable6-20170118
> > 2) Platform: Ubuntu 16.04 LTS
> > 3) unpack.log : see attached
> >
> > Regards
> >
> >
> > --
> > *Maryam Tayebi*
> >
> > PhD Candidate of Bioengineering
> > Auckland Bioengineering Institute, University of Auckland, Auckland,
> > New Zealand
> >
> >
> >
> > MSc of Medical Imaging
> > University of Manchester, Manchester, UK
> >
> >
> > ___
> > 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



-- 
*Maryam Tayebi*

PhD Candidate of Bioengineering
Auckland Bioengineering Institute, University of Auckland, Auckland, New
Zealand



MSc of Medical Imaging
University of Manchester, Manchester, UK

cd /hpc_htom/mtay316/tutorial4/practice_with_data/Subj01
/hpc/mtay316/freesurfer/bin/dcmunpack -src . -targ /hpc/mtay316/tutorial4/practice_with_data/mprage -run 4 /hpc/mtay316/tutorial4/practice_with_data/Subj01/ nii.gz 1.nii.gz

$Id: dcmunpack,v 1.19.2.1 2016/08/02 21:12:01 greve Exp $
-rwxr-xr-x 1 mtay316 graduate 23759 Jan 19  2017 /hpc/mtay316/freesurfer/bin/dcmunpack
Linux bn390370 4.15.0-36-generic #39~16.04.1-Ubuntu SMP Tue Sep 25 08:59:23 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
Thu Nov  8 15:26:20 NZDT 2018
---
  1 4 /hpc/mtay316/tutorial4/practice_with_data/Subj01/ 1 0 0
---
Searching for matching files
Thu Nov  8 15:26:20 NZDT 2018
Searching .
Thu Nov  8 15:26:20 NZDT 2018
Found 177 total files.
#@# 2/177 Thu Nov  8 15:26:20 NZDT 2018
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#@# 47/177 Thu Nov  8 

Re: [Freesurfer] dcmunpack Error

[Greve, Douglas N.,Ph.D.]

You have to specify an output directory with -targ and the runs you want 
to unpack with -run. See the help (ie, run dcmunpack with -help)

On 11/07/2018 05:38 PM, Maryam Tayebi wrote:
>
> External Email - Use Caution
>
> Hello Freesurfer Developers,
> I was going to reconstruct MPRAGE images from GE 3T machine.
> First I used this command:
> /dcmunpack -src . -scanonly scan.log/
>
> It made just /scan.log/ file for me. Then I used this command:
> /unpacksdcmdir -src / -targ  
> -scanonly scan.log/
>
> However, it made 3 files for me; dicomdir.sumfile, parse.status and 
> unpack.log, but they were 0 bites. Furthermore, the following message 
> also appeared on the terminal:
>
> /ERROR: parsing /hpc/mtay316/tutorial4/practice_with_data/dicoms/
> See logfile /hpc/mtay316/tutorial4/practice_with_data//unpack.log for 
> more details/
>
> I used this command for SIEMENS data and it worked. Apparently this 
> code just works on SIEMENS data not GE. So now what is the code that I 
> can use for GE dcm images?
>
> 1) FREESURFER Version: 
> freesurfer-x86_64-unknown-linux-gnu-stable6-20170118
> 2) Platform: Ubuntu 16.04 LTS
> 3) unpack.log : see attached
>
> Regards
>
>
> -- 
> *Maryam Tayebi*
>
> PhD Candidate of Bioengineering
> Auckland Bioengineering Institute, University of Auckland, Auckland, 
> New Zealand
>
>
>
> MSc of Medical Imaging
> University of Manchester, Manchester, UK
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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[Freesurfer] dcmunpack Error

[Maryam Tayebi]

External Email - Use Caution

Hello Freesurfer Developers,
I was going to reconstruct MPRAGE images from GE 3T machine.
First I used this command:
*dcmunpack -src . -scanonly scan.log*

It made just *scan.log* file for me. Then I used this command:
*unpacksdcmdir -src / -targ 
-scanonly scan.log*

However, it made 3 files for me; dicomdir.sumfile, parse.status and
unpack.log, but they were 0 bites. Furthermore, the following message also
appeared on the terminal:


*ERROR: parsing /hpc/mtay316/tutorial4/practice_with_data/dicoms/ See
logfile /hpc/mtay316/tutorial4/practice_with_data//unpack.log for more
details*

I used this command for SIEMENS data and it worked. Apparently this code
just works on SIEMENS data not GE. So now what is the code that I can use
for GE dcm images?

1) FREESURFER Version: freesurfer-x86_64-unknown-linux-gnu-stable6-20170118
2) Platform: Ubuntu 16.04 LTS
3) unpack.log : see attached

Regards


-- 
*Maryam Tayebi*

PhD Candidate of Bioengineering
Auckland Bioengineering Institute, University of Auckland, Auckland, New
Zealand



MSc of Medical Imaging
University of Manchester, Manchester, UK
Log file created by unpacksdcmdir
$Id: unpacksdcmdir,v 1.25 2015/02/06 19:19:50 greve Exp $
/hpc/mtay316/tutorial4/practice_with_data//unpack.log
/hpc_htom/mtay316/tutorial4/practice_with_data/dicoms
Thu Nov  8 10:59:10 NZDT 2018
-src /hpc/mtay316/tutorial4/practice_with_data/dicoms/ -targ /hpc/mtay316/tutorial4/practice_with_data/ -scanonly scan.log
mri_convert.bin -all-info 
ProgramName: mri_convert.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/11/07-21:59:10-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $  User: mtay316  Machine: bn390370  Platform: Linux  PlatformVersion: 4.15.0-36-generic  CompilerName: GCC  CompilerVersion: 40400 
bn390370
Linux bn390370 4.15.0-36-generic #39~16.04.1-Ubuntu SMP Tue Sep 25 08:59:23 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
SkipMoCo 0
dicomdir /hpc/mtay316/tutorial4/practice_with_data/dicoms/
Scanning source directory ...
INFO: summary file is /hpc/mtay316/tutorial4/practice_with_data//dicomdir.sumfile
INFO: status file is /hpc/mtay316/tutorial4/practice_with_data//parse.status
mri_parse_sdcmdir --sortbyrun --d /hpc/mtay316/tutorial4/practice_with_data/dicoms/ --o /hpc/mtay316/tutorial4/practice_with_data//dicomdir.sumfile --status /hpc/mtay316/tutorial4/practice_with_data//parse.status
INFO: scanning path to Siemens DICOM DIR:
   /hpc/mtay316/tutorial4/practice_with_data/dicoms
INFO: Found 175 files in /hpc/mtay316/tutorial4/practice_with_data/dicoms
INFO: counting Siemens Files
$Id: mri_parse_sdcmdir.c,v 1.22 2015/05/21 16:37:12 greve Exp $
cwd /hpc_htom/mtay316/tutorial4/practice_with_data/dicoms
cmdline --sortbyrun --d /hpc/mtay316/tutorial4/practice_with_data/dicoms/ --o /hpc/mtay316/tutorial4/practice_with_data//dicomdir.sumfile --status /hpc/mtay316/tutorial4/practice_with_data//parse.status 
sysname  Linux
hostname bn390370
machine  x86_64
user mtay316
INFO: found 0 Siemens Files
ERROR: scanning directory /hpc/mtay316/tutorial4/practice_with_data/dicoms
ERROR: parsing /hpc/mtay316/tutorial4/practice_with_data/dicoms/ 
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