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.
> <DGREVE@mgh.harvard.edu <mailto:DGREVE@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 /<my dicoms pathways> -targ <my output
>     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
>     >
>     >
>     > _______________________________________________
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>
>
>     _______________________________________________
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>
>
>
> --
> *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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