External Email - Use Caution Dear Greve, Thank you sooooo much. It s finally fixed and now is working properly.
Regards On Fri, 9 Nov 2018 at 02:50, Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu> 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. > > <dgr...@mgh.harvard.edu <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 /<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 > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto: > 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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