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
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?
- 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
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 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 CautionHello 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?
- 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
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 > > > _______________________________________________ > 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
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. DGREVE@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 CautionI 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 > > > _______________________________________________ > 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
freesurfer@nmr.mgh.harvard.edu
-
Greve, Douglas N.,Ph.D. -
Maryam Tayebi