Good day,
I'm getting the following error when I try to convert my DICOM files. Some of the files do not have the issue, but others do. The error is below.
WARNING: file /Users/marc/Desktop/brainscan/DICOM/PA000000/ST000000/SE000001/IM000000 does not contain a Siemens ASCII header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header
Darwin Marcs-MacBook-Air.local 15.0.0 Darwin Kernel Version 15.0.0: Sat Sep 19 15:53:46 PDT 2015; root:xnu-3247.10.11~1/RELEASE_X86_64 x86_64
recon-all -s my_brain exited with ERRORS at Fri Dec 4 20:02:27 CST 2015
For more details, see the log file /Applications/freesurfer/subjects/my_brain/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
I need help figuring out how to solve this if anyone can. I'd really appreciate it.
Thanks,
Marc
Did you see the question "has this file been anonymized?" ?
On 12/5/15 10:04 AM, Marc Callison wrote:
Good day,
I'm getting the following error when I try to convert my DICOM files. Some of the files do not have the issue, but others do. The error is below.
WARNING: file /Users/marc/Desktop/brainscan/DICOM/PA000000/ST000000/SE000001/IM000000 does not contain a Siemens ASCII header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header
Darwin Marcs-MacBook-Air.local 15.0.0 Darwin Kernel Version 15.0.0: Sat Sep 19 15:53:46 PDT 2015; root:xnu-3247.10.11~1/RELEASE_X86_64 x86_64
recon-all -s my_brain exited with ERRORS at Fri Dec 4 20:02:27 CST 2015
For more details, see the log file /Applications/freesurfer/subjects/my_brain/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
I need help figuring out how to solve this if anyone can. I'd really appreciate it.
Thanks,
Marc
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Yes I don't think that is it because it processes some of the files. Not sure though.
I did try the mri_convert command but I'd have to run it hundreds or times unless there is some way to make it loop through all the files in the different folders.
On Saturday, December 5, 2015, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Did you see the question "has this file been anonymized?" ?
On 12/5/15 10:04 AM, Marc Callison wrote:
Good day,
I'm getting the following error when I try to convert my DICOM files. Some of the files do not have the issue, but others do. The error is below.
WARNING: file /Users/marc/Desktop/brainscan/DICOM/PA000000/ST000000/SE000001/IM000000 does not contain a Siemens ASCII header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header
Darwin Marcs-MacBook-Air.local 15.0.0 Darwin Kernel Version 15.0.0: Sat Sep 19 15:53:46 PDT 2015; root:xnu-3247.10.11~1/RELEASE_X86_64 x86_64
recon-all -s my_brain exited with ERRORS at Fri Dec 4 20:02:27 CST 2015
For more details, see the log file /Applications/freesurfer/subjects/my_brain/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
I need help figuring out how to solve this if anyone can. I'd really appreciate it.
Thanks,
Marc
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu javascript:_e(%7B%7D,'cvml','Freesurfer@nmr.mgh.harvard.edu');https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
can you send me /Users/marc/Desktop/brainscan/DICOM/PA000000/ST000000/SE000001/IM000000 ? Also, what version of FS are you using?
On 12/05/2015 01:39 PM, Marc Callison wrote:
Yes I don't think that is it because it processes some of the files. Not sure though.
I did try the mri_convert command but I'd have to run it hundreds or times unless there is some way to make it loop through all the files in the different folders.
On Saturday, December 5, 2015, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Did you see the question "has this file been anonymized?" ? On 12/5/15 10:04 AM, Marc Callison wrote:Good day, I'm getting the following error when I try to convert my DICOM files. Some of the files do not have the issue, but others do. The error is below. WARNING: file /Users/marc/Desktop/brainscan/DICOM/PA000000/ST000000/SE000001/IM000000 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header Darwin Marcs-MacBook-Air.local 15.0.0 Darwin Kernel Version 15.0.0: Sat Sep 19 15:53:46 PDT 2015; root:xnu-3247.10.11~1/RELEASE_X86_64 x86_64 recon-all -s my_brain exited with ERRORS at Fri Dec 4 20:02:27 CST 2015 For more details, see the log file /Applications/freesurfer/subjects/my_brain/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I need help figuring out how to solve this if anyone can. I'd really appreciate it. Thanks, Marc _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <javascript:_e(%7B%7D,'cvml','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
See attached.
I am running the most current version, 5.3.0
On Mon, Dec 7, 2015 at 12:37 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
can you send me /Users/marc/Desktop/brainscan/DICOM/PA000000/ST000000/SE000001/IM000000 ? Also, what version of FS are you using?
On 12/05/2015 01:39 PM, Marc Callison wrote:
Yes I don't think that is it because it processes some of the files. Not sure though.
I did try the mri_convert command but I'd have to run it hundreds or times unless there is some way to make it loop through all the files in the different folders.
On Saturday, December 5, 2015, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Did you see the question "has this file been anonymized?" ? On 12/5/15 10:04 AM, Marc Callison wrote:Good day, I'm getting the following error when I try to convert my DICOM files. Some of the files do not have the issue, but others do. The error is below. WARNING: file/Users/marc/Desktop/brainscan/DICOM/PA000000/ST000000/SE000001/IM000000
does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header Darwin Marcs-MacBook-Air.local 15.0.0 Darwin Kernel Version 15.0.0: Sat Sep 19 15:53:46 PDT 2015; root:xnu-3247.10.11~1/RELEASE_X86_64 x86_64 recon-all -s my_brain exited with ERRORS at Fri Dec 4 20:02:27 CST 2015 For more details, see the log file /Applications/freesurfer/subjects/my_brain/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I need help figuring out how to solve this if anyone can. I'd really appreciate it. Thanks, Marc _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <javascript:_e(%7B%7D,'cvml','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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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 http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
I can convert that ok with version 6. Try using the mri_convert from here (make a backup of the one you have) ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert
On 12/08/2015 08:08 PM, Marc Callison wrote:
See attached.
I am running the most current version, 5.3.0
On Mon, Dec 7, 2015 at 12:37 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
can you send me /Users/marc/Desktop/brainscan/DICOM/PA000000/ST000000/SE000001/IM000000 ? Also, what version of FS are you using? On 12/05/2015 01:39 PM, Marc Callison wrote: > Yes I don't think that is it because it processes some of the files. > Not sure though. > > I did try the mri_convert command but I'd have to run it hundreds or > times unless there is some way to make it loop through all the files > in the different folders. > > > > On Saturday, December 5, 2015, Douglas Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > Did you see the question "has this file been anonymized?" ? > > On 12/5/15 10:04 AM, Marc Callison wrote: >> Good day, >> >> I'm getting the following error when I try to convert my DICOM >> files. Some of the files do not have the issue, but others do. >> The error is below. >> >> WARNING: file >> /Users/marc/Desktop/brainscan/DICOM/PA000000/ST000000/SE000001/IM000000 >> does not contain a Siemens ASCII header >> >> has this file been anonymized? >> >> ERROR: cannot unpack mosiacs without ASCII header >> >> Darwin Marcs-MacBook-Air.local 15.0.0 Darwin Kernel Version >> 15.0.0: Sat Sep 19 15:53:46 PDT 2015; >> root:xnu-3247.10.11~1/RELEASE_X86_64 x86_64 >> >> >> recon-all -s my_brain exited with ERRORS at Fri Dec 4 20:02:27 >> CST 2015 >> >> >> For more details, see the log file >> /Applications/freesurfer/subjects/my_brain/scripts/recon-all.log >> >> To report a problem, see >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> >> >> I need help figuring out how to solve this if anyone can. I'd >> really appreciate it. >> >> >> Thanks, >> >> Marc >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <javascript:_e(%7B%7D,'cvml','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 -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Douglas N Greve
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Marc Callison