Hello FreeSurfer develpers I'm attempting to run " recon-all " command on a file of dicom data, and encounter with an error command:
recon-all -s dyegmoh exited with ERRORS at Thu Feb 8 17:08:16 +0330 2018
how can i understand why this error happens and what should i do to solve it?
can you send us the complete command you ran, the entire screen output and the recon-all.log file?
cheers Bruce On Thu, 8 Feb 2018, Z Hessam wrote:
Hello FreeSurfer develpers I'm attempting to run " recon-all " command on a file of dicom data, and encounter with an error command:
recon-all -s dyegmoh exited with ERRORS at Thu Feb 8 17:08:16 +0330 2018
how can i understand why this error happens and what should i do to solve it?
sure... with first code i convert *.dcm files. with second code i want to segment data:
1) recon-all -i /media/hessam91/driver2/data/1.dcm -autorecon1 -subjid dyegmoh 2) recon-all -s dyegmoh -all
and the log file is attached(recon-all_dyegmoh.log).
On Thu, Feb 8, 2018 at 7:05 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
can you send us the complete command you ran, the entire screen output and the recon-all.log file?
cheers Bruce
On Thu, 8 Feb 2018, Z Hessam wrote:
Hello FreeSurfer develpers
I'm attempting to run " recon-all " command on a file of dicom data, and encounter with an error command:
recon-all -s dyegmoh exited with ERRORS at Thu Feb 8 17:08:16 +0330 2018
how can i understand why this error happens and what should i do to solve it?
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when i use first code for another data set, it sent me an error:
ERROR: /tmp/hessam91.tmp.decompressed.dcm.PV8Mal is not a dicom file
why this error happens?
On Thu, Feb 8, 2018 at 9:48 PM, Z Hessam z.hessam@gmail.com wrote:
sure... with first code i convert *.dcm files. with second code i want to segment data:
- recon-all -i /media/hessam91/driver2/data/1.dcm -autorecon1 -subjid
dyegmoh 2) recon-all -s dyegmoh -all
and the log file is attached(recon-all_dyegmoh.log).
On Thu, Feb 8, 2018 at 7:05 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
can you send us the complete command you ran, the entire screen output and the recon-all.log file?
cheers Bruce
On Thu, 8 Feb 2018, Z Hessam wrote:
Hello FreeSurfer develpers
I'm attempting to run " recon-all " command on a file of dicom data, and encounter with an error command:
recon-all -s dyegmoh exited with ERRORS at Thu Feb 8 17:08:16 +0330 2018
how can i understand why this error happens and what should i do to solve it?
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.
looks like the acquisition is not what you would need to run FreeSurfer on. Looking at the log I think your input is a T2-weighted image (we require a T1) with a slice thickness of 9mm (we require all voxel dimensions to be <=1.5mm or so)
cheers Bruce
On Thu, 8 Feb 2018, Z Hessam wrote:
sure... with first code i convert *.dcm files. with second code i want to segment data:
- recon-all -i /media/hessam91/driver2/data/1.dcm -autorecon1 -subjid dyegmoh
- recon-all -s dyegmoh -all
and the log file is attached(recon-all_dyegmoh.log).
On Thu, Feb 8, 2018 at 7:05 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: can you send us the complete command you ran, the entire screen output and the recon-all.log file?
cheers Bruce On Thu, 8 Feb 2018, Z Hessam wrote: Hello FreeSurfer develpers I'm attempting to run " recon-all " command on a file of dicom data, and encounter with an error command: recon-all -s dyegmoh exited with ERRORS at Thu Feb 8 17:08:16 +0330 2018 how can i understand why this error happens and what should i do to solve it?
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.
thank you for your attention
regards
On Fri, Feb 9, 2018 at 1:04 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
looks like the acquisition is not what you would need to run FreeSurfer on. Looking at the log I think your input is a T2-weighted image (we require a T1) with a slice thickness of 9mm (we require all voxel dimensions to be <=1.5mm or so)
cheers Bruce
On Thu, 8 Feb 2018, Z Hessam wrote:
sure...
with first code i convert *.dcm files. with second code i want to segment data:
- recon-all -i /media/hessam91/driver2/data/1.dcm -autorecon1 -subjid
dyegmoh 2) recon-all -s dyegmoh -all
and the log file is attached(recon-all_dyegmoh.log).
On Thu, Feb 8, 2018 at 7:05 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: can you send us the complete command you ran, the entire screen output and the recon-all.log file?
cheers Bruce On Thu, 8 Feb 2018, Z Hessam wrote: Hello FreeSurfer develpers I'm attempting to run " recon-all " command on a file ofdicom data, and encounter with an error command:
recon-all -s dyegmoh exited with ERRORS at Thu Feb 817:08:16 +0330 2018
how can i understand why this error happens and what shouldi do to solve it?
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.
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.
hello, i have problem again with a new data set. this is the recon-all.log file in attach
thanks a lot
On Fri, Feb 9, 2018 at 2:22 PM, Z Hessam z.hessam@gmail.com wrote:
thank you for your attention
regards
On Fri, Feb 9, 2018 at 1:04 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
looks like the acquisition is not what you would need to run FreeSurfer on. Looking at the log I think your input is a T2-weighted image (we require a T1) with a slice thickness of 9mm (we require all voxel dimensions to be <=1.5mm or so)
cheers Bruce
On Thu, 8 Feb 2018, Z Hessam wrote:
sure...
with first code i convert *.dcm files. with second code i want to segment data:
- recon-all -i /media/hessam91/driver2/data/1.dcm -autorecon1 -subjid
dyegmoh 2) recon-all -s dyegmoh -all
and the log file is attached(recon-all_dyegmoh.log).
On Thu, Feb 8, 2018 at 7:05 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: can you send us the complete command you ran, the entire screen output and the recon-all.log file?
cheers Bruce On Thu, 8 Feb 2018, Z Hessam wrote: Hello FreeSurfer develpers I'm attempting to run " recon-all " command on a file ofdicom data, and encounter with an error command:
recon-all -s dyegmoh exited with ERRORS at Thu Feb 817:08:16 +0330 2018
how can i understand why this error happens and what shouldi do to solve it?
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.
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.
Your input here is a localizer image:
Protocol t2_haste_localizer_p2
On Mon, Mar 19, 2018 at 12:51 PM, Z Hessam z.hessam@gmail.com wrote:
hello, i have problem again with a new data set. this is the recon-all.log file in attach
thanks a lot
On Fri, Feb 9, 2018 at 2:22 PM, Z Hessam z.hessam@gmail.com wrote:
thank you for your attention
regards
On Fri, Feb 9, 2018 at 1:04 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
looks like the acquisition is not what you would need to run FreeSurfer
on. Looking at the log I think your input is a T2-weighted image (we require a T1) with a slice thickness of 9mm (we require all voxel dimensions to be <=1.5mm or so)
cheers Bruce
On Thu, 8 Feb 2018, Z Hessam wrote:
sure... with first code i convert *.dcm files. with second code i want to segment data:
- recon-all -i /media/hessam91/driver2/data/1.dcm -autorecon1 -subjid
dyegmoh
- recon-all -s dyegmoh -all
and the log file is attached(recon-all_dyegmoh.log).
On Thu, Feb 8, 2018 at 7:05 PM, Bruce Fischl <
fischl@nmr.mgh.harvard.edu> wrote:
can you send us the complete command you ran, the entire screen
output and the
recon-all.log file? cheers Bruce On Thu, 8 Feb 2018, Z Hessam wrote: Hello FreeSurfer develpers I'm attempting to run " recon-all " command on a file of
dicom data, and
encounter with an error command: recon-all -s dyegmoh exited with ERRORS at Thu Feb 8
17:08:16 +0330 2018
how can i understand why this error happens and what
should i do to solve
it?
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
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
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
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
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
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.
This one has 9mm thick slices. This web page:
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferBeginnersGuide
has some discussion about what types of inputs are needed.
cheers Bruce
On Mon, 19 Mar 2018, Z Hessam wrote:
hello, i have problem again with a new data set. this is the recon-all.log file in attach
thanks a lot
On Fri, Feb 9, 2018 at 2:22 PM, Z Hessam z.hessam@gmail.com wrote: thank you for your attention
regards
On Fri, Feb 9, 2018 at 1:04 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: looks like the acquisition is not what you would need to run FreeSurfer on. Looking at the log I think your input is a T2-weighted image (we require a T1) with a slice thickness of 9mm (we require all voxel dimensions to be <=1.5mm or so)
cheers Bruce On Thu, 8 Feb 2018, Z Hessam wrote: sure... with first code i convert *.dcm files. with second code i want to segment data: 1) recon-all -i /media/hessam91/driver2/data/1.dcm -autorecon1 -subjid dyegmoh 2) recon-all -s dyegmoh -all and the log file is attached(recon-all_dyegmoh.log). On Thu, Feb 8, 2018 at 7:05 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: can you send us the complete command you ran, the entire screen output and the recon-all.log file? cheers Bruce On Thu, 8 Feb 2018, Z Hessam wrote: Hello FreeSurfer develpers I'm attempting to run " recon-all " command on a file of dicom data, and encounter with an error command: recon-all -s dyegmoh exited with ERRORS at Thu Feb 8 17:08:16 +0330 2018 how can i understand why this error happens and what should i do to solve it? _______________________________________________ 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.
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.
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Niels Bergsland -
Z Hessam