Re: [Freesurfer] mri_segment error

2018-03-19 Thread Bruce Fischl 

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  wrote:
  thank you for your attention

regards

On Fri, Feb 9, 2018 at 1:04 AM, Bruce Fischl  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
 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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Re: [Freesurfer] mri_segment error

2018-03-19 Thread Niels Bergsland 
Your input here is a localizer image:

Protocol  t2_haste_localizer_p2



On Mon, Mar 19, 2018 at 12:51 PM, 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  wrote:
>>
>> thank you for your attention
>>
>> regards
>>
>> On Fri, Feb 9, 2018 at 1:04 AM, Bruce Fischl 
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 <
fis...@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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 addressed. If you believe this e-mail was sent to you in error and the
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 contains patient information, please contact the Partners Compliance
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 dispose of the e-mail.



>>>
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>>>
>>>
>>> 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
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in error
>>> but does not contain patient information, please contact the sender and
properly
>>> dispose of the e-mail.
>>>
>>
>
>
> ___
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>
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is
> addressed. If you believe this e-mail was sent to you in error and the
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> contains patient information, please contact the Partners Compliance
HelpLine at
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properly
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Re: [Freesurfer] mri_segment error

2018-03-19 Thread Z Hessam 
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  wrote:

> thank you for your attention
>
> regards
>
> On Fri, Feb 9, 2018 at 1:04 AM, Bruce Fischl 
> 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 
>>> 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.
>>
>>
>


recon-all.log
Description: Binary data
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Re: [Freesurfer] mri_segment error

2018-02-09 Thread Z Hessam 
thank you for your attention

regards

On Fri, Feb 9, 2018 at 1:04 AM, Bruce Fischl 
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 
>> 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.
>
>
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Re: [Freesurfer] mri_segment error

2018-02-08 Thread Bruce Fischl 
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  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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Re: [Freesurfer] mri_segment error

2018-02-08 Thread Z Hessam 
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  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 
> 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.
>>
>>
>
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Re: [Freesurfer] mri_segment error

2018-02-08 Thread Bruce Fischl 
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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[Freesurfer] mri_segment error

2018-02-08 Thread Z Hessam 
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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