Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

[Anastasia Yendiki]

You get the same error as trac-all because trac-all runs mri_convert. I'd 
send the mri_convert error in a new email with mri_convert somewhere in 
the title, so that someone else can help you.


On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:


Also when I run mir_convert on the DICOMs I get the same error as the one I
got when I used DICOMs :
WARNING: 
file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/3T2/MR.1.3.12.2.1107.5.2.19.
45306.2014091812330393354083931 does not contain a Siemens ASCII header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header

Any idea what this could be ?

Thanks,

Ismail

  On Jul 4, 2016, at 3:15 PM, Koubiyr, Ismail
   wrote:

It says 1 … I don’t understand why I get that knowing that when I open
the nifti I can go through the frames …

Ismail

  On Jul 4, 2016, at 3:11 PM, Anastasia Yendiki
   wrote:


  I do not know why the dicoms do not work. When you run
  mri_info on your nifti, what is the number of frames that
  shows up?

  On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:

Hi Anastasia,

This is what’s weird, my nifti volume contains
64 frames as my bvecs/bvals. So this shouldn’t
be the reason.
Also why the DICOMs wouldn’t work at the
beginning ?

Thanks,
Ismail

  On Jul 4, 2016, at 2:41 PM,
  Anastasia Yendiki
  
  wrote:


  Hi Ismail - You can see from the
  log file that the command that
  causes the error is this:

  mri_convert --frame 31
  
/Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi.nii.gz
  
/Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi_frame31.nii.gz

  It's trying to extract the 32nd
  frame of your nifti file, but from
  the error message it looks like
  your nifti file doesn't have a
  32nd frame. So either the nifti
  file has too few volumes, or the
  bvecs/bvals have too many lines.
  You'll have to figure that out.

  a.y

  On Mon, 4 Jul 2016, Koubiyr,
  Ismail wrote:

Hi Anastasia,
Here it is.
But how could the
problem be related to
the nifti volume since
I have errors
when using the DICOMs
too ?
Thanks again,
Ismail
  On Jul 4,
  2016, at
  1:44 PM,
  Anastasia
  Yendiki


wrote:


  Hi Ismail
  - It
  sounds
  like the
  error has
  to do with
  the nifti
  volume,
  not

the bvecs/bvals. Can
you send the log file
from
scripts/trac-all.log?

  Thanks,
  a.y

  On Mon, 4
  Jul 2016,
  Koubiyr,
  Ismail
  wrote:

Hi
Anastasia,
Thank
you
for
getting
back
to
me.
Here
are
more
details
about
my
problem,
I
think
it
should
help
you
understand
more.
I
run
 

Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

[Koubiyr, Ismail]

Also when I run mir_convert on the DICOMs I get the same error as the one I got 
when I used DICOMs :
WARNING: file 
/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/3T2/MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931
 does not contain a Siemens ASCII header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header

Any idea what this could be ?

Thanks,

Ismail

On Jul 4, 2016, at 3:15 PM, Koubiyr, Ismail 
> wrote:

It says 1 … I don’t understand why I get that knowing that when I open the 
nifti I can go through the frames …

Ismail

On Jul 4, 2016, at 3:11 PM, Anastasia Yendiki 
> wrote:


I do not know why the dicoms do not work. When you run mri_info on your nifti, 
what is the number of frames that shows up?

On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:

Hi Anastasia,

This is what’s weird, my nifti volume contains 64 frames as my bvecs/bvals. So 
this shouldn’t be the reason.
Also why the DICOMs wouldn’t work at the beginning ?

Thanks,
Ismail

On Jul 4, 2016, at 2:41 PM, Anastasia Yendiki 
> wrote:


Hi Ismail - You can see from the log file that the command that causes the 
error is this:

mri_convert --frame 31 
/Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi.nii.gz 
/Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi_frame31.nii.gz

It's trying to extract the 32nd frame of your nifti file, but from the error 
message it looks like your nifti file doesn't have a 32nd frame. So either the 
nifti file has too few volumes, or the bvecs/bvals have too many lines. You'll 
have to figure that out.

a.y

On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:

Hi Anastasia,
Here it is.
But how could the problem be related to the nifti volume since I have errors
when using the DICOMs too ?
Thanks again,
Ismail
On Jul 4, 2016, at 1:44 PM, Anastasia Yendiki
> wrote:


Hi Ismail - It sounds like the error has to do with the nifti volume, not
the bvecs/bvals. Can you send the log file from scripts/trac-all.log?

Thanks,
a.y

On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:

Hi Anastasia,
Thank you for getting back to me.
Here are more details about my problem, I think it should help you
understand more.
I run trac-all -prep -c on some DICOM files but I had the following error
:
WARNING:file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.368
0043
.6.8878.22551.20150806120704.648.1017 does not contain a Siemens ASCII
header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header
I also tried to de-mosiac the DICOMs, it gave me the same error.
Then I converted the DICOMs into NIFTI, which allowed me not to get the
previous error but something else weird happened. Now I get :
ERROR: fMRIframe: frame >= nframes
I checked the bvecs and bvals files, they seem normal, no additional
space,
but when the new bvecs  and bvals are created, they seem messed up. I
will
attach you all the bvecs and bvals I used and the ones I get too.
Ideally, the DICOMs should work fine but I have no idea why I get these
errors.
The bvecs and bvals are obtained from dcm2nii and then corrected to avoid
any additional space.
Thank you in advance for your help.
Best,
Ismail
P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used.

   On Jul 4, 2016, at 3:32 AM, Anastasia Yendiki
   > wrote:
Hi Ismail - Are you passing the nifti volume as input to trac-all?
It's
hard to tell without looking at your configuration file.
Best,
a.y
On Tue, 28 Jun 2016, Koubiyr, Ismail wrote:

   Hi everyone,

   I have some problems trying to run TRACULA on some DWI
   data. It is a mosaic Siemens DWI. I first converted the
   DICOM files with dcm2nii to get the bvec and bval files.
   Then I run the trac-all -prep -c command and I get the
   following error :

   WARNING: file /My/path/to/dicom does not contain a Siemens
   ASCII header
   has this file been anonymized?
   ERROR: cannot unpack mosiacs without ASCII header

   I tried to unpack the mosaics with gdcmtar, but I got the
   same error.

   Thank you in advance for your help,

   Ismail
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Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

[Koubiyr, Ismail]

It says 1 … I don’t understand why I get that knowing that when I open the 
nifti I can go through the frames …

Ismail

> On Jul 4, 2016, at 3:11 PM, Anastasia Yendiki  
> wrote:
> 
> 
> I do not know why the dicoms do not work. When you run mri_info on your 
> nifti, what is the number of frames that shows up?
> 
> On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
> 
>> Hi Anastasia,
>> 
>> This is what’s weird, my nifti volume contains 64 frames as my bvecs/bvals. 
>> So this shouldn’t be the reason.
>> Also why the DICOMs wouldn’t work at the beginning ?
>> 
>> Thanks,
>> Ismail
>> 
>>> On Jul 4, 2016, at 2:41 PM, Anastasia Yendiki 
>>>  wrote:
>>> 
>>> 
>>> Hi Ismail - You can see from the log file that the command that causes the 
>>> error is this:
>>> 
>>> mri_convert --frame 31 
>>> /Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi.nii.gz 
>>> /Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi_frame31.nii.gz
>>> 
>>> It's trying to extract the 32nd frame of your nifti file, but from the 
>>> error message it looks like your nifti file doesn't have a 32nd frame. So 
>>> either the nifti file has too few volumes, or the bvecs/bvals have too many 
>>> lines. You'll have to figure that out.
>>> 
>>> a.y
>>> 
>>> On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
>>> 
 Hi Anastasia,
 Here it is.
 But how could the problem be related to the nifti volume since I have 
 errors
 when using the DICOMs too ?
 Thanks again,
 Ismail
> On Jul 4, 2016, at 1:44 PM, Anastasia Yendiki
  wrote:
> 
> 
> Hi Ismail - It sounds like the error has to do with the nifti volume, not
 the bvecs/bvals. Can you send the log file from scripts/trac-all.log?
> 
> Thanks,
> a.y
> 
> On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
> 
>> Hi Anastasia,
>> Thank you for getting back to me.
>> Here are more details about my problem, I think it should help you
>> understand more.
>> I run trac-all -prep -c on some DICOM files but I had the following error
 :
>> WARNING:file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.368
 0043
>> .6.8878.22551.20150806120704.648.1017 does not contain a Siemens ASCII
>> header
>> has this file been anonymized?
>> ERROR: cannot unpack mosiacs without ASCII header
>> I also tried to de-mosiac the DICOMs, it gave me the same error.
>> Then I converted the DICOMs into NIFTI, which allowed me not to get the
>> previous error but something else weird happened. Now I get :
>> ERROR: fMRIframe: frame >= nframes
>> I checked the bvecs and bvals files, they seem normal, no additional
 space,
>> but when the new bvecs  and bvals are created, they seem messed up. I
 will
>> attach you all the bvecs and bvals I used and the ones I get too.
>> Ideally, the DICOMs should work fine but I have no idea why I get these
>> errors.
>> The bvecs and bvals are obtained from dcm2nii and then corrected to avoid
>> any additional space.
>> Thank you in advance for your help.
>> Best,
>> Ismail
>> P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used.
>> 
>> On Jul 4, 2016, at 3:32 AM, Anastasia Yendiki
>>  wrote:
>> Hi Ismail - Are you passing the nifti volume as input to trac-all?
>> It's
>> hard to tell without looking at your configuration file.
>> Best,
>> a.y
>> On Tue, 28 Jun 2016, Koubiyr, Ismail wrote:
>> 
>> Hi everyone,
>> 
>> I have some problems trying to run TRACULA on some DWI
>> data. It is a mosaic Siemens DWI. I first converted the
>> DICOM files with dcm2nii to get the bvec and bval files.
>> Then I run the trac-all -prep -c command and I get the
>> following error :
>> 
>> WARNING: file /My/path/to/dicom does not contain a Siemens
>> ASCII header
>> has this file been anonymized?
>> ERROR: cannot unpack mosiacs without ASCII header
>> 
>> I tried to unpack the mosaics with gdcmtar, but I got the
>> same error.
>> 
>> Thank you in advance for your help,
>> 
>> Ismail
>> ___
>> 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
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> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

[Anastasia Yendiki]

I do not know why the dicoms do not work. When you run mri_info on your 
nifti, what is the number of frames that shows up?


On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:


Hi Anastasia,

This is what’s weird, my nifti volume contains 64 frames as my bvecs/bvals. So 
this shouldn’t be the reason.
Also why the DICOMs wouldn’t work at the beginning ?

Thanks,
Ismail


On Jul 4, 2016, at 2:41 PM, Anastasia Yendiki  
wrote:


Hi Ismail - You can see from the log file that the command that causes the 
error is this:

mri_convert --frame 31 
/Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi.nii.gz 
/Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi_frame31.nii.gz

It's trying to extract the 32nd frame of your nifti file, but from the error 
message it looks like your nifti file doesn't have a 32nd frame. So either the 
nifti file has too few volumes, or the bvecs/bvals have too many lines. You'll 
have to figure that out.

a.y

On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:


Hi Anastasia,
Here it is.
But how could the problem be related to the nifti volume since I have errors
when using the DICOMs too ?
Thanks again,
Ismail

On Jul 4, 2016, at 1:44 PM, Anastasia Yendiki

 wrote:



Hi Ismail - It sounds like the error has to do with the nifti volume, not

the bvecs/bvals. Can you send the log file from scripts/trac-all.log?


Thanks,
a.y

On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:


Hi Anastasia,
Thank you for getting back to me.
Here are more details about my problem, I think it should help you
understand more.
I run trac-all -prep -c on some DICOM files but I had the following error

:

WARNING:file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.368

0043

.6.8878.22551.20150806120704.648.1017 does not contain a Siemens ASCII
header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header
I also tried to de-mosiac the DICOMs, it gave me the same error.
Then I converted the DICOMs into NIFTI, which allowed me not to get the
previous error but something else weird happened. Now I get :
ERROR: fMRIframe: frame >= nframes
I checked the bvecs and bvals files, they seem normal, no additional

space,

but when the new bvecs  and bvals are created, they seem messed up. I

will

attach you all the bvecs and bvals I used and the ones I get too.
Ideally, the DICOMs should work fine but I have no idea why I get these
errors.
The bvecs and bvals are obtained from dcm2nii and then corrected to avoid
any additional space.
Thank you in advance for your help.
Best,
Ismail
P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used.

 On Jul 4, 2016, at 3:32 AM, Anastasia Yendiki
  wrote:
Hi Ismail - Are you passing the nifti volume as input to trac-all?
It's
hard to tell without looking at your configuration file.
Best,
a.y
On Tue, 28 Jun 2016, Koubiyr, Ismail wrote:

 Hi everyone,

 I have some problems trying to run TRACULA on some DWI
 data. It is a mosaic Siemens DWI. I first converted the
 DICOM files with dcm2nii to get the bvec and bval files.
 Then I run the trac-all -prep -c command and I get the
 following error :

 WARNING: file /My/path/to/dicom does not contain a Siemens
 ASCII header
 has this file been anonymized?
 ERROR: cannot unpack mosiacs without ASCII header

 I tried to unpack the mosaics with gdcmtar, but I got the
 same error.

 Thank you in advance for your help,

 Ismail
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Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

[Koubiyr, Ismail]

Hi Anastasia,

This is what’s weird, my nifti volume contains 64 frames as my bvecs/bvals. So 
this shouldn’t be the reason.
Also why the DICOMs wouldn’t work at the beginning ?

Thanks,
Ismail

> On Jul 4, 2016, at 2:41 PM, Anastasia Yendiki  
> wrote:
> 
> 
> Hi Ismail - You can see from the log file that the command that causes the 
> error is this:
> 
> mri_convert --frame 31 
> /Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi.nii.gz 
> /Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi_frame31.nii.gz
> 
> It's trying to extract the 32nd frame of your nifti file, but from the error 
> message it looks like your nifti file doesn't have a 32nd frame. So either 
> the nifti file has too few volumes, or the bvecs/bvals have too many lines. 
> You'll have to figure that out.
> 
> a.y
> 
> On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
> 
>> Hi Anastasia,
>> Here it is.
>> But how could the problem be related to the nifti volume since I have errors
>> when using the DICOMs too ?
>> Thanks again,
>> Ismail
>> > On Jul 4, 2016, at 1:44 PM, Anastasia Yendiki
>>  wrote:
>> >
>> >
>> > Hi Ismail - It sounds like the error has to do with the nifti volume, not
>> the bvecs/bvals. Can you send the log file from scripts/trac-all.log?
>> >
>> > Thanks,
>> > a.y
>> >
>> > On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
>> >
>> >> Hi Anastasia,
>> >> Thank you for getting back to me.
>> >> Here are more details about my problem, I think it should help you
>> >> understand more.
>> >> I run trac-all -prep -c on some DICOM files but I had the following error
>> :
>> >> WARNING:file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.368
>> 0043
>> >> .6.8878.22551.20150806120704.648.1017 does not contain a Siemens ASCII
>> >> header
>> >> has this file been anonymized?
>> >> ERROR: cannot unpack mosiacs without ASCII header
>> >> I also tried to de-mosiac the DICOMs, it gave me the same error.
>> >> Then I converted the DICOMs into NIFTI, which allowed me not to get the
>> >> previous error but something else weird happened. Now I get :
>> >> ERROR: fMRIframe: frame >= nframes
>> >> I checked the bvecs and bvals files, they seem normal, no additional
>> space,
>> >> but when the new bvecs  and bvals are created, they seem messed up. I
>> will
>> >> attach you all the bvecs and bvals I used and the ones I get too.
>> >> Ideally, the DICOMs should work fine but I have no idea why I get these
>> >> errors.
>> >> The bvecs and bvals are obtained from dcm2nii and then corrected to avoid
>> >> any additional space.
>> >> Thank you in advance for your help.
>> >> Best,
>> >> Ismail
>> >> P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used.
>> >>
>> >>  On Jul 4, 2016, at 3:32 AM, Anastasia Yendiki
>> >>   wrote:
>> >> Hi Ismail - Are you passing the nifti volume as input to trac-all?
>> >> It's
>> >> hard to tell without looking at your configuration file.
>> >> Best,
>> >> a.y
>> >> On Tue, 28 Jun 2016, Koubiyr, Ismail wrote:
>> >>
>> >>  Hi everyone,
>> >>
>> >>  I have some problems trying to run TRACULA on some DWI
>> >>  data. It is a mosaic Siemens DWI. I first converted the
>> >>  DICOM files with dcm2nii to get the bvec and bval files.
>> >>  Then I run the trac-all -prep -c command and I get the
>> >>  following error :
>> >>
>> >>  WARNING: file /My/path/to/dicom does not contain a Siemens
>> >>  ASCII header
>> >>  has this file been anonymized?
>> >>  ERROR: cannot unpack mosiacs without ASCII header
>> >>
>> >>  I tried to unpack the mosaics with gdcmtar, but I got the
>> >>  same error.
>> >>
>> >>  Thank you in advance for your help,
>> >>
>> >>  Ismail
>> >>  ___
>> >>  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 mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> ___
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Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

[Anastasia Yendiki]

Hi Ismail - You can see from the log file that the command that causes the 
error is this:


mri_convert --frame 31 
/Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi.nii.gz 
/Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi_frame31.nii.gz

It's trying to extract the 32nd frame of your nifti file, but from the 
error message it looks like your nifti file doesn't have a 32nd frame. So 
either the nifti file has too few volumes, or the bvecs/bvals have too 
many lines. You'll have to figure that out.


a.y

On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:


Hi Anastasia,

Here it is.
But how could the problem be related to the nifti volume since I have errors
when using the DICOMs too ?
Thanks again,

Ismail



> On Jul 4, 2016, at 1:44 PM, Anastasia Yendiki
 wrote:
>
>
> Hi Ismail - It sounds like the error has to do with the nifti volume, not
the bvecs/bvals. Can you send the log file from scripts/trac-all.log?
>
> Thanks,
> a.y
>
> On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
>
>> Hi Anastasia,
>> Thank you for getting back to me.
>> Here are more details about my problem, I think it should help you
>> understand more.
>> I run trac-all -prep -c on some DICOM files but I had the following error
:
>> 
WARNING:file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.368
0043
>> .6.8878.22551.20150806120704.648.1017 does not contain a Siemens ASCII
>> header
>> has this file been anonymized?
>> ERROR: cannot unpack mosiacs without ASCII header
>> I also tried to de-mosiac the DICOMs, it gave me the same error.
>> Then I converted the DICOMs into NIFTI, which allowed me not to get the
>> previous error but something else weird happened. Now I get :
>> ERROR: fMRIframe: frame >= nframes
>> I checked the bvecs and bvals files, they seem normal, no additional
space,
>> but when the new bvecs  and bvals are created, they seem messed up. I
will
>> attach you all the bvecs and bvals I used and the ones I get too.
>> Ideally, the DICOMs should work fine but I have no idea why I get these
>> errors.
>> The bvecs and bvals are obtained from dcm2nii and then corrected to avoid
>> any additional space.
>> Thank you in advance for your help.
>> Best,
>> Ismail
>> P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used.
>>
>>  On Jul 4, 2016, at 3:32 AM, Anastasia Yendiki
>>   wrote:
>> Hi Ismail - Are you passing the nifti volume as input to trac-all?
>> It's
>> hard to tell without looking at your configuration file.
>> Best,
>> a.y
>> On Tue, 28 Jun 2016, Koubiyr, Ismail wrote:
>>
>>  Hi everyone,
>>
>>  I have some problems trying to run TRACULA on some DWI
>>  data. It is a mosaic Siemens DWI. I first converted the
>>  DICOM files with dcm2nii to get the bvec and bval files.
>>  Then I run the trac-all -prep -c command and I get the
>>  following error :
>>
>>  WARNING: file /My/path/to/dicom does not contain a Siemens
>>  ASCII header
>>  has this file been anonymized?
>>  ERROR: cannot unpack mosiacs without ASCII header
>>
>>  I tried to unpack the mosaics with gdcmtar, but I got the
>>  same error.
>>
>>  Thank you in advance for your help,
>>
>>  Ismail
>>  ___
>>  Freesurfer mailing list
>>  Freesurfer@nmr.mgh.harvard.edu
>>  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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>> Freesurfer mailing list
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Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

[Koubiyr, Ismail]

Hi Anastasia,

Here it is.
But how could the problem be related to the nifti volume since I have errors 
when using the DICOMs too ?
Thanks again,

Ismail



> On Jul 4, 2016, at 1:44 PM, Anastasia Yendiki  
> wrote:
>
>
> Hi Ismail - It sounds like the error has to do with the nifti volume, not the 
> bvecs/bvals. Can you send the log file from scripts/trac-all.log?
>
> Thanks,
> a.y
>
> On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
>
>> Hi Anastasia,
>> Thank you for getting back to me.
>> Here are more details about my problem, I think it should help you
>> understand more.
>> I run trac-all -prep -c on some DICOM files but I had the following error :
>> WARNING: 
>> file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.3680043
>> .6.8878.22551.20150806120704.648.1017 does not contain a Siemens ASCII
>> header
>> has this file been anonymized?
>> ERROR: cannot unpack mosiacs without ASCII header
>> I also tried to de-mosiac the DICOMs, it gave me the same error.
>> Then I converted the DICOMs into NIFTI, which allowed me not to get the
>> previous error but something else weird happened. Now I get :
>> ERROR: fMRIframe: frame >= nframes
>> I checked the bvecs and bvals files, they seem normal, no additional space,
>> but when the new bvecs  and bvals are created, they seem messed up. I will
>> attach you all the bvecs and bvals I used and the ones I get too.
>> Ideally, the DICOMs should work fine but I have no idea why I get these
>> errors.
>> The bvecs and bvals are obtained from dcm2nii and then corrected to avoid
>> any additional space.
>> Thank you in advance for your help.
>> Best,
>> Ismail
>> P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used.
>>
>>  On Jul 4, 2016, at 3:32 AM, Anastasia Yendiki
>>   wrote:
>> Hi Ismail - Are you passing the nifti volume as input to trac-all?
>> It's
>> hard to tell without looking at your configuration file.
>> Best,
>> a.y
>> On Tue, 28 Jun 2016, Koubiyr, Ismail wrote:
>>
>>  Hi everyone,
>>
>>  I have some problems trying to run TRACULA on some DWI
>>  data. It is a mosaic Siemens DWI. I first converted the
>>  DICOM files with dcm2nii to get the bvec and bval files.
>>  Then I run the trac-all -prep -c command and I get the
>>  following error :
>>
>>  WARNING: file /My/path/to/dicom does not contain a Siemens
>>  ASCII header
>>  has this file been anonymized?
>>  ERROR: cannot unpack mosiacs without ASCII header
>>
>>  I tried to unpack the mosaics with gdcmtar, but I got the
>>  same error.
>>
>>  Thank you in advance for your help,
>>
>>  Ismail
>>  ___
>>  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 mailing list
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trac-all.log
Description: trac-all.log
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Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

[Anastasia Yendiki]

Hi Ismail - It sounds like the error has to do with the nifti volume, not 
the bvecs/bvals. Can you send the log file from scripts/trac-all.log?


Thanks,
a.y

On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:


Hi Anastasia,

Thank you for getting back to me.
Here are more details about my problem, I think it should help you
understand more.

I run trac-all -prep -c on some DICOM files but I had the following error :
WARNING: 
file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.3680043
.6.8878.22551.20150806120704.648.1017 does not contain a Siemens ASCII
header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header
I also tried to de-mosiac the DICOMs, it gave me the same error.

Then I converted the DICOMs into NIFTI, which allowed me not to get the
previous error but something else weird happened. Now I get :
ERROR: fMRIframe: frame >= nframes
I checked the bvecs and bvals files, they seem normal, no additional space,
but when the new bvecs  and bvals are created, they seem messed up. I will
attach you all the bvecs and bvals I used and the ones I get too.

Ideally, the DICOMs should work fine but I have no idea why I get these
errors.
The bvecs and bvals are obtained from dcm2nii and then corrected to avoid
any additional space.

Thank you in advance for your help.

Best,

Ismail

P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used.


  On Jul 4, 2016, at 3:32 AM, Anastasia Yendiki
   wrote:


Hi Ismail - Are you passing the nifti volume as input to trac-all?
It's
hard to tell without looking at your configuration file.

Best,
a.y

On Tue, 28 Jun 2016, Koubiyr, Ismail wrote:

  Hi everyone,

  I have some problems trying to run TRACULA on some DWI
  data. It is a mosaic Siemens DWI. I first converted the
  DICOM files with dcm2nii to get the bvec and bval files.
  Then I run the trac-all -prep -c command and I get the
  following error :

  WARNING: file /My/path/to/dicom does not contain a Siemens
  ASCII header
  has this file been anonymized?
  ERROR: cannot unpack mosiacs without ASCII header

  I tried to unpack the mosaics with gdcmtar, but I got the
  same error.

  Thank you in advance for your help,

  Ismail
  ___
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

[Koubiyr, Ismail]

Hi Anastasia,

Thank you for getting back to me.
Here are more details about my problem, I think it should help you understand 
more.

I run trac-all -prep -c on some DICOM files but I had the following error :
WARNING: file 
/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.3680043.6.8878.22551.20150806120704.648.1017
 does not contain a Siemens ASCII header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header
I also tried to de-mosiac the DICOMs, it gave me the same error.

Then I converted the DICOMs into NIFTI, which allowed me not to get the 
previous error but something else weird happened. Now I get :
ERROR: fMRIframe: frame >= nframes
I checked the bvecs and bvals files, they seem normal, no additional space, but 
when the new bvecs  and bvals are created, they seem messed up. I will attach 
you all the bvecs and bvals I used and the ones I get too.

Ideally, the DICOMs should work fine but I have no idea why I get these errors.
The bvecs and bvals are obtained from dcm2nii and then corrected to avoid any 
additional space.

Thank you in advance for your help.

Best,

Ismail

P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used.


On Jul 4, 2016, at 3:32 AM, Anastasia Yendiki 
> wrote:


Hi Ismail - Are you passing the nifti volume as input to trac-all? It's
hard to tell without looking at your configuration file.

Best,
a.y

On Tue, 28 Jun 2016, Koubiyr, Ismail wrote:

Hi everyone,

I have some problems trying to run TRACULA on some DWI data. It is a mosaic 
Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and 
bval files.
Then I run the trac-all -prep -c command and I get the following error :

WARNING: file /My/path/to/dicom does not contain a Siemens ASCII header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header

I tried to unpack the mosaics with gdcmtar, but I got the same error.

Thank you in advance for your help,

Ismail
___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



___
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bvals
Description: bvals


bvecs
Description: bvecs


bvecs.norot
Description: bvecs.norot


dwi_orig.mghdti.bvecs
Description: dwi_orig.mghdti.bvecs


dwi_orig.mghdti.bvals
Description: dwi_orig.mghdti.bvals
0
1000
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0
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0
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0.400451 0.175928 -0.899271
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-0.857087 0.178312 0.48333
0.00074441 0.735199 0.677851
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0.656176 0.522342 0.544602
0.331016 0.523908 0.784824
0.197021 -0.176144 -0.964446
0.20548 0.177881 0.96236
0.651496 0.731864 0.199821
0.324279 0.941458 0.0921958
0.200221 0.939774 -0.277014
0.402681 0.730255 -0.551883
0.730024 0.176561 -0.66022
0.726896 0.519093 -0.449628
0.851743 0.519522 -0.0680449
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0.979641 0.177715 0.0933861
0 0 0
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0.19699 0.519109 -0.831697
0.400451 0.175928 -0.899271
-0.402681 0.730255 -0.551883
-0.201801 0.940841 -0.272204
-0.852534 0.518969 -0.0621066
-0.729693 0.519789 -0.444259
-0.406 0.176399 -0.896687
-0.730687 0.176545 -0.659491
-0.650821 0.731986 0.201565
-0.321998 0.941721 0.0973547
-0.325885 0.523495 0.787243
-0.652464 0.522204 0.549176
-0.979115 0.177805 0.0985869
-0.857087 0.178312 0.48333
0.00074441 0.735199 0.677851
0.00317198 0.943882 0.330266
0.656176 0.522342 0.544602
0.331016 0.523908 0.784824
0.197021 -0.176144 -0.964446
0.20548 0.177881 0.96236
0.651496 0.731864 0.199821
0.324279 0.941458 0.0921958
0.200221 0.939774 -0.277014
0.402681 0.730255 -0.551883
0.730024 0.176561 -0.66022
0.726896 0.519093 -0.449628
0.851743 0.519522 -0.0680449
0.859934 0.178306 0.478247
0.979641 0.177715 0.0933861
0 0 0
0 0 0___
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Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

[Anastasia Yendiki]

Hi Ismail - Are you passing the nifti volume as input to trac-all? It's 
hard to tell without looking at your configuration file.

Best,
a.y

On Tue, 28 Jun 2016, Koubiyr, Ismail wrote:

> Hi everyone,
>
> I have some problems trying to run TRACULA on some DWI data. It is a mosaic 
> Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec 
> and bval files.
> Then I run the trac-all -prep -c command and I get the following error :
>
> WARNING: file /My/path/to/dicom does not contain a Siemens ASCII header
> has this file been anonymized?
> ERROR: cannot unpack mosiacs without ASCII header
>
> I tried to unpack the mosaics with gdcmtar, but I got the same error.
>
> Thank you in advance for your help,
>
> Ismail
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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[Freesurfer] Tracula : ERROR: cannot unpack mosiacs without ASCII header

[Koubiyr, Ismail]

Hi everyone,

I’m reposting my problem if someone could help me I would really appreciate it.

I have some problems trying to run TRACULA on some DWI data. It is a mosaic 
Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and 
bval files.
Then I run the trac-all -prep -c command and I get the following error :

WARNING: file /My/path/to/dicom does not contain a Siemens ASCII header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header

I tried to unpack the mosaics with gdcmtar, but I got the same error.

P.S : DTIFIT works on FSL (FDT) but gives a poor quality in the reconstruction 
not as the one expected with Tracula.

Thank you in advance for your help,

Ismail

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[Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

[Koubiyr, Ismail]

Hi everyone,

I have some problems trying to run TRACULA on some DWI data. It is a mosaic 
Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and 
bval files.
Then I run the trac-all -prep -c command and I get the following error :

WARNING: file /My/path/to/dicom does not contain a Siemens ASCII header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header

I tried to unpack the mosaics with gdcmtar, but I got the same error.

Thank you in advance for your help,

Ismail
___
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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