subject:"\[Freesurfer\] mri_convert \: ERROR\: cannot unpack mosiacs without ASCII header"

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

2016-07-21 Thread Koubiyr, Ismail

Doug, Zeke,

Thank you very much for your help.

Best,

Ismail

On Jul 21, 2016, at 1:15 AM,
zkauf...@nmr.mgh.harvard.edu wrote:

Current versions of the Mac freesurfer binaries are not compatible with
the v5.3 release. Too much has changed since then. If you wanted to use
the newest version on the code you will need to download the latest dev
version of freesurfer from this page (see "Development Version"):

https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall#Download

Hope this helps.

-Zeke

There was an obscure error having to do with the ascii header when
unpacking skyra data on the mac, that might be it. Zeke, can you get
Ismail a version of mri_convert appropriate for his OS?

doug

On 7/20/16 10:34 AM, Koubiyr, Ismail wrote:
Hi Doug,

I tried it on the cluster and it worked, which is weird because it was
not working before . Any idea what might be the problem on my system ?
Thanks again.

Ismail

On Jul 19, 2016, at 10:32 PM, Douglas Greve

> wrote:

I used the same version, but I used it on linux. Do you have a linux
box with FS installed that you can try it on?

On 7/19/16 1:57 PM, Koubiyr, Ismail wrote:
I used the same command line as you did. And when I check with
mri_probedicom I can see the ASCII header.

Here is the version of FS I am using :
freesurfer-i386-apple-darwin11.4.2-stable5-20130514

Do you think it might be related ?

Thanks again.

Ismail

On Jul 19, 2016, at 1:27 PM, Douglas N Greve

> wrote:

What is your exact command line?

The version of the file that you gave me definitely has an ascii
header,
and I don't get that warning when I convert. What version of FS are
you
using on what platform? To check whether that file has an ascii
header, run

mri_probedicom --i
MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931

There should be a line like below

### ASCCONV BEGIN

On 07/19/2016 01:16 PM, Koubiyr, Ismail wrote:
Hi Doug,

That's weird because I can't convert it using only mri_convert, here
is the error I get :

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 why ?

Best,

Ismail

On Jul 19, 2016, at 1:11 PM, Douglas N Greve

>
wrote:

I was able to convert it fine with
mri_convert MR.1.3.12.2.1107.5.2.19.45306.2014091812372179441003292
output.nii.gz
If I included -it dicom, the conversion did not have an error,
but the
output had only one slice. Since these are mosaics, they need the
Siemens ascii header which is ignored with -it dicom. So ...
don't use
-it dicom

On 07/19/2016 11:06 AM, Koubiyr, Ismail wrote:
Hi Doug,

It is still an issue. I uploaded the DICOMs to you. Hope it could
be
useful.
Thanks.

Ismail

On Jul 18, 2016, at 6:14 PM, Douglas N Greve

>
wrote:

Is this still a problem? If so, can you upload the dicom files
to our
file drop?

On 07/05/2016 11:24 AM, Koubiyr, Ismail wrote:
The file has not been anonymized.

Thanks,

Ismail

On Jul 5, 2016, at 11:20 AM, Douglas N Greve

>
wrote:

can you answer the question that it asks?

On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote:
Hi everyone,

I'm having some issues converting my DICOMs (DWI) into NIFTI
using
mri_convert. I looked for other topics with people having
the same
kind of problem but couldn't find an answer.

Each time I run mri_convert on my DICOMs I get the following
error :
WARNING: file
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

Here are the following DICOMs informations :
Identification
NumarisVer syngo MR D13
ScannerModel Skyra
PatientName x
Date and time
StudyDate 20140918
StudyTime 121037.203000
SeriesTime 123450.60
AcqTime 123257.367500
Acquisition parameters
PulseSeq ep_b0
Protocol AX DTI no angle MS NEX 4 2
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 96
InversionTime -1
RepetitionTime 4700
PhEncFOV 0
ReadoutFOV 0
Image information
RunNo 4
SeriesNo 5
ImageNo 1
NImageRows 990
NImageCols 990
NFrames 64
SliceArraylSize 0
IsMosaic 1
ImgPos 1075.1575

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

2016-07-20 Thread zkaufman


Current versions of the Mac freesurfer binaries are not compatible with
the v5.3 release. Too much has changed since then. If you wanted to use
the newest version on the code you will need to download the latest dev
version of freesurfer from this page (see "Development Version"):

  https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall#Download

Hope this helps.

-Zeke

> There was an obscure error having to do with the ascii header when
> unpacking skyra data on the mac, that might be it. Zeke, can you get
> Ismail a version of mri_convert appropriate for his OS?
>
> doug
>
>
>
> On 7/20/16 10:34 AM, Koubiyr, Ismail wrote:
>> Hi Doug,
>>
>> I tried it on the cluster and it worked, which is weird because it was
>> not working before  Any idea what might be the problem on my system ?
>> Thanks again.
>>
>> Ismail
>>
>>> On Jul 19, 2016, at 10:32 PM, Douglas Greve
>>> > wrote:
>>>
>>> I used the same version, but I used it on linux. Do you have a linux
>>> box with FS installed that you can try it on?
>>>
>>>
>>> On 7/19/16 1:57 PM, Koubiyr, Ismail wrote:
 I used the same command line as you did. And when I check with
 mri_probedicom I can see the ASCII header.

 Here is the version of FS I am using :
 freesurfer-i386-apple-darwin11.4.2-stable5-20130514

 Do you think it might be related ?

 Thanks again.

 Ismail

> On Jul 19, 2016, at 1:27 PM, Douglas N Greve
> > wrote:
>
> What is your exact command line?
>
> The version of the file that you gave me definitely has an ascii
> header,
> and I don't get that warning when I convert. What version of FS are
> you
> using on what platform? To check whether that file has an ascii
> header, run
>
> mri_probedicom --i
> MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931
>
> There should be a line like below
>
> ### ASCCONV BEGIN
>
>
> On 07/19/2016 01:16 PM, Koubiyr, Ismail wrote:
>> Hi Doug,
>>
>> Thats weird because I cant convert it using only mri_convert, here
>> is the error I get :
>>
>> 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 why ?
>>
>> Best,
>>
>> Ismail
>>
>>> On Jul 19, 2016, at 1:11 PM, Douglas N Greve
>>> >> >
>>> wrote:
>>>
>>> I was able to convert it fine with
>>> mri_convert MR.1.3.12.2.1107.5.2.19.45306.2014091812372179441003292
>>> output.nii.gz
>>> If I included -it dicom, the conversion did not have an error,
>>> but the
>>> output had only one slice. Since these are mosaics, they need the
>>> Siemens ascii header which is ignored with -it dicom. So ...
>>> don't use
>>> -it dicom
>>>
>>>
>>> On 07/19/2016 11:06 AM, Koubiyr, Ismail wrote:
 Hi Doug,

 It is still an issue. I uploaded the DICOMs to you. Hope it could
 be
 useful.
 Thanks.

 Ismail

> On Jul 18, 2016, at 6:14 PM, Douglas N Greve
>  >
> wrote:
>
> Is this still a problem? If so, can you upload the dicom files
> to our
> file drop?
>
> On 07/05/2016 11:24 AM, Koubiyr, Ismail wrote:
>> The file has not been anonymized.
>>
>> Thanks,
>>
>> Ismail
>>
>>> On Jul 5, 2016, at 11:20 AM, Douglas N Greve
>>> >> >
>>> wrote:
>>>
>>> can you answer the question that it asks?
>>>
>>> On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote:
 Hi everyone,

 Im having some issues converting my DICOMs (DWI) into NIFTI
 using
 mri_convert. I looked for other topics with people having
 the same
 kind of problem but couldnt find an answer.

 Each time I run mri_convert on my DICOMs I get the following
 error :
 WARNING: file
 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

 Here are the following DICOMs

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

2016-07-20 Thread Douglas Greve

There was an obscure error having to do with the ascii header when
unpacking skyra data on the mac, that might be it. Zeke, can you get
Ismail a version of mri_convert appropriate for his OS?

doug

On 7/20/16 10:34 AM, Koubiyr, Ismail wrote:

Hi Doug,

I tried it on the cluster and it worked, which is weird because it was
not working before … Any idea what might be the problem on my system ?

Thanks again.

Ismail

On Jul 19, 2016, at 10:32 PM, Douglas Greve
> wrote:

I used the same version, but I used it on linux. Do you have a linux
box with FS installed that you can try it on?

On 7/19/16 1:57 PM, Koubiyr, Ismail wrote:
I used the same command line as you did. And when I check with
mri_probedicom I can see the ASCII header.

Here is the version of FS I am using :
freesurfer-i386-apple-darwin11.4.2-stable5-20130514

Do you think it might be related ?

Thanks again.

Ismail

On Jul 19, 2016, at 1:27 PM, Douglas N Greve
> wrote:

What is your exact command line?

The version of the file that you gave me definitely has an ascii
header,

and I don't get that warning when I convert. What version of FS are you
using on what platform? To check whether that file has an ascii
header, run

mri_probedicom --i
MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931

There should be a line like below

### ASCCONV BEGIN

On 07/19/2016 01:16 PM, Koubiyr, Ismail wrote:

Hi Doug,

That’s weird because I can’t convert it using only mri_convert, here
is the error I get :

Any idea why ?

Best,

Ismail

On Jul 19, 2016, at 1:11 PM, Douglas N Greve
>
wrote:

I was able to convert it fine with
mri_convert MR.1.3.12.2.1107.5.2.19.45306.2014091812372179441003292
output.nii.gz
If I included -it dicom, the conversion did not have an error,
but the

output had only one slice. Since these are mosaics, they need the
Siemens ascii header which is ignored with -it dicom. So ...
don't use

-it dicom

On 07/19/2016 11:06 AM, Koubiyr, Ismail wrote:

Hi Doug,

It is still an issue. I uploaded the DICOMs to you. Hope it could be
useful.
Thanks.

Ismail

On Jul 18, 2016, at 6:14 PM, Douglas N Greve
>
wrote:

Is this still a problem? If so, can you upload the dicom files
to our

file drop?

On 07/05/2016 11:24 AM, Koubiyr, Ismail wrote:

The file has not been anonymized.

Thanks,

Ismail

On Jul 5, 2016, at 11:20 AM, Douglas N Greve
>
wrote:

can you answer the question that it asks?

On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote:

Hi everyone,

I’m having some issues converting my DICOMs (DWI) into NIFTI
using
mri_convert. I looked for other topics with people having
the same

kind of problem but couldn’t find an answer.

Each time I run mri_convert on my DICOMs I get the following
error :

WARNING: file
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

Then I try using mri_convert -it dicom, it converts the files
but not
as it is expected, you could notice the difference when I run
mri_info
on my output :
Volume information for output.nii.gz
type: nii
dimensions: 990 x 990 x 1 x 64
voxel sizes: 2.1818, 2.1818, 2.
type: SHORT (4)
fov: 2160.000
dof: 0

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

2016-07-20 Thread Koubiyr, Ismail

Hi Doug,

I tried it on the cluster and it worked, which is weird because it was not 
working before … Any idea what might be the problem on my system ?
Thanks again.

Ismail

On Jul 19, 2016, at 10:32 PM, Douglas Greve 
> wrote:

I used the same version, but I used it on linux. Do you have a linux box with 
FS installed that you can try it on?

On 7/19/16 1:57 PM, Koubiyr, Ismail wrote:
I used the same command line as you did. And when I check with mri_probedicom I 
can see the ASCII header.

Here is the version of FS I am using : 
freesurfer-i386-apple-darwin11.4.2-stable5-20130514

Do you think it might be related ?

Thanks again.

Ismail

On Jul 19, 2016, at 1:27 PM, Douglas N Greve 
> wrote:

What is your exact command line?

The version of the file that you gave me definitely has an ascii header,
and I don't get that warning when I convert. What version of FS are you
using on what platform? To check whether that file has an ascii header, run

mri_probedicom --i MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931

There should be a line like below

### ASCCONV BEGIN

On 07/19/2016 01:16 PM, Koubiyr, Ismail wrote:
Hi Doug,

That’s weird because I can’t convert it using only mri_convert, here
is the error I get :

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 why ?

Best,

Ismail

On Jul 19, 2016, at 1:11 PM, Douglas N Greve

> wrote:

I was able to convert it fine with
mri_convert MR.1.3.12.2.1107.5.2.19.45306.2014091812372179441003292
output.nii.gz
If I included -it dicom, the conversion did not have an error, but the
output had only one slice. Since these are mosaics, they need the
Siemens ascii header which is ignored with -it dicom. So ... don't use
-it dicom

On 07/19/2016 11:06 AM, Koubiyr, Ismail wrote:
Hi Doug,

It is still an issue. I uploaded the DICOMs to you. Hope it could be
useful.
Thanks.

Ismail

On Jul 18, 2016, at 6:14 PM, Douglas N Greve

> wrote:

Is this still a problem? If so, can you upload the dicom files to our
file drop?

On 07/05/2016 11:24 AM, Koubiyr, Ismail wrote:
The file has not been anonymized.

Thanks,

Ismail

On Jul 5, 2016, at 11:20 AM, Douglas N Greve

> wrote:

can you answer the question that it asks?

On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote:
Hi everyone,

I’m having some issues converting my DICOMs (DWI) into NIFTI using
mri_convert. I looked for other topics with people having the same
kind of problem but couldn’t find an answer.

Each time I run mri_convert on my DICOMs I get the following error :
WARNING: file
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

Here are the following DICOMs informations :
Identification
NumarisVer   syngo MR D13
ScannerModel Skyra
PatientName   x
Date and time
StudyDate 20140918
StudyTime 121037.203000
SeriesTime   123450.60
AcqTime   123257.367500
Acquisition parameters
PulseSeq ep_b0
Protocol AX DTI no angle MS NEX 4 2
PhEncDir COL
EchoNo   1
FlipAngle 90
EchoTime 96
InversionTime -1
RepetitionTime   4700
PhEncFOV 0
ReadoutFOV   0
Image information
RunNo 4
SeriesNo 5
ImageNo   1
NImageRows   990
NImageCols   990
NFrames   64
SliceArraylSize   0
IsMosaic 1
ImgPos   1075.1575 1069.8385 -48.6769
VolRes 2.1818   2.1818   2.
VolDim 000
Vc -1.  -0.   0.
Vr -0.  -1.   0.
Vs 0.   0.   0.
VolCenter   0.   0.   0.
TransferSyntaxUID 1.2.840.10008.1.2.1

Then I try using mri_convert -it dicom, it converts the files
but not
as it is expected, you could notice the difference when I run
mri_info
on my output :
Volume information for output.nii.gz
type: nii
  dimensions: 990 x 990 x 1 x 64
 voxel sizes: 2.1818, 2.1818, 2.
type: SHORT (4)
 fov: 2160.000
 dof: 0
  xstart: -1080.0, xend: 1080.0
  ystart: -1080.0, yend: 1080.0
  zstart: -1.0, zend: 1.0
  TR: 4700.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip
angle: 0.00 degrees
 nframes: 64
 PhEncDir: UNKNOWN
ras xform present
  xform info: x_r =  -1., y_r =  -0., z_r =

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

2016-07-19 Thread Douglas Greve

I used the same version, but I used it on linux. Do you have a linux box 
with FS installed that you can try it on?

On 7/19/16 1:57 PM, Koubiyr, Ismail wrote:
I used the same command line as you did. And when I check with 
mri_probedicom I can see the ASCII header.

Here is the version of FS I am using : 
freesurfer-i386-apple-darwin11.4.2-stable5-20130514

Do you think it might be related ?

Thanks again.

Ismail

On Jul 19, 2016, at 1:27 PM, Douglas N Greve 
> wrote:

What is your exact command line?

The version of the file that you gave me definitely has an ascii header,
and I don't get that warning when I convert. What version of FS are you
using on what platform? To check whether that file has an ascii 
header, run

mri_probedicom --i 
MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931

There should be a line like below

### ASCCONV BEGIN

On 07/19/2016 01:16 PM, Koubiyr, Ismail wrote:

Hi Doug,

That’s weird because I can’t convert it using only mri_convert, here
is the error I get :

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 why ?

Best,

Ismail

On Jul 19, 2016, at 1:11 PM, Douglas N Greve
> 
wrote:

I was able to convert it fine with
mri_convert MR.1.3.12.2.1107.5.2.19.45306.2014091812372179441003292
output.nii.gz
If I included -it dicom, the conversion did not have an error, but the
output had only one slice. Since these are mosaics, they need the
Siemens ascii header which is ignored with -it dicom. So ... don't use
-it dicom

On 07/19/2016 11:06 AM, Koubiyr, Ismail wrote:

Hi Doug,

It is still an issue. I uploaded the DICOMs to you. Hope it could be
useful.
Thanks.

Ismail

On Jul 18, 2016, at 6:14 PM, Douglas N Greve
> 
wrote:

Is this still a problem? If so, can you upload the dicom files to our
file drop?

On 07/05/2016 11:24 AM, Koubiyr, Ismail wrote:

The file has not been anonymized.

Thanks,

Ismail

On Jul 5, 2016, at 11:20 AM, Douglas N Greve
> 
wrote:

can you answer the question that it asks?

On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote:

Hi everyone,

I’m having some issues converting my DICOMs (DWI) into NIFTI using
mri_convert. I looked for other topics with people having the same
kind of problem but couldn’t find an answer.

Each time I run mri_convert on my DICOMs I get the following 
error :

WARNING: file
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

Here are the following DICOMs informations :
Identification
NumarisVer   syngo MR D13
ScannerModel Skyra
PatientName   x
Date and time
StudyDate 20140918
StudyTime 121037.203000
SeriesTime   123450.60
AcqTime   123257.367500
Acquisition parameters
PulseSeq ep_b0
Protocol AX DTI no angle MS NEX 4 2
PhEncDir COL
EchoNo   1
FlipAngle 90
EchoTime 96
InversionTime -1
RepetitionTime   4700
PhEncFOV 0
ReadoutFOV   0
Image information
RunNo 4
SeriesNo 5
ImageNo   1
NImageRows   990
NImageCols   990
NFrames   64
SliceArraylSize   0
IsMosaic 1
ImgPos   1075.1575 1069.8385 -48.6769
VolRes 2.1818   2.1818   2.
VolDim 000
Vc -1.  -0.   0.
Vr -0.  -1.   0.
Vs 0.   0.   0.
VolCenter   0.   0.   0.
TransferSyntaxUID 1.2.840.10008.1.2.1

Then I try using mri_convert -it dicom, it converts the files
but not
as it is expected, you could notice the difference when I run
mri_info
on my output :
Volume information for output.nii.gz
type: nii
  dimensions: 990 x 990 x 1 x 64
 voxel sizes: 2.1818, 2.1818, 2.
type: SHORT (4)
 fov: 2160.000
 dof: 0
  xstart: -1080.0, xend: 1080.0
  ystart: -1080.0, yend: 1080.0
  zstart: -1.0, zend: 1.0
  TR: 4700.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip
angle: 0.00 degrees
 nframes: 64
 PhEncDir: UNKNOWN
ras xform present
  xform info: x_r =  -1., y_r =  -0., z_r = -0., c_r =
-4.8425
: x_a =  -0., y_a =  -1., z_a = -0., c_a =
-10.1615
: x_s =   0., y_s =   0., z_s = 1., c_s =
-47.6769
Orientation   : LPS
Primary Slice Direction: axial

voxel to ras transform:
 -2.1818

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

2016-07-19 Thread Koubiyr, Ismail

I used the same command line as you did. And when I check with mri_probedicom I 
can see the ASCII header.

Here is the version of FS I am using : 
freesurfer-i386-apple-darwin11.4.2-stable5-20130514

Do you think it might be related ?

Thanks again.

Ismail

On Jul 19, 2016, at 1:27 PM, Douglas N Greve 
> wrote:

What is your exact command line?

The version of the file that you gave me definitely has an ascii header,
and I don't get that warning when I convert. What version of FS are you
using on what platform? To check whether that file has an ascii header, run

mri_probedicom --i MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931

There should be a line like below

### ASCCONV BEGIN

On 07/19/2016 01:16 PM, Koubiyr, Ismail wrote:
Hi Doug,

That’s weird because I can’t convert it using only mri_convert, here
is the error I get :

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 why ?

Best,

Ismail

On Jul 19, 2016, at 1:11 PM, Douglas N Greve

> wrote:

I was able to convert it fine with
mri_convert MR.1.3.12.2.1107.5.2.19.45306.2014091812372179441003292
output.nii.gz
If I included -it dicom, the conversion did not have an error, but the
output had only one slice. Since these are mosaics, they need the
Siemens ascii header which is ignored with -it dicom. So ... don't use
-it dicom

On 07/19/2016 11:06 AM, Koubiyr, Ismail wrote:
Hi Doug,

It is still an issue. I uploaded the DICOMs to you. Hope it could be
useful.
Thanks.

Ismail

On Jul 18, 2016, at 6:14 PM, Douglas N Greve

> wrote:

Is this still a problem? If so, can you upload the dicom files to our
file drop?

On 07/05/2016 11:24 AM, Koubiyr, Ismail wrote:
The file has not been anonymized.

Thanks,

Ismail

On Jul 5, 2016, at 11:20 AM, Douglas N Greve

> wrote:

can you answer the question that it asks?

On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote:
Hi everyone,

I’m having some issues converting my DICOMs (DWI) into NIFTI using
mri_convert. I looked for other topics with people having the same
kind of problem but couldn’t find an answer.

Each time I run mri_convert on my DICOMs I get the following error :
WARNING: file
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

Here are the following DICOMs informations :
Identification
NumarisVer   syngo MR D13
ScannerModel Skyra
PatientName   x
Date and time
StudyDate 20140918
StudyTime 121037.203000
SeriesTime   123450.60
AcqTime   123257.367500
Acquisition parameters
PulseSeq ep_b0
Protocol AX DTI no angle MS NEX 4 2
PhEncDir COL
EchoNo   1
FlipAngle 90
EchoTime 96
InversionTime -1
RepetitionTime   4700
PhEncFOV 0
ReadoutFOV   0
Image information
RunNo 4
SeriesNo 5
ImageNo   1
NImageRows   990
NImageCols   990
NFrames   64
SliceArraylSize   0
IsMosaic 1
ImgPos   1075.1575 1069.8385 -48.6769
VolRes 2.1818   2.1818   2.
VolDim 000
Vc -1.  -0.   0.
Vr -0.  -1.   0.
Vs 0.   0.   0.
VolCenter   0.   0.   0.
TransferSyntaxUID 1.2.840.10008.1.2.1

Then I try using mri_convert -it dicom, it converts the files
but not
as it is expected, you could notice the difference when I run
mri_info
on my output :
Volume information for output.nii.gz
type: nii
  dimensions: 990 x 990 x 1 x 64
 voxel sizes: 2.1818, 2.1818, 2.
type: SHORT (4)
 fov: 2160.000
 dof: 0
  xstart: -1080.0, xend: 1080.0
  ystart: -1080.0, yend: 1080.0
  zstart: -1.0, zend: 1.0
  TR: 4700.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip
angle: 0.00 degrees
 nframes: 64
 PhEncDir: UNKNOWN
ras xform present
  xform info: x_r =  -1., y_r =  -0., z_r = -0., c_r =
-4.8425
: x_a =  -0., y_a =  -1., z_a = -0., c_a =
-10.1615
: x_s =   0., y_s =   0., z_s = 1., c_s =
-47.6769
Orientation   : LPS
Primary Slice Direction: axial

voxel to ras transform:
 -2.1818  -0.  -0.  1075.1575
 -0.  -2.1818  -0.  1069.8385
  0.   0.   2.   -48.6769
  0.   0.   0. 1.

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

2016-07-19 Thread Douglas N Greve

What is your exact command line?

The version of the file that you gave me definitely has an ascii header, 
and I don't get that warning when I convert. What version of FS are you 
using on what platform? To check whether that file has an ascii header, run

mri_probedicom --i MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931

There should be a line like below

### ASCCONV BEGIN


On 07/19/2016 01:16 PM, Koubiyr, Ismail wrote:
> Hi Doug,
>
> That’s weird because I can’t convert it using only mri_convert, here 
> is the error I get :
>
> 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 why ?
>
> Best,
>
> Ismail
>
>> On Jul 19, 2016, at 1:11 PM, Douglas N Greve 
>> > wrote:
>>
>> I was able to convert it fine with
>>  mri_convert MR.1.3.12.2.1107.5.2.19.45306.2014091812372179441003292
>> output.nii.gz
>> If I included -it dicom, the conversion did not have an error, but the
>> output had only one slice. Since these are mosaics, they need the
>> Siemens ascii header which is ignored with -it dicom. So ... don't use
>> -it dicom
>>
>>
>> On 07/19/2016 11:06 AM, Koubiyr, Ismail wrote:
>>> Hi Doug,
>>>
>>> It is still an issue. I uploaded the DICOMs to you. Hope it could be 
>>> useful.
>>> Thanks.
>>>
>>> Ismail
>>>
 On Jul 18, 2016, at 6:14 PM, Douglas N Greve 
 > wrote:

 Is this still a problem? If so, can you upload the dicom files to our
 file drop?

 On 07/05/2016 11:24 AM, Koubiyr, Ismail wrote:
> The file has not been anonymized.
>
> Thanks,
>
> Ismail
>
>> On Jul 5, 2016, at 11:20 AM, Douglas N Greve 
>> > wrote:
>>
>> can you answer the question that it asks?
>>
>> On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote:
>>> Hi everyone,
>>>
>>> I’m having some issues converting my DICOMs (DWI) into NIFTI using
>>> mri_convert. I looked for other topics with people having the same
>>> kind of problem but couldn’t find an answer.
>>>
>>> Each time I run mri_convert on my DICOMs I get the following error :
>>> WARNING: file 
>>> 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
>>>
>>> Here are the following DICOMs informations :
>>> Identification
>>> NumarisVer   syngo MR D13
>>> ScannerModel Skyra
>>> PatientName   x
>>> Date and time
>>> StudyDate 20140918
>>> StudyTime 121037.203000
>>> SeriesTime   123450.60
>>> AcqTime   123257.367500
>>> Acquisition parameters
>>> PulseSeq ep_b0
>>> Protocol AX DTI no angle MS NEX 4 2
>>> PhEncDir COL
>>> EchoNo   1
>>> FlipAngle 90
>>> EchoTime 96
>>> InversionTime -1
>>> RepetitionTime   4700
>>> PhEncFOV 0
>>> ReadoutFOV   0
>>> Image information
>>> RunNo 4
>>> SeriesNo 5
>>> ImageNo   1
>>> NImageRows   990
>>> NImageCols   990
>>> NFrames   64
>>> SliceArraylSize   0
>>> IsMosaic 1
>>> ImgPos   1075.1575 1069.8385 -48.6769
>>> VolRes 2.1818   2.1818   2.
>>> VolDim 000
>>> Vc -1.  -0.   0.
>>> Vr -0.  -1.   0.
>>> Vs 0.   0.   0.
>>> VolCenter   0.   0.   0.
>>> TransferSyntaxUID 1.2.840.10008.1.2.1
>>>
>>>
>>> Then I try using mri_convert -it dicom, it converts the files 
>>> but not
>>> as it is expected, you could notice the difference when I run 
>>> mri_info
>>> on my output :
>>> Volume information for output.nii.gz
>>>  type: nii
>>>dimensions: 990 x 990 x 1 x 64
>>>   voxel sizes: 2.1818, 2.1818, 2.
>>>  type: SHORT (4)
>>>   fov: 2160.000
>>>   dof: 0
>>>xstart: -1080.0, xend: 1080.0
>>>ystart: -1080.0, yend: 1080.0
>>>zstart: -1.0, zend: 1.0
>>>TR: 4700.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip
>>> angle: 0.00 degrees
>>>   nframes: 64
>>>   PhEncDir: UNKNOWN
>>> ras xform present
>>>xform info: x_r =  -1., y_r =  -0., z_r = -0., c_r =
>>>  -4.8425
>>>  : x_a =  -0., y_a =  -1., z_a = -0., c_a =
>>>

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

2016-07-19 Thread Koubiyr, Ismail

Hi Doug,

That’s weird because I can’t convert it using only mri_convert, here is the 
error I get :

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 why ?

Best,

Ismail

On Jul 19, 2016, at 1:11 PM, Douglas N Greve 
> wrote:

I was able to convert it fine with
 mri_convert MR.1.3.12.2.1107.5.2.19.45306.2014091812372179441003292
output.nii.gz
If I included -it dicom, the conversion did not have an error, but the
output had only one slice. Since these are mosaics, they need the
Siemens ascii header which is ignored with -it dicom. So ... don't use
-it dicom

On 07/19/2016 11:06 AM, Koubiyr, Ismail wrote:
Hi Doug,

It is still an issue. I uploaded the DICOMs to you. Hope it could be useful.
Thanks.

Ismail

On Jul 18, 2016, at 6:14 PM, Douglas N Greve 
> wrote:

Is this still a problem? If so, can you upload the dicom files to our
file drop?

On 07/05/2016 11:24 AM, Koubiyr, Ismail wrote:
The file has not been anonymized.

Thanks,

Ismail

On Jul 5, 2016, at 11:20 AM, Douglas N Greve 
> wrote:

can you answer the question that it asks?

On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote:
Hi everyone,

I’m having some issues converting my DICOMs (DWI) into NIFTI using
mri_convert. I looked for other topics with people having the same
kind of problem but couldn’t find an answer.

Each time I run mri_convert on my DICOMs I get the following error :
WARNING: file 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

Here are the following DICOMs informations :
Identification
NumarisVer   syngo MR D13
ScannerModel Skyra
PatientName   x
Date and time
StudyDate 20140918
StudyTime 121037.203000
SeriesTime   123450.60
AcqTime   123257.367500
Acquisition parameters
PulseSeq ep_b0
Protocol AX DTI no angle MS NEX 4 2
PhEncDir COL
EchoNo   1
FlipAngle 90
EchoTime 96
InversionTime -1
RepetitionTime   4700
PhEncFOV 0
ReadoutFOV   0
Image information
RunNo 4
SeriesNo 5
ImageNo   1
NImageRows   990
NImageCols   990
NFrames   64
SliceArraylSize   0
IsMosaic 1
ImgPos   1075.1575 1069.8385 -48.6769
VolRes 2.1818   2.1818   2.
VolDim 000
Vc -1.  -0.   0.
Vr -0.  -1.   0.
Vs 0.   0.   0.
VolCenter   0.   0.   0.
TransferSyntaxUID 1.2.840.10008.1.2.1

Then I try using mri_convert -it dicom, it converts the files but not
as it is expected, you could notice the difference when I run mri_info
on my output :
Volume information for output.nii.gz
 type: nii
   dimensions: 990 x 990 x 1 x 64
  voxel sizes: 2.1818, 2.1818, 2.
 type: SHORT (4)
  fov: 2160.000
  dof: 0
   xstart: -1080.0, xend: 1080.0
   ystart: -1080.0, yend: 1080.0
   zstart: -1.0, zend: 1.0
   TR: 4700.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip
angle: 0.00 degrees
  nframes: 64
  PhEncDir: UNKNOWN
ras xform present
   xform info: x_r =  -1., y_r =  -0., z_r = -0., c_r =
 -4.8425
 : x_a =  -0., y_a =  -1., z_a = -0., c_a =
-10.1615
 : x_s =   0., y_s =   0., z_s = 1., c_s =
-47.6769
Orientation   : LPS
Primary Slice Direction: axial

voxel to ras transform:
  -2.1818  -0.  -0.  1075.1575
  -0.  -2.1818  -0.  1069.8385
   0.   0.   2.   -48.6769
   0.   0.   0. 1.

voxel-to-ras determinant 9.52066

ras to voxel transform:
  -0.4583   0.   0.   492.7805
   0.  -0.4583   0.   490.3426
  -0.  -0.   0.500024.3384
   0.   0.   0. 1.

I would really appreciate your help, thank you.

Best,

Ismail

___
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
gr...@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:

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

2016-07-19 Thread Douglas N Greve

I was able to convert it fine with
  mri_convert MR.1.3.12.2.1107.5.2.19.45306.2014091812372179441003292 
output.nii.gz
If I included -it dicom, the conversion did not have an error, but the 
output had only one slice. Since these are mosaics, they need the 
Siemens ascii header which is ignored with -it dicom. So ... don't use 
-it dicom


On 07/19/2016 11:06 AM, Koubiyr, Ismail wrote:
> Hi Doug,
>
> It is still an issue. I uploaded the DICOMs to you. Hope it could be useful.
> Thanks.
>
> Ismail
>
>> On Jul 18, 2016, at 6:14 PM, Douglas N Greve  
>> wrote:
>>
>> Is this still a problem? If so, can you upload the dicom files to our
>> file drop?
>>
>> On 07/05/2016 11:24 AM, Koubiyr, Ismail wrote:
>>> The file has not been anonymized.
>>>
>>> Thanks,
>>>
>>> Ismail
>>>
 On Jul 5, 2016, at 11:20 AM, Douglas N Greve  
 wrote:

 can you answer the question that it asks?

 On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote:
> Hi everyone,
>
> I’m having some issues converting my DICOMs (DWI) into NIFTI using
> mri_convert. I looked for other topics with people having the same
> kind of problem but couldn’t find an answer.
>
> Each time I run mri_convert on my DICOMs I get the following error :
> WARNING: file 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
>
> Here are the following DICOMs informations :
> Identification
> NumarisVer   syngo MR D13
> ScannerModel Skyra
> PatientName   x
> Date and time
> StudyDate 20140918
> StudyTime 121037.203000
> SeriesTime   123450.60
> AcqTime   123257.367500
> Acquisition parameters
> PulseSeq ep_b0
> Protocol AX DTI no angle MS NEX 4 2
> PhEncDir COL
> EchoNo   1
> FlipAngle 90
> EchoTime 96
> InversionTime -1
> RepetitionTime   4700
> PhEncFOV 0
> ReadoutFOV   0
> Image information
> RunNo 4
> SeriesNo 5
> ImageNo   1
> NImageRows   990
> NImageCols   990
> NFrames   64
> SliceArraylSize   0
> IsMosaic 1
> ImgPos   1075.1575 1069.8385 -48.6769
> VolRes 2.1818   2.1818   2.
> VolDim 000
> Vc -1.  -0.   0.
> Vr -0.  -1.   0.
> Vs 0.   0.   0.
> VolCenter   0.   0.   0.
> TransferSyntaxUID 1.2.840.10008.1.2.1
>
>
> Then I try using mri_convert -it dicom, it converts the files but not
> as it is expected, you could notice the difference when I run mri_info
> on my output :
> Volume information for output.nii.gz
>   type: nii
> dimensions: 990 x 990 x 1 x 64
>voxel sizes: 2.1818, 2.1818, 2.
>   type: SHORT (4)
>fov: 2160.000
>dof: 0
> xstart: -1080.0, xend: 1080.0
> ystart: -1080.0, yend: 1080.0
> zstart: -1.0, zend: 1.0
> TR: 4700.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip
> angle: 0.00 degrees
>nframes: 64
>PhEncDir: UNKNOWN
> ras xform present
> xform info: x_r =  -1., y_r =  -0., z_r = -0., c_r =
>   -4.8425
>   : x_a =  -0., y_a =  -1., z_a = -0., c_a =
> -10.1615
>   : x_s =   0., y_s =   0., z_s = 1., c_s =
> -47.6769
> Orientation   : LPS
> Primary Slice Direction: axial
>
> voxel to ras transform:
>-2.1818  -0.  -0.  1075.1575
>-0.  -2.1818  -0.  1069.8385
> 0.   0.   2.   -48.6769
> 0.   0.   0. 1.
>
> voxel-to-ras determinant 9.52066
>
> ras to voxel transform:
>-0.4583   0.   0.   492.7805
> 0.  -0.4583   0.   490.3426
>-0.  -0.   0.500024.3384
> 0.   0.   0. 1.
>
> I would really appreciate your help, thank you.
>
> Best,
>
> Ismail
>
>
>
> ___
> 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
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop:

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

2016-07-19 Thread Koubiyr, Ismail

Hi Doug,

It is still an issue. I uploaded the DICOMs to you. Hope it could be useful.
Thanks.

Ismail 

> On Jul 18, 2016, at 6:14 PM, Douglas N Greve  
> wrote:
> 
> Is this still a problem? If so, can you upload the dicom files to our 
> file drop?
> 
> On 07/05/2016 11:24 AM, Koubiyr, Ismail wrote:
>> The file has not been anonymized.
>> 
>> Thanks,
>> 
>> Ismail
>> 
>>> On Jul 5, 2016, at 11:20 AM, Douglas N Greve  
>>> wrote:
>>> 
>>> can you answer the question that it asks?
>>> 
>>> On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote:
 Hi everyone,
 
 I’m having some issues converting my DICOMs (DWI) into NIFTI using
 mri_convert. I looked for other topics with people having the same
 kind of problem but couldn’t find an answer.
 
 Each time I run mri_convert on my DICOMs I get the following error :
 WARNING: file 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
 
 Here are the following DICOMs informations :
 Identification
 NumarisVer   syngo MR D13
 ScannerModel Skyra
 PatientName   x
 Date and time
 StudyDate 20140918
 StudyTime 121037.203000
 SeriesTime   123450.60
 AcqTime   123257.367500
 Acquisition parameters
 PulseSeq ep_b0
 Protocol AX DTI no angle MS NEX 4 2
 PhEncDir COL
 EchoNo   1
 FlipAngle 90
 EchoTime 96
 InversionTime -1
 RepetitionTime   4700
 PhEncFOV 0
 ReadoutFOV   0
 Image information
 RunNo 4
 SeriesNo 5
 ImageNo   1
 NImageRows   990
 NImageCols   990
 NFrames   64
 SliceArraylSize   0
 IsMosaic 1
 ImgPos   1075.1575 1069.8385 -48.6769
 VolRes 2.1818   2.1818   2.
 VolDim 000
 Vc -1.  -0.   0.
 Vr -0.  -1.   0.
 Vs 0.   0.   0.
 VolCenter   0.   0.   0.
 TransferSyntaxUID 1.2.840.10008.1.2.1
 
 
 Then I try using mri_convert -it dicom, it converts the files but not
 as it is expected, you could notice the difference when I run mri_info
 on my output :
 Volume information for output.nii.gz
  type: nii
dimensions: 990 x 990 x 1 x 64
   voxel sizes: 2.1818, 2.1818, 2.
  type: SHORT (4)
   fov: 2160.000
   dof: 0
xstart: -1080.0, xend: 1080.0
ystart: -1080.0, yend: 1080.0
zstart: -1.0, zend: 1.0
TR: 4700.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip
 angle: 0.00 degrees
   nframes: 64
   PhEncDir: UNKNOWN
 ras xform present
xform info: x_r =  -1., y_r =  -0., z_r = -0., c_r =
  -4.8425
  : x_a =  -0., y_a =  -1., z_a = -0., c_a =
 -10.1615
  : x_s =   0., y_s =   0., z_s = 1., c_s =
 -47.6769
 Orientation   : LPS
 Primary Slice Direction: axial
 
 voxel to ras transform:
   -2.1818  -0.  -0.  1075.1575
   -0.  -2.1818  -0.  1069.8385
0.   0.   2.   -48.6769
0.   0.   0. 1.
 
 voxel-to-ras determinant 9.52066
 
 ras to voxel transform:
   -0.4583   0.   0.   492.7805
0.  -0.4583   0.   490.3426
   -0.  -0.   0.500024.3384
0.   0.   0. 1.
 
 I would really appreciate your help, thank you.
 
 Best,
 
 Ismail
 
 
 
 ___
 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
>>> gr...@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
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>> 
>

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

2016-07-18 Thread Douglas N Greve

Is this still a problem? If so, can you upload the dicom files to our 
file drop?

On 07/05/2016 11:24 AM, Koubiyr, Ismail wrote:
> The file has not been anonymized.
>
> Thanks,
>
> Ismail
>
>> On Jul 5, 2016, at 11:20 AM, Douglas N Greve  
>> wrote:
>>
>> can you answer the question that it asks?
>>
>> On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote:
>>> Hi everyone,
>>>
>>> I’m having some issues converting my DICOMs (DWI) into NIFTI using
>>> mri_convert. I looked for other topics with people having the same
>>> kind of problem but couldn’t find an answer.
>>>
>>> Each time I run mri_convert on my DICOMs I get the following error :
>>> WARNING: file 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
>>>
>>> Here are the following DICOMs informations :
>>> Identification
>>> NumarisVer   syngo MR D13
>>> ScannerModel Skyra
>>> PatientName   x
>>> Date and time
>>> StudyDate 20140918
>>> StudyTime 121037.203000
>>> SeriesTime   123450.60
>>> AcqTime   123257.367500
>>> Acquisition parameters
>>> PulseSeq ep_b0
>>> Protocol AX DTI no angle MS NEX 4 2
>>> PhEncDir COL
>>> EchoNo   1
>>> FlipAngle 90
>>> EchoTime 96
>>> InversionTime -1
>>> RepetitionTime   4700
>>> PhEncFOV 0
>>> ReadoutFOV   0
>>> Image information
>>> RunNo 4
>>> SeriesNo 5
>>> ImageNo   1
>>> NImageRows   990
>>> NImageCols   990
>>> NFrames   64
>>> SliceArraylSize   0
>>> IsMosaic 1
>>> ImgPos   1075.1575 1069.8385 -48.6769
>>> VolRes 2.1818   2.1818   2.
>>> VolDim 000
>>> Vc -1.  -0.   0.
>>> Vr -0.  -1.   0.
>>> Vs 0.   0.   0.
>>> VolCenter   0.   0.   0.
>>> TransferSyntaxUID 1.2.840.10008.1.2.1
>>>
>>>
>>> Then I try using mri_convert -it dicom, it converts the files but not
>>> as it is expected, you could notice the difference when I run mri_info
>>> on my output :
>>> Volume information for output.nii.gz
>>>   type: nii
>>> dimensions: 990 x 990 x 1 x 64
>>>voxel sizes: 2.1818, 2.1818, 2.
>>>   type: SHORT (4)
>>>fov: 2160.000
>>>dof: 0
>>> xstart: -1080.0, xend: 1080.0
>>> ystart: -1080.0, yend: 1080.0
>>> zstart: -1.0, zend: 1.0
>>> TR: 4700.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip
>>> angle: 0.00 degrees
>>>nframes: 64
>>>PhEncDir: UNKNOWN
>>> ras xform present
>>> xform info: x_r =  -1., y_r =  -0., z_r = -0., c_r =
>>>   -4.8425
>>>   : x_a =  -0., y_a =  -1., z_a = -0., c_a =
>>> -10.1615
>>>   : x_s =   0., y_s =   0., z_s = 1., c_s =
>>> -47.6769
>>> Orientation   : LPS
>>> Primary Slice Direction: axial
>>>
>>> voxel to ras transform:
>>>-2.1818  -0.  -0.  1075.1575
>>>-0.  -2.1818  -0.  1069.8385
>>> 0.   0.   2.   -48.6769
>>> 0.   0.   0. 1.
>>>
>>> voxel-to-ras determinant 9.52066
>>>
>>> ras to voxel transform:
>>>-0.4583   0.   0.   492.7805
>>> 0.  -0.4583   0.   490.3426
>>>-0.  -0.   0.500024.3384
>>> 0.   0.   0. 1.
>>>
>>> I would really appreciate your help, thank you.
>>>
>>> Best,
>>>
>>> Ismail
>>>
>>>
>>>
>>> ___
>>> 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
>> gr...@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
>
> ___
> 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
gr...@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:

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

2016-07-06 Thread Koubiyr, Ismail

Hi,

This is a repost. Would anyone have a solution to this problem ?
Thanks for your help.

Best,

Ismail

> On Jul 5, 2016, at 11:24 AM, Koubiyr, Ismail  wrote:
> 
> The file has not been anonymized.
> 
> Thanks,
> 
> Ismail 
> 
>> On Jul 5, 2016, at 11:20 AM, Douglas N Greve  
>> wrote:
>> 
>> can you answer the question that it asks?
>> 
>> On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote:
>>> Hi everyone,
>>> 
>>> I’m having some issues converting my DICOMs (DWI) into NIFTI using 
>>> mri_convert. I looked for other topics with people having the same 
>>> kind of problem but couldn’t find an answer.
>>> 
>>> Each time I run mri_convert on my DICOMs I get the following error :
>>> WARNING: file 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
>>> 
>>> Here are the following DICOMs informations :
>>> Identification
>>> NumarisVer   syngo MR D13
>>> ScannerModel Skyra
>>> PatientName   x
>>> Date and time
>>> StudyDate 20140918
>>> StudyTime 121037.203000
>>> SeriesTime   123450.60
>>> AcqTime   123257.367500
>>> Acquisition parameters
>>> PulseSeq ep_b0
>>> Protocol AX DTI no angle MS NEX 4 2
>>> PhEncDir COL
>>> EchoNo   1
>>> FlipAngle 90
>>> EchoTime 96
>>> InversionTime -1
>>> RepetitionTime   4700
>>> PhEncFOV 0
>>> ReadoutFOV   0
>>> Image information
>>> RunNo 4
>>> SeriesNo 5
>>> ImageNo   1
>>> NImageRows   990
>>> NImageCols   990
>>> NFrames   64
>>> SliceArraylSize   0
>>> IsMosaic 1
>>> ImgPos   1075.1575 1069.8385 -48.6769
>>> VolRes 2.1818   2.1818   2.
>>> VolDim 000
>>> Vc -1.  -0.   0.
>>> Vr -0.  -1.   0.
>>> Vs 0.   0.   0.
>>> VolCenter   0.   0.   0.
>>> TransferSyntaxUID 1.2.840.10008.1.2.1
>>> 
>>> 
>>> Then I try using mri_convert -it dicom, it converts the files but not 
>>> as it is expected, you could notice the difference when I run mri_info 
>>> on my output :
>>> Volume information for output.nii.gz
>>> type: nii
>>>   dimensions: 990 x 990 x 1 x 64
>>>  voxel sizes: 2.1818, 2.1818, 2.
>>> type: SHORT (4)
>>>  fov: 2160.000
>>>  dof: 0
>>>   xstart: -1080.0, xend: 1080.0
>>>   ystart: -1080.0, yend: 1080.0
>>>   zstart: -1.0, zend: 1.0
>>>   TR: 4700.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip 
>>> angle: 0.00 degrees
>>>  nframes: 64
>>>  PhEncDir: UNKNOWN
>>> ras xform present
>>>   xform info: x_r =  -1., y_r =  -0., z_r = -0., c_r =  
>>> -4.8425
>>> : x_a =  -0., y_a =  -1., z_a = -0., c_a =   
>>> -10.1615
>>> : x_s =   0., y_s =   0., z_s = 1., c_s =   
>>> -47.6769
>>> Orientation   : LPS
>>> Primary Slice Direction: axial
>>> 
>>> voxel to ras transform:
>>>  -2.1818  -0.  -0.  1075.1575
>>>  -0.  -2.1818  -0.  1069.8385
>>>   0.   0.   2.   -48.6769
>>>   0.   0.   0. 1.
>>> 
>>> voxel-to-ras determinant 9.52066
>>> 
>>> ras to voxel transform:
>>>  -0.4583   0.   0.   492.7805
>>>   0.  -0.4583   0.   490.3426
>>>  -0.  -0.   0.500024.3384
>>>   0.   0.   0. 1.
>>> 
>>> I would really appreciate your help, thank you.
>>> 
>>> Best,
>>> 
>>> Ismail
>>> 
>>> 
>>> 
>>> ___
>>> 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
>> gr...@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
> 


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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] mri_convert : ERROR: cannot unpack mosiacs without ASCII header

2016-07-05 Thread Douglas N Greve

can you answer the question that it asks?

On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote:
> Hi everyone,
>
> I’m having some issues converting my DICOMs (DWI) into NIFTI using 
> mri_convert. I looked for other topics with people having the same 
> kind of problem but couldn’t find an answer.
>
> Each time I run mri_convert on my DICOMs I get the following error :
> WARNING: file 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
>
> Here are the following DICOMs informations :
> Identification
> NumarisVer   syngo MR D13
> ScannerModel Skyra
> PatientName   x
> Date and time
> StudyDate 20140918
> StudyTime 121037.203000
> SeriesTime   123450.60
> AcqTime   123257.367500
> Acquisition parameters
> PulseSeq ep_b0
> Protocol AX DTI no angle MS NEX 4 2
> PhEncDir COL
> EchoNo   1
> FlipAngle 90
> EchoTime 96
> InversionTime -1
> RepetitionTime   4700
> PhEncFOV 0
> ReadoutFOV   0
> Image information
> RunNo 4
> SeriesNo 5
> ImageNo   1
> NImageRows   990
> NImageCols   990
> NFrames   64
> SliceArraylSize   0
> IsMosaic 1
> ImgPos   1075.1575 1069.8385 -48.6769
> VolRes 2.1818   2.1818   2.
> VolDim 000
> Vc -1.  -0.   0.
> Vr -0.  -1.   0.
> Vs 0.   0.   0.
> VolCenter   0.   0.   0.
> TransferSyntaxUID 1.2.840.10008.1.2.1
>
>
> Then I try using mri_convert -it dicom, it converts the files but not 
> as it is expected, you could notice the difference when I run mri_info 
> on my output :
> Volume information for output.nii.gz
>   type: nii
> dimensions: 990 x 990 x 1 x 64
>voxel sizes: 2.1818, 2.1818, 2.
>   type: SHORT (4)
>fov: 2160.000
>dof: 0
> xstart: -1080.0, xend: 1080.0
> ystart: -1080.0, yend: 1080.0
> zstart: -1.0, zend: 1.0
> TR: 4700.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip 
> angle: 0.00 degrees
>nframes: 64
>PhEncDir: UNKNOWN
> ras xform present
> xform info: x_r =  -1., y_r =  -0., z_r = -0., c_r =  
>   -4.8425
>   : x_a =  -0., y_a =  -1., z_a = -0., c_a =   
> -10.1615
>   : x_s =   0., y_s =   0., z_s = 1., c_s =   
> -47.6769
> Orientation   : LPS
> Primary Slice Direction: axial
>
> voxel to ras transform:
>-2.1818  -0.  -0.  1075.1575
>-0.  -2.1818  -0.  1069.8385
> 0.   0.   2.   -48.6769
> 0.   0.   0. 1.
>
> voxel-to-ras determinant 9.52066
>
> ras to voxel transform:
>-0.4583   0.   0.   492.7805
> 0.  -0.4583   0.   490.3426
>-0.  -0.   0.500024.3384
> 0.   0.   0. 1.
>
> I would really appreciate your help, thank you.
>
> Best,
>
> Ismail
>
>
>
> ___
> 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
gr...@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/

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

2016-07-05 Thread Koubiyr, Ismail

The file has not been anonymized.

Thanks,

Ismail 

> On Jul 5, 2016, at 11:20 AM, Douglas N Greve  
> wrote:
> 
> can you answer the question that it asks?
> 
> On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote:
>> Hi everyone,
>> 
>> I’m having some issues converting my DICOMs (DWI) into NIFTI using 
>> mri_convert. I looked for other topics with people having the same 
>> kind of problem but couldn’t find an answer.
>> 
>> Each time I run mri_convert on my DICOMs I get the following error :
>> WARNING: file 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
>> 
>> Here are the following DICOMs informations :
>> Identification
>> NumarisVer   syngo MR D13
>> ScannerModel Skyra
>> PatientName   x
>> Date and time
>> StudyDate 20140918
>> StudyTime 121037.203000
>> SeriesTime   123450.60
>> AcqTime   123257.367500
>> Acquisition parameters
>> PulseSeq ep_b0
>> Protocol AX DTI no angle MS NEX 4 2
>> PhEncDir COL
>> EchoNo   1
>> FlipAngle 90
>> EchoTime 96
>> InversionTime -1
>> RepetitionTime   4700
>> PhEncFOV 0
>> ReadoutFOV   0
>> Image information
>> RunNo 4
>> SeriesNo 5
>> ImageNo   1
>> NImageRows   990
>> NImageCols   990
>> NFrames   64
>> SliceArraylSize   0
>> IsMosaic 1
>> ImgPos   1075.1575 1069.8385 -48.6769
>> VolRes 2.1818   2.1818   2.
>> VolDim 000
>> Vc -1.  -0.   0.
>> Vr -0.  -1.   0.
>> Vs 0.   0.   0.
>> VolCenter   0.   0.   0.
>> TransferSyntaxUID 1.2.840.10008.1.2.1
>> 
>> 
>> Then I try using mri_convert -it dicom, it converts the files but not 
>> as it is expected, you could notice the difference when I run mri_info 
>> on my output :
>> Volume information for output.nii.gz
>>  type: nii
>>dimensions: 990 x 990 x 1 x 64
>>   voxel sizes: 2.1818, 2.1818, 2.
>>  type: SHORT (4)
>>   fov: 2160.000
>>   dof: 0
>>xstart: -1080.0, xend: 1080.0
>>ystart: -1080.0, yend: 1080.0
>>zstart: -1.0, zend: 1.0
>>TR: 4700.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip 
>> angle: 0.00 degrees
>>   nframes: 64
>>   PhEncDir: UNKNOWN
>> ras xform present
>>xform info: x_r =  -1., y_r =  -0., z_r = -0., c_r =  
>>  -4.8425
>>  : x_a =  -0., y_a =  -1., z_a = -0., c_a =   
>> -10.1615
>>  : x_s =   0., y_s =   0., z_s = 1., c_s =   
>> -47.6769
>> Orientation   : LPS
>> Primary Slice Direction: axial
>> 
>> voxel to ras transform:
>>   -2.1818  -0.  -0.  1075.1575
>>   -0.  -2.1818  -0.  1069.8385
>>0.   0.   2.   -48.6769
>>0.   0.   0. 1.
>> 
>> voxel-to-ras determinant 9.52066
>> 
>> ras to voxel transform:
>>   -0.4583   0.   0.   492.7805
>>0.  -0.4583   0.   490.3426
>>   -0.  -0.   0.500024.3384
>>0.   0.   0. 1.
>> 
>> I would really appreciate your help, thank you.
>> 
>> Best,
>> 
>> Ismail
>> 
>> 
>> 
>> ___
>> 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
> gr...@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


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

2016-07-05 Thread Koubiyr, Ismail

Hi everyone,

I’m having some issues converting my DICOMs (DWI) into NIFTI using mri_convert. 
I looked for other topics with people having the same kind of problem but 
couldn’t find an answer.

Each time I run mri_convert on my DICOMs I get the following error :
WARNING: file 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

Here are the following DICOMs informations :
Identification
NumarisVersyngo MR D13
ScannerModel  Skyra
PatientName   x
Date and time
StudyDate 20140918
StudyTime 121037.203000
SeriesTime123450.60
AcqTime   123257.367500
Acquisition parameters
PulseSeq  ep_b0
Protocol  AX DTI no angle MS NEX 4 2
PhEncDir  COL
EchoNo1
FlipAngle 90
EchoTime  96
InversionTime -1
RepetitionTime4700
PhEncFOV  0
ReadoutFOV0
Image information
RunNo 4
SeriesNo  5
ImageNo   1
NImageRows990
NImageCols990
NFrames   64
SliceArraylSize   0
IsMosaic  1
ImgPos1075.1575 1069.8385 -48.6769
VolRes  2.1818   2.1818   2.
VolDim  000
Vc -1.  -0.   0.
Vr -0.  -1.   0.
Vs  0.   0.   0.
VolCenter   0.   0.   0.
TransferSyntaxUID 1.2.840.10008.1.2.1


Then I try using mri_convert -it dicom, it converts the files but not as it is 
expected, you could notice the difference when I run mri_info on my output :
Volume information for output.nii.gz
  type: nii
dimensions: 990 x 990 x 1 x 64
   voxel sizes: 2.1818, 2.1818, 2.
  type: SHORT (4)
   fov: 2160.000
   dof: 0
xstart: -1080.0, xend: 1080.0
ystart: -1080.0, yend: 1080.0
zstart: -1.0, zend: 1.0
TR: 4700.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 
degrees
   nframes: 64
   PhEncDir: UNKNOWN
ras xform present
xform info: x_r =  -1., y_r =  -0., z_r =  -0., c_r =-4.8425
  : x_a =  -0., y_a =  -1., z_a =  -0., c_a =   -10.1615
  : x_s =   0., y_s =   0., z_s =   1., c_s =   -47.6769
Orientation   : LPS
Primary Slice Direction: axial

voxel to ras transform:
   -2.1818  -0.  -0.  1075.1575
   -0.  -2.1818  -0.  1069.8385
0.   0.   2.   -48.6769
0.   0.   0. 1.

voxel-to-ras determinant 9.52066

ras to voxel transform:
   -0.4583   0.   0.   492.7805
0.  -0.4583   0.   490.3426
   -0.  -0.   0.500024.3384
0.   0.   0. 1.

I would really appreciate your help, thank you.

Best,

Ismail

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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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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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