Re: [Freesurfer] aparc+aseg.mgz for network analysis

[Koubiyr, Ismail]

I think you can use mri_binarize and set the match values as you like.
Hope it can help.

Best,

Ismail

> On Jul 21, 2016, at 2:13 PM, Jinsong Tang  wrote:
> 
> Hello freesurfers,
> 
> I want to select the subcortical structures (thalamus, pallidum, caudate, 
> putamen, accumbens, hippocampus, and amygdala) and the 68 distinct brain 
> regions as nodes of the individual brain networks. The labels are 
> [9,11:13,17:18,26,48,50:54,58, 1002:1035, 2002:2035].  However, in the 
> aparc+aseg.mgz files, there are also some other labels. Is there any way to 
> delete all other unselected labels?
> 
> Thank you so much!
> Best,
> 
> Jinsong
> ___
> Freesurfer mailing list
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Re: [Freesurfer] mri_convert : ERROR: cannot unpack mosiacs without ASCII header

[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<mailto: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
<gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu> 
<mailto:gr...@nmr.mgh.harvard.edu>> 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
<gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu> 
<mailto:gr...@nmr.mgh.harvard.edu>> 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
<gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>
<mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu>>
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
<gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>
<mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu>>
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
<gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>
<mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu>>
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
NIma

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

[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 
<gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>> 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 
<gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>> 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
<gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu> 
<mailto:gr...@nmr.mgh.harvard.edu>> 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
<gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu> 
<mailto:gr...@nmr.mgh.harvard.edu>> 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
<gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu> 
<mailto:gr...@nmr.mgh.harvard.edu>> 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
 PhEncDi

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

[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 
<gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>> 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
<gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu> 
<mailto:gr...@nmr.mgh.harvard.edu>> 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
<gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu> 
<mailto:gr...@nmr.mgh.harvard.edu>> 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
<gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu> 
<mailto:gr...@nmr.mgh.harvard.edu>> 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

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

[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 
<gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>> 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 
<gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>> 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 
<gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>> 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



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Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358
Fax: 617-726-7422

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FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Out

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

[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 <gr...@nmr.mgh.harvard.edu> 
> 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 <gr...@nmr.mgh.harvard.edu> 
>>> 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
>>>>

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

[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 <ikoub...@bwh.harvard.edu> wrote:
> 
> The file has not been anonymized.
> 
> Thanks,
> 
> Ismail 
> 
>> On Jul 5, 2016, at 11:20 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> 
>> 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
>>

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

[Koubiyr, Ismail]

The file has not been anonymized.

Thanks,

Ismail 

> On Jul 5, 2016, at 11:20 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> 
> 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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[Freesurfer] mri_convert : ERROR: cannot unpack mosiacs without ASCII header

[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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but does not contain patient information, please contact the sender and properly
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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 
<ikoub...@bwh.harvard.edu<mailto:ikoub...@bwh.harvard.edu>> 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 
<ayend...@nmr.mgh.harvard.edu<mailto:ayend...@nmr.mgh.harvard.edu>> 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 
<ayend...@nmr.mgh.harvard.edu<mailto:ayend...@nmr.mgh.harvard.edu>> 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
<ayend...@nmr.mgh.harvard.edu<mailto:ayend...@nmr.mgh.harvard.edu>> 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
   <ayend...@nmr.mgh.harvard.edu<mailto:ayend...@nmr.mgh.harvard.edu>> 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 <ayend...@nmr.mgh.harvard.edu> 
> 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 
>>> <ayend...@nmr.mgh.harvard.edu> 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
>>>> <ayend...@nmr.mgh.harvard.edu> 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
>>>>>> <ayend...@nmr.mgh.harvard.edu> 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,
>>>>>> 
>>&

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 <ayend...@nmr.mgh.harvard.edu> 
> 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
>> <ayend...@nmr.mgh.harvard.edu> 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
>> >>  <ayend...@nmr.mgh.harvard.edu> 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
>> >> __

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 <ayend...@nmr.mgh.harvard.edu> 
> 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
>>      <ayend...@nmr.mgh.harvard.edu> 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



trac-all.log
Description: trac-all.log
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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 
<ayend...@nmr.mgh.harvard.edu<mailto:ayend...@nmr.mgh.harvard.edu>> 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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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
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0.651496 0.731864 0.199821
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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] trac-all error (bvecs and bvals don't have same number of entries)

[Koubiyr, Ismail]

Hi Lars,

I had the same problem. You can notice in your bvec file that there are some 
unusual blank spaces sometimes. Try to look at each space between two numbers 
and make sure it’s fine. You can also make sure about the number of entries by 
running wc -w on each of your bvec or bval file.
Hope it’s gonna help you.

Cheers,

Ismail

> On Jul 2, 2016, at 4:27 AM, Lars M. Rimol  wrote:
> 
> Hi,
> 
> Trying to run trac-all -c dmric_file -prep,  I get an error message stating 
> that there are different numbers of entries in the bval and bvec files. I 
> don't understand why, since both have the same number of rows (64). 
> 
> OS = Ubuntu 14.04.4
> Software: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0; I have updated 
> Tracula and FSL (v 5.0.9). 
> 
> 
> Error message:
> 
> #@# Tensor fit fr. 01. juli 19:20:29 +0200 2016
> dtifit -k /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dwi.nii.gz -m 
> /media/lmr2/subjects/DTI/tracula_2016/4_FS/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
>  -r /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvecs -b 
> /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvals -o 
> /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dtifit
> Error: bvecs and bvals don't have the same number of entries
> Linux dmed4870 3.19.0-31-generic #36~14.04.1-Ubuntu SMP Thu Oct 8 10:21:08 
> UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
> 
> trac-preproc exited with ERRORS at fr. 01. juli 19:20:30 +0200 2016
> 
> --
> I also tried flipping the bvec/bval files, but got the same error. 
> I don't know if there's anything wrong with the bval/bvec files, or if this 
> error message is indicative of some other problem. Is the updated Tracula 
> version only compatible with the dev version of FS? 
> 
> I have attached the bval/bvec files and the trac-all.log.
> 
> ---
> The contents of the dmric file is:
> 
> setenv SUBJECTS_DIR  /media/lmr2/subjects/DTI
> set dtroot =  /media/lmr2/subjects/DTI/tracula_2016_nativerows
> set subjlist = (4_FS)
> set dcmroot =  /media/lmr2/subjects/DTI
> set dcmlist =   ( 4/5/1.dcm )
> set bvalfile = /media/lmr2/subjects/DTI/bvals_rows.csv
> set bvecfile = /media/lmr2/subjects/DTI/bvec_rows.csv
> 
> 
> 
> Thank you!
> 
> 
> yours,
> 
> Lars M. Rimol, PhD
> Senior researcher, 
> Norwegian Advisory Unit for functional MRI
> Department of Radiology, 
> St. Olav's University hospital,
> 7006 Trondheim, 
> Norway
> 
> 
> 
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[Freesurfer] TRACULA problems

[Koubiyr, Ismail]

Hi everyone,

It’s been two weeks that I’ve been facing some issues with Tracula. I hope you 
could help me with that.

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 this 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.





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
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0.197021 -0.176144 -0.964446
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0 0 0
0 0 0___
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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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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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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[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
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.