Doug, Zeke,

Thank you very much for your help.

Best,

Ismail


On Jul 21, 2016, at 1:15 AM, zkaufman@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
<greve@nmr.mgh.harvard.edu <mailto:greve@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
<greve@nmr.mgh.harvard.edu <mailto:greve@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
<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu><mailto:greve@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
<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu><mailto:greve@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
<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu><mailto:greve@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       xxxxx
Date and time
StudyDate         20140918
StudyTime         121037.203000
SeriesTime       123450.600000
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   2.0000
VolDim             0        0        0
Vc                 -1.0000  -0.0000   0.0000
Vr                 -0.0000  -1.0000   0.0000
Vs                 0.0000   0.0000   0.0000
VolCenter           0.0000   0.0000   0.0000
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, 2.0000
       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 =  -1.0000, y_r =  -0.0000, z_r = -0.0000,
c_r =
-4.8425
           : x_a =  -0.0000, y_a =  -1.0000, z_a = -0.0000,
c_a =
-10.1615
           : x_s =   0.0000, y_s =   0.0000, z_s = 1.0000,
c_s =
-47.6769
Orientation   : LPS
Primary Slice Direction: axial

voxel to ras transform:
            -2.1818  -0.0000  -0.0000  1075.1575
            -0.0000  -2.1818  -0.0000  1069.8385
             0.0000   0.0000   2.0000   -48.6769
             0.0000   0.0000   0.0000     1.0000

voxel-to-ras determinant 9.52066

ras to voxel transform:
            -0.4583   0.0000   0.0000   492.7805
             0.0000  -0.4583   0.0000   490.3426
            -0.0000  -0.0000   0.5000    24.3384
             0.0000   0.0000   0.0000     1.0000

I would really appreciate your help, thank you.

Best,

Ismail



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MGH-NMR Center
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MGH-NMR Center
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Phone Number: 617-724-2358
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