On Jul 19, 2016, at 10:32 PM, Douglas Greve <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> 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>> 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>> 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>> 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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Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@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
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@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
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@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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