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.edumailto: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.edumailto: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.edumailto: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.edumailto: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.edumailto: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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto: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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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