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.edumailto: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.edumailto: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.edumailto: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 >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> greve@nmr.mgh.harvard.edu >>>> mailto: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/BugReporting >>>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 >>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> http://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 >>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve@nmr.mgh.harvard.edu >> mailto: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/BugReporting >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> http://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 >> mailto:Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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