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>> 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 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> >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> -- >>>>>> 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 >>>>>> >>>>>> 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 >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> 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 >>>> gr...@nmr.mgh.harvard.edu <mailto: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 >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> 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 >> gr...@nmr.mgh.harvard.edu <mailto: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 > > > > _______________________________________________ > 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 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.
