Hi, This is a repost. Would anyone have a solution to this problem ? Thanks for your help.
Best, Ismail > On Jul 5, 2016, at 11:24 AM, Koubiyr, Ismail <ikoub...@bwh.harvard.edu> 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> >> 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 >>> 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 > _______________________________________________ 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.
