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. IsmailOn Jul 19, 2016, at 10:32 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu <mailto:gr...@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-stable5-20130514Do you think it might be related ? Thanks again. IsmailOn Jul 19, 2016, at 1:27 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu <mailto:gr...@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 youusing on what platform? To check whether that file has an ascii header, runmri_probedicom --i MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931There 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, IsmailOn Jul 19, 2016, at 1:11 PM, Douglas N Greve<gr...@nmr.mgh.harvard.edu <mailto: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.gzIf I included -it dicom, the conversion did not have an error, but theoutput had only one slice. Since these are mosaics, they need theSiemens 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. IsmailOn Jul 18, 2016, at 6:14 PM, Douglas N Greve<gr...@nmr.mgh.harvard.edu <mailto: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 ourfile drop? On 07/05/2016 11:24 AM, Koubiyr, Ismail wrote:The file has not been anonymized. Thanks, IsmailOn Jul 5, 2016, at 11:20 AM, Douglas N Greve<gr...@nmr.mgh.harvard.edu <mailto: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 samekind 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 presentxform 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 listFreesurfer@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 Centergr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu>Phone Number: 617-724-2358 Fax: 617-726-7422Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2www.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 listFreesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing listFreesurfer@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 Centergr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu>Phone Number: 617-724-2358 Fax: 617-726-7422Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2www.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 listFreesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing listFreesurfer@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 Centergr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu>Phone Number: 617-724-2358 Fax: 617-726-7422Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2www.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 listFreesurfer@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.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Douglas N. 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