Doug, Zeke, Thank you very much for your help.
Best, Ismail On Jul 21, 2016, at 1:15 AM, zkauf...@nmr.mgh.harvard.edu<mailto:zkauf...@nmr.mgh.harvard.edu> wrote: Current versions of the Mac freesurfer binaries are not compatible with the v5.3 release. Too much has changed since then. If you wanted to use the newest version on the code you will need to download the latest dev version of freesurfer from this page (see "Development Version"): https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall#Download Hope this helps. -Zeke 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 <gr...@nmr.mgh.harvard.edu<mailto: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-stable5-20130514 Do you think it might be related ? Thanks again. Ismail On Jul 19, 2016, at 1:27 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu<mailto: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 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> <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.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> <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 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> <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 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> <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> <mailto: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 <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2<http://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> <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> <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> <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 gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu> <mailto: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 <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2<http://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> <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> <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> <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 gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu> <mailto: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 <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2<http://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> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/<http://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ 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 _______________________________________________ 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 gr...@nmr.mgh.harvard.edu<mailto: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 <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2<http://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> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/<http://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ 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 _______________________________________________ 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.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
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