Re: [Freesurfer] Cannot run unpacksdcmdir on buckner_data/014-anon
Hi Doug, I ran the command you suggested and it appears to run without any errors or warnings. *OUTPUT: * anders@debian:~/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon$ mri_convert 001.dcm deleteme.mgh mri_convert 001.dcm deleteme.mgh $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from 001.dcm... Getting Series No Scanning Directory INFO: Found 132 files in /home/anders/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon INFO: Scanning for Series Number 14 INFO: found 128 files in series INFO: loading series header info. INFO: sorting. RunNo = 13 INFO: (256 256 128), nframes = 1, ismosaic=0 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix - 0.993 -0.117 0.033 1.187; 0.122 0.973 -0.197 -0.637; -0.009 0.200 0.980 5.207; 0.000 0.000 0.000 1.000; FileName /home/anders/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon/001.dcm Identification NumarisVersyngo MR 2004V 4VB11A ScannerModel Avanto PatientName anon Date and time StudyDate StudyTime 00 SeriesTime00 AcqTime 00 Acquisition parameters PulseSeq *tfl3d1_ns Protocol anon PhEncDir ROW EchoNo0 FlipAngle 7 EchoTime 3.26 InversionTime 1000 RepetitionTime2730 PhEncFOV 256 ReadoutFOV256 Image information RunNo 13 SeriesNo 14 ImageNo 1 NImageRows256 NImageCols256 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 68.8536 138.9441 135.4929 VolRes 1. 1. 1.3300 VolDim256 256 128 Vc 0.1217 -0.9924 -0.0169 Vr 0.0065 0.0178 -0.9998 Vs -0.9925 -0.1216 -0.0086 VolCenter 0.7783 3.8396 4.6268 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) INFO: no Siemens slice order reversal detected (good!). TR=2730.00, TE=3.26, TI=1000.00, flip angle=7.00 i_ras = (0.121728, -0.99242, -0.0168585) j_ras = (0.00647436, 0.0177783, -0.999821) k_ras = (-0.992542, -0.121597, -0.008589) writing to deleteme.mgh... * *As far as I can tell, the Avanto is a Siemens model, which does not explain why unpacksdcmdir does not work, since unpacksdcmdir can find the slice with -scanonly but cannot unpack it. Any other ideas? Venlig hilsen | Kind regards Anders Dreisig Olsen anders.d.ol...@gmail.com mailto:anders.d.ol...@gmail.com On 07-01-2014 01:09, Douglas N Greve wrote: Not sure. Try running mri_convert 001.dcm deleteme.mgh if it fails, capture the screen output and send it to the list doug On 01/06/2014 06:31 PM, Anders Olsen wrote: Hello FreeSurfer team. I am currently trying to learn the general usage of FreeSurfer and have run into problems with unpacking DICOM files. When I run: unpacksdcmdir -src ~/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon -targ ~/fs_subjects/014-anon -scanonly ~/fs_subjects/014-anon/scan.info It completes and gives me the following output: 14anon ok 256 256 128 001.dcm I then try to unpack slice number 14 by running: unpacksdcmdir -src ~/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon -targ ~/fs_subjects/014-anon -fsfast -run 14 bold nii f.nii And it gives me the message: ERROR: reading ~/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon/001.dcm tag 28 30 I have done md5sum buckner_data-tutorial_subjs.tar.gz and got the hash: 14618f42ffa6b21d5714f37e159357c4 which matches the md5sum in ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.md5sum.txt Am I doing something wrong or is there a problem with the dcm files in the test data? -- Venlig hilsen | Kind regards Anders Dreisig Olsen anders.d.ol...@gmail.com mailto:anders.d.ol...@gmail.com ___ 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
[Freesurfer] Cannot run unpacksdcmdir on buckner_data/014-anon
Hello FreeSurfer team. I am currently trying to learn the general usage of FreeSurfer and have run into problems with unpacking DICOM files. When I run: unpacksdcmdir -src ~/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon -targ ~/fs_subjects/014-anon -scanonly ~/fs_subjects/014-anon/scan.info It completes and gives me the following output: 14anon ok 256 256 128 001.dcm I then try to unpack slice number 14 by running: unpacksdcmdir -src ~/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon -targ ~/fs_subjects/014-anon -fsfast -run 14 bold nii f.nii And it gives me the message: ERROR: reading ~/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon/001.dcm tag 28 30 I have done md5sum buckner_data-tutorial_subjs.tar.gz and got the hash: 14618f42ffa6b21d5714f37e159357c4 which matches the md5sum in ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.md5sum.txt Am I doing something wrong or is there a problem with the dcm files in the test data? -- Venlig hilsen | Kind regards Anders Dreisig Olsen anders.d.ol...@gmail.com mailto:anders.d.ol...@gmail.com ___ 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.
Re: [Freesurfer] Cannot run unpacksdcmdir on buckner_data/014-anon
Not sure. Try running mri_convert 001.dcm deleteme.mgh if it fails, capture the screen output and send it to the list doug On 01/06/2014 06:31 PM, Anders Olsen wrote: Hello FreeSurfer team. I am currently trying to learn the general usage of FreeSurfer and have run into problems with unpacking DICOM files. When I run: unpacksdcmdir -src ~/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon -targ ~/fs_subjects/014-anon -scanonly ~/fs_subjects/014-anon/scan.info It completes and gives me the following output: 14anon ok 256 256 128 001.dcm I then try to unpack slice number 14 by running: unpacksdcmdir -src ~/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon -targ ~/fs_subjects/014-anon -fsfast -run 14 bold nii f.nii And it gives me the message: ERROR: reading ~/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon/001.dcm tag 28 30 I have done md5sum buckner_data-tutorial_subjs.tar.gz and got the hash: 14618f42ffa6b21d5714f37e159357c4 which matches the md5sum in ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.md5sum.txt Am I doing something wrong or is there a problem with the dcm files in the test data? -- Venlig hilsen | Kind regards Anders Dreisig Olsen anders.d.ol...@gmail.com mailto:anders.d.ol...@gmail.com ___ 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.
