---------- Forwarded message ---------- From: Luc Amdahl luc.amdahl@gmail.com Date: Mon, Jun 17, 2013 at 3:45 PM Subject: Re: [Freesurfer] DICOM unpacking error To: Bruce Fischl fischl@nmr.mgh.harvard.edu
Hi Bruce,
Thanks for responding.
Here is the command line and screen output:
[Sheinberg-Lab-MRI-iMac:~/MRI/Solar_System] lab% unpacksdcmdir -src DICOM -targ subj_4 -fsfast -run 5 bold nii f.nii -run 6 bold nii f.nii -run 7 bold nii f.nii -run 8 bold nii f.nii -run 9 bold nii f.nii -run 10 bold nii f.nii
$Id: unpacksdcmdir,v 1.23 2008/12/15 21:42:16 greve Exp $
/Users/lab/MRI/Solar_System -src DICOM -targ subj_4 -fsfast -run 5 bold nii f.nii -run 6 bold nii f.nii -run 7 bold nii f.nii -run 8 bold nii f.nii -run 9 bold nii f.nii -run 10 bold nii f.nii
Fri Jun 14 09:47:20 EDT 2013
mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/14-13:47:20-GMT BuildTimeStamp: May 13 2013 16:45:47 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: lab Machine: Sheinberg-Lab-MRI-iMac.local Platform: Darwin PlatformVersion: 10.8.0 CompilerName: GCC CompilerVersion: 40000
Sheinberg-Lab-MRI-iMac.local Darwin Sheinberg-Lab-MRI-iMac.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
Fri Jun 14 09:47:20 EDT 2013 Log File is subj_4/unpack.log INFO: Logfile is subj_4/unpack.log SkipMoCo 0 Scanning source directory ... INFO: summary file is subj_4/dicomdir.sumfile INFO: status file is subj_4/parse.status Scanning directory Fri Jun 14 09:47:20 EDT 2013 mri_parse_sdcmdir --sortbyrun --d DICOM --o subj_4/dicomdir.sumfile --status subj_4/parse.status 0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 70 72 74 76 78 80 82 84 86 88 90 92 94 96 98 100 Done scanning Fri Jun 14 09:48:46 EDT 2013 ------------------------------------------ 1 localizer ok 512 512 3 1 59198979 2 T1_MEMPRAGE_freesurfer ok 256 256 176 4 59199008 3 T1_MEMPRAGE_freesurfer ok 256 256 176 4 59187534 4 T1_MEMPRAGE_freesurfer ok 256 256 176 1 59175542 5 ep_TR2500_128 ok 64 64 42 128 59175096 6 ep_TR2500_128 ok 64 64 42 128 59170659 7 ep_TR2500_128 ok 64 64 42 128 59169456 8 ep_TR2500_128 ok 64 64 42 128 59168253 9 ep_TR2500_128 ok 64 64 42 128 59167050 10 ep_TR2500_128 ok 64 64 42 128 59162613 11 ep_TR2500_113 ok 64 64 42 113 59299072 12 t2_3DFLAIR ok 256 240 176 1 59297629 unpacking config ------------------ {5 bold nii f.nii} {6 bold nii f.nii} {7 bold nii f.nii} {8 bold nii f.nii} {9 bold nii f.nii} {10 bold nii f.nii} ----------------------------------- --------------------------------------------------------- Run 5 ----------------------------------------- Fri Jun 14 09:48:46 EDT 2013 5 bold nii f.nii ERROR: reading DICOM/59175096 tag 28 30
Here is the version of FS I'm using: freesurfer-i386-apple-darwin10.8.0-stable5-20130513
What exactly do you mean when you ask where the DICOM's are from? I receive them from Brown's MRF facility, and we've been successful in converting them on other iMac's using the same version of FS.
Thanks,
Luc
On Mon, Jun 17, 2013 at 2:36 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
can you send the complete command line and screen output, and tell us what version of FS you are using and where the dicoms are from?
On Mon, 17 Jun 2013, Luc Amdahl wrote:
Hi Freesurfers,
I am trying to use Freesurfer to convert DICOM files to nii f.nii files. Freesurfer is able to find all the DICOM files but always gives me an error: "ERROR: reading DICOM/59175096 tag 28 30".
Can anyone help?
Thanks,
Luc
-- Luc Amdahl Brown University '14 Sc.B. Neuroscience 69 Brown St., #6137 Providence, RI 02912 603.252.4441
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/**compliancelinehttp://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.
Luc, it is missing the pixel spacing (ie, voxel size), which is a fundamental quantity which should not be missing. Have you anonymized the data or done something else too it? doug
On 6/17/13 2:36 PM, Luc Amdahl wrote:
---------- Forwarded message ---------- From: *Luc Amdahl* <luc.amdahl@gmail.com mailto:luc.amdahl@gmail.com> Date: Mon, Jun 17, 2013 at 3:45 PM Subject: Re: [Freesurfer] DICOM unpacking error To: Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>
Hi Bruce,
Thanks for responding.
Here is the command line and screen output:
[Sheinberg-Lab-MRI-iMac:~/MRI/Solar_System] lab% unpacksdcmdir -src DICOM -targ subj_4 -fsfast -run 5 bold nii f.nii -run 6 bold nii f.nii -run 7 bold nii f.nii -run 8 bold nii f.nii -run 9 bold nii f.nii -run 10 bold nii f.nii
$Id: unpacksdcmdir,v 1.23 2008/12/15 21:42:16 greve Exp $
/Users/lab/MRI/Solar_System -src DICOM -targ subj_4 -fsfast -run 5 bold nii f.nii -run 6 bold nii f.nii -run 7 bold nii f.nii -run 8 bold nii f.nii -run 9 bold nii f.nii -run 10 bold nii f.nii
Fri Jun 14 09:47:20 EDT 2013
mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/14-13:47:20-GMT BuildTimeStamp: May 13 2013 16:45:47 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: lab Machine: Sheinberg-Lab-MRI-iMac.local Platform: Darwin PlatformVersion: 10.8.0 CompilerName: GCC CompilerVersion: 40000
Sheinberg-Lab-MRI-iMac.local Darwin Sheinberg-Lab-MRI-iMac.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
Fri Jun 14 09:47:20 EDT 2013 Log File is subj_4/unpack.log INFO: Logfile is subj_4/unpack.log SkipMoCo 0 Scanning source directory ... INFO: summary file is subj_4/dicomdir.sumfile INFO: status file is subj_4/parse.status Scanning directory Fri Jun 14 09:47:20 EDT 2013 mri_parse_sdcmdir --sortbyrun --d DICOM --o subj_4/dicomdir.sumfile --status subj_4/parse.status 0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 70 72 74 76 78 80 82 84 86 88 90 92 94 96 98 100 Done scanning Fri Jun 14 09:48:46 EDT 2013
1 localizer ok 512 512 3 1 59198979 2 T1_MEMPRAGE_freesurfer ok 256 256 176 4 tel:256%20256%20176%20%C2%A0%204 59199008 3 T1_MEMPRAGE_freesurfer ok 256 256 176 4 tel:256%20256%20176%20%C2%A0%204 59187534 4 T1_MEMPRAGE_freesurfer ok 256 256 176 1 tel:256%20256%20176%20%C2%A0%201 59175542 5 ep_TR2500_128 ok 64 64 42 128 59175096 6 ep_TR2500_128 ok 64 64 42 128 59170659 7 ep_TR2500_128 ok 64 64 42 128 59169456 8 ep_TR2500_128 ok 64 64 42 128 59168253 9 ep_TR2500_128 ok 64 64 42 128 59167050 10 ep_TR2500_128 ok 64 64 42 128 59162613 11 ep_TR2500_113 ok 64 64 42 113 59299072 12 t2_3DFLAIR ok 256 240 176 1 tel:256%20240%20176%20%C2%A0%201 59297629 unpacking config ------------------ {5 bold nii f.nii} {6 bold nii f.nii} {7 bold nii f.nii} {8 bold nii f.nii} {9 bold nii f.nii} {10 bold nii f.nii}
Run 5 ----------------------------------------- Fri Jun 14 09:48:46 EDT 2013 5 bold nii f.nii ERROR: reading DICOM/59175096 tag 28 30
Here is the version of FS I'm using: freesurfer-i386-apple-darwin10.8.0-stable5-20130513
What exactly do you mean when you ask where the DICOM's are from? I receive them from Brown's MRF facility, and we've been successful in converting them on other iMac's using the same version of FS.
Thanks,
Luc
On Mon, Jun 17, 2013 at 2:36 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
can you send the complete command line and screen output, and tell us what version of FS you are using and where the dicoms are from? On Mon, 17 Jun 2013, Luc Amdahl wrote: Hi Freesurfers, I am trying to use Freesurfer to convert DICOM files to nii f.nii files. Freesurfer is able to find all the DICOM files but always gives me an error: "ERROR: reading DICOM/59175096 tag 28 30". Can anyone help? Thanks, Luc -- Luc Amdahl Brown University '14 Sc.B. Neuroscience 69 Brown St., #6137 Providence, RI 02912 603.252.4441 <tel:603.252.4441> 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.
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