Is it straight off the scanner? It does not have the siemens ascii header which usually means that it has been manipulated in some way. You can try using mri_convert with --it dicom doug
On 05/23/2013 12:57 PM, Cat Chong wrote:
no it has not.
*From:* Douglas N Greve greve@nmr.mgh.harvard.edu *To:* freesurfer@nmr.mgh.harvard.edu *Sent:* Thursday, May 23, 2013 9:43 AM *Subject:* Re: [Freesurfer] Siemens dicom error on mri_convert
has this file been anonymized? On 05/23/2013 12:39 PM, Cat Chong wrote:
Hello Experts, I am trying to run the mri_convert command prior to the recon-all command on Siemens T1 dicoms (as suggested in the archives). I am using freesurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0, Mac OS X Lion 10.7.5 I am using the command below: mri_convert -it siemens_dicom -ot mgz 1002/IM-0001-0001.dcm 2001.mgz Below is the command line error I receive, it is a similar error I receive when I try to use the command recon-all on the Siemens dicoms. I have used freesurfer before on GE dicoms and never had a problem running recon-all. Is this error message particular to the Siemens dicoms, and would you be able to tell me how to proceed? Thank you very much for you help, Cat reading from 1002/IM-0001-0001.dcm... Getting Series No Scanning Directory INFO: Found 130 files in 1002 INFO: Scanning for Series Number 2 INFO: found 128 files in series INFO: loading series header info. INFO: sorting. RunNo = 1 WARNING: Run 1 appears to be truncated Files Found: 128, Files Expected (lRep+1): 1 FileName 1002/IM-0001-0001.dcm Identification NumarisVer syngo MR D11 ScannerModel Skyra PatientName RS-FMRI^RS-FMRI Date and time StudyDate 20130222 StudyTime 082109.140000 SeriesTime 082812.906000 AcqTime 082237.315000 Acquisition parameters PulseSeq *tfl3d1_16ns Protocol SAG MP Rage PhEncDir ROW EchoNo 1 FlipAngle 8 EchoTime 3.03 InversionTime 1000 RepetitionTime 2400 PhEncFOV 0 ReadoutFOV 0 Image information RunNo 1 SeriesNo 2 ImageNo 1 NImageRows 256 NImageCols 256 NFrames 128 SliceArraylSize 0 IsMosaic 1 ImgPos -78.6002 128.0000 93.1332 VolRes 1.0000 1.0000 1.2500 VolDim 0 0 0 Vc -0.0000 -1.0000 0.0000 Vr -0.0000 -0.0000 -1.0000 Vs 0.0000 0.0000 0.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 WARNING: file 1002/IM-0001-0001.dcm does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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Dear Doug Yes, the data is straight off the scanner, I don't think it has been manipulated, but I will check. When I run the the command suggested I get the below error message: mri_convert –it dicom -ot mgz 1002/IM-0001-0001.dcm 1002.mgz mri_convert –it dicom -ot mgz 1002/IM-0001-0001.dcm 1002.mgz
mri_convert: extra arguments ("1002/IM-0001-0001.dcm" and following)
type mri_convert -u for usage
I am not quite sure where I am making an error. Cat
________________________________ From: Douglas N Greve greve@nmr.mgh.harvard.edu To: Cat Chong cavecreekcutter@yahoo.com; "Freesurfer@nmr.mgh.harvard.edu" Freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 23, 2013 10:06 AM Subject: Re: [Freesurfer] Siemens dicom error on mri_convert
Is it straight off the scanner? It does not have the siemens ascii header which usually means that it has been manipulated in some way. You can try using mri_convert with --it dicom doug
On 05/23/2013 12:57 PM, Cat Chong wrote:
no it has not.
*From:* Douglas N Greve greve@nmr.mgh.harvard.edu *To:* freesurfer@nmr.mgh.harvard.edu *Sent:* Thursday, May 23, 2013 9:43 AM *Subject:* Re: [Freesurfer] Siemens dicom error on mri_convert
has this file been anonymized? On 05/23/2013 12:39 PM, Cat Chong wrote:
Hello Experts, I am trying to run the mri_convert command prior to the recon-all command on Siemens T1 dicoms (as suggested in the archives). I am using freesurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0, Mac OS X Lion 10.7.5 I am using the command below: mri_convert -it siemens_dicom -ot mgz 1002/IM-0001-0001.dcm 2001.mgz Below is the command line error I receive, it is a similar error I receive when I try to use the command recon-all on the Siemens dicoms. I have used freesurfer before on GE dicoms and never had a problem running recon-all. Is this error message particular to the Siemens dicoms, and would you be able to tell me how to proceed? Thank you very much for you help, Cat reading from 1002/IM-0001-0001.dcm... Getting Series No Scanning Directory INFO: Found 130 files in 1002 INFO: Scanning for Series Number 2 INFO: found 128 files in series INFO: loading series header info. INFO: sorting. RunNo = 1 WARNING: Run 1 appears to be truncated Files Found: 128, Files Expected (lRep+1): 1 FileName 1002/IM-0001-0001.dcm Identification NumarisVer syngo MR D11 ScannerModel Skyra PatientName RS-FMRI^RS-FMRI Date and time StudyDate 20130222 StudyTime 082109.140000 SeriesTime 082812.906000 AcqTime 082237.315000 Acquisition parameters PulseSeq *tfl3d1_16ns Protocol SAG MP Rage PhEncDir ROW EchoNo 1 FlipAngle 8 EchoTime 3.03 InversionTime 1000 RepetitionTime 2400 PhEncFOV 0 ReadoutFOV 0 Image information RunNo 1 SeriesNo 2 ImageNo 1 NImageRows 256 NImageCols 256 NFrames 128 SliceArraylSize 0 IsMosaic 1 ImgPos -78.6002 128.0000 93.1332 VolRes 1.0000 1.0000 1.2500 VolDim 0 0 0 Vc -0.0000 -1.0000 0.0000 Vr -0.0000 -0.0000 -1.0000 Vs 0.0000 0.0000 0.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 WARNING: file 1002/IM-0001-0001.dcm does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header
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. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@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 mailto: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 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.
freesurfer@nmr.mgh.harvard.edu
-
Cat Chong -
Douglas N Greve