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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