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 <gr...@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 > 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 > 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. > > > -- 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
