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 > 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.
